SRX5798296 1017aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729531 1017aArc1 1017aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798297 1021aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729530 1021aEub1 1021aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798298 1021aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729532 1021aArc1 1021aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798299 1093aCil17 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729533 1093aCil17 1093aCil17 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798300 1093aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729534 1093aEub1 1093aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798301 1091aCil10 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729535 1091aCil10 1091aCil10 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798302 1091aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729536 1091aEub1 1091aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798303 1090aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729537 1090aEub1 1090aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798304 1091aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729538 1091aArc1 1091aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798305 1092aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729539 1092aEub1 1092aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798306 1093aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729540 1093aArc1 1093aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798307 1092aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729541 1092aArc1 1092aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798308 1092aCil14 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729542 1092aCil14 1092aCil14 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798309 1056aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729543 1056aArc1 1056aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798310 1059aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729544 1059aArc1 1059aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798311 1059aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729545 1059aEub1 1059aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798312 1058aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729546 1058aArc1 1058aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798313 1058aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729547 1058aEub1 1058aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798314 1061aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729548 1061aArc1 1061aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798315 1061aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729549 1061aEub1 1061aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798316 1060aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729550 1060aArc1 1060aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798317 1060aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729551 1060aEub1 1060aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798318 1062aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729552 1062aArc1 1062aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798319 1062aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729553 1062aEub1 1062aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798320 1012aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729554 1012aArc1 1012aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798321 1012aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729555 1012aEub1 1012aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798322 1013aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729556 1013aArc1 1013aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798323 1013aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729557 1013aEub1 1013aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798324 1014aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729558 1014aArc1 1014aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798325 1014aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729559 1014aEub1 1014aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798326 1015aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729560 1015aArc1 1015aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798327 1015aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729561 1015aEub1 1015aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798328 1016aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729562 1016aArc1 1016aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798329 1016aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729563 1016aEub1 1016aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798330 1097aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729564 1097aArc1 1097aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798331 1096aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729565 1096aEub1 1096aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798332 1094aCil24 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729566 1094aCil24 1094aCil24 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798333 1094aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729567 1094aArc1 1094aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798334 1095aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729568 1095aArc1 1095aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798335 1094aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729569 1094aEub1 1094aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798336 1095aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729570 1095aEub1 1095aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798337 1095aCil4 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729571 1095aCil4 1095aCil4 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798338 1096aCil16 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729572 1096aCil16 1096aCil16 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798339 1096aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729573 1096aArc1 1096aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798340 1063aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729574 1063aEub1 1063aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798341 1063aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729576 1063aArc1 1063aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798342 1064aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729575 1064aEub1 1064aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798343 1064aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729577 1064aArc1 1064aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798344 1065aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729578 1065aEub1 1065aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798345 1065aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729580 1065aArc1 1065aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798346 1066aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729579 1066aEub1 1066aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798347 1066aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729581 1066aArc1 1066aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798348 1067aCil8 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729582 1067aCil8 1067aCil8 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798349 1067aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729583 1067aArc1 1067aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798350 1100aCil9 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729584 1100aCil9 1100aCil9 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798351 1100aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729585 1100aArc1 1100aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798352 1025aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729586 1025aArc1 1025aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798353 1030aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729587 1030aEub1 1030aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798354 1030aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729589 1030aArc1 1030aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798355 1027aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729588 1027aEub1 1027aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798356 1027aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729590 1027aArc1 1027aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798357 1028aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729591 1028aEub1 1028aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798358 1028aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729592 1028aArc1 1028aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798359 1097aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729593 1097aEub1 1097aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798360 1097aCil20 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729594 1097aCil20 1097aCil20 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798361 1098aCil12 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729595 1098aCil12 1098aCil12 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798362 1098aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729596 1098aArc1 1098aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798363 1099aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729598 1099aArc1 1099aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798364 1098aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729597 1098aEub1 1098aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798365 1099aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729600 1099aEub1 1099aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798366 1099aCil25 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729599 1099aCil25 1099aCil25 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798367 1071aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729601 1071aEub1 1071aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798368 1072aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729602 1072aArc1 1072aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798369 1069aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729603 1069aEub1 1069aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798370 1070aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729605 1070aArc1 1070aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798371 1070aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729604 1070aEub1 1070aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798372 1071aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729606 1071aArc1 1071aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798373 1067aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729607 1067aEub1 1067aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798374 1068aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729608 1068aArc1 1068aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798375 1068aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729609 1068aEub1 1068aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798376 1069aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729610 1069aArc1 1069aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798377 1001aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729611 1001aEub1 1001aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798378 1001aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729612 1001aArc1 1001aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798379 1002aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729613 1002aEub1 1002aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798380 1002aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729614 1002aArc1 1002aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798381 1003aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729615 1003aEub1 1003aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798382 1003aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729616 1003aArc1 1003aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798383 1005aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729617 1005aEub1 1005aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798384 1005aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729618 1005aArc1 1005aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798385 1006aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729619 1006aEub1 1006aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798386 1006aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729620 1006aArc1 1006aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798387 1025aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729621 1025aEub1 1025aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798388 1024aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729622 1024aArc1 1024aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798389 1024aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729623 1024aEub1 1024aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798390 1023aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729624 1023aArc1 1023aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798391 1023aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729625 1023aEub1 1023aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798392 1022aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729626 1022aArc1 1022aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798393 1022aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729627 1022aEub1 1022aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798394 1026aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729628 1026aArc1 1026aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798395 1026aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729629 1026aEub1 1026aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798396 1077aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729630 1077aArc1 1077aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798397 1076aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729631 1076aEub1 1076aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798398 1074aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729632 1074aArc1 1074aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798399 1073aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729633 1073aEub1 1073aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798400 1073aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729634 1073aArc1 1073aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798401 1072aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729636 1072aEub1 1072aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798402 1076aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729635 1076aArc1 1076aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798403 1075aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729637 1075aEub1 1075aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798404 1075aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729639 1075aArc1 1075aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798405 1074aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729638 1074aEub1 1074aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798406 1038aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729640 1038aEub1 1038aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798407 1038aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729641 1038aArc1 1038aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798408 1037aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729642 1037aEub1 1037aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798409 1037aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729643 1037aArc1 1037aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798410 1040aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729644 1040aEub1 1040aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798411 1040aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729645 1040aArc1 1040aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798412 1039aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729646 1039aEub1 1039aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798413 1039aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729647 1039aArc1 1039aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798414 1041aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729648 1041aEub1 1041aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798415 1041aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729649 1041aArc1 1041aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798416 1080aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729650 1080aArc1 1080aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798417 1080aCil3 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729651 1080aCil3 1080aCil3 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798418 1079aCil19 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729652 1079aCil19 1079aCil19 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798419 1079aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729653 1079aEub1 1079aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798420 1078aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729654 1078aEub1 1078aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798421 1079aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729655 1079aArc1 1079aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798422 1078aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729656 1078aArc1 1078aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798423 1078aCil18 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729657 1078aCil18 1078aCil18 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798424 1077aCil2 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729658 1077aCil2 1077aCil2 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798425 1077aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729659 1077aEub1 1077aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798426 1036aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729660 1036aArc1 1036aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798427 1036aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729661 1036aEub1 1036aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798428 1034aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729662 1034aArc1 1034aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798429 1034aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729663 1034aEub1 1034aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798430 1035aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729664 1035aArc1 1035aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798431 1035aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729665 1035aEub1 1035aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798432 1032aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729666 1032aArc1 1032aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798433 1032aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729667 1032aEub1 1032aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798434 1033aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729668 1033aArc1 1033aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798435 1033aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729669 1033aEub1 1033aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798436 1053aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729670 1053aArc1 1053aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798437 1100aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729671 1100aEub1 1100aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798438 1083aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729672 1083aEub1 1083aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798439 1083aCil7 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729673 1083aCil7 1083aCil7 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798440 1082aCil6 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729674 1082aCil6 1082aCil6 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798441 1082aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729675 1082aArc1 1082aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798442 1083aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729676 1083aArc1 1083aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798443 1082aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729677 1082aEub1 1082aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798444 1081aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729678 1081aArc1 1081aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798445 1080aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729679 1080aEub1 1080aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798446 1081aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729680 1081aEub1 1081aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798447 1081aCil1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729681 1081aCil1 1081aCil1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798448 1011aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729682 1011aEub1 1011aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798449 1011aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729683 1011aArc1 1011aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798450 1007aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729684 1007aEub1 1007aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798451 1007aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729685 1007aArc1 1007aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798452 1008aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729686 1008aEub1 1008aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798453 1008aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729687 1008aArc1 1008aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798454 1009aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729688 1009aEub1 1009aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798455 1009aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729689 1009aArc1 1009aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798456 1010aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729690 1010aEub1 1010aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798457 1010aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729691 1010aArc1 1010aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798458 1053aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729692 1053aEub1 1053aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798459 1029aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729693 1029aEub1 1029aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798460 1054aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729694 1054aEub1 1054aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798461 1054aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729695 1054aArc1 1054aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798462 1055aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729696 1055aEub1 1055aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798463 1055aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729697 1055aArc1 1055aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798464 1056aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729698 1056aEub1 1056aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798465 1029aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729699 1029aArc1 1029aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798466 1057aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729700 1057aEub1 1057aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798467 1057aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729701 1057aArc1 1057aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798468 1086aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729702 1086aEub1 1086aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798469 1087aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729703 1087aArc1 1087aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798470 1084aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729704 1084aArc1 1084aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798471 1084aCil15 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729705 1084aCil15 1084aCil15 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798472 1084aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729706 1084aEub1 1084aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798473 1085aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729707 1085aArc1 1085aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798474 1085aCil21 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729708 1085aCil21 1085aCil21 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798475 1085aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729709 1085aEub1 1085aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798476 1086aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729710 1086aArc1 1086aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798477 1086aCil13 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729711 1086aCil13 1086aCil13 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798478 1044aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729712 1044aArc1 1044aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798479 1044aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729713 1044aEub1 1044aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798480 1043aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729714 1043aArc1 1043aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798481 1043aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729716 1043aEub1 1043aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798482 1046aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729715 1046aArc1 1046aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798483 1046aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729718 1046aEub1 1046aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798484 1045aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729717 1045aArc1 1045aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798485 1045aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729719 1045aEub1 1045aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798486 1031aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729720 1031aEub1 1031aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798487 1047aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729722 1047aArc1 1047aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798488 1047aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729721 1047aEub1 1047aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798489 1031aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729723 1031aArc1 1031aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798490 1089aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729724 1089aEub1 1089aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798491 1089aCil11 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729725 1089aCil11 1089aCil11 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798492 1089aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729726 1089aArc1 1089aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798493 1088aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729727 1088aEub1 1088aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798494 1088aCil23 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729728 1088aCil23 1088aCil23 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798495 1088aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729729 1088aArc1 1088aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798496 1087aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729730 1087aEub1 1087aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798497 1087aCil5 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729731 1087aCil5 1087aCil5 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798498 1090aCil22 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729733 1090aCil22 1090aCil22 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798499 1090aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729732 1090aArc1 1090aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798500 1020aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729734 1020aEub1 1020aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798501 1020aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729735 1020aArc1 1020aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798502 1019aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729736 1019aEub1 1019aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798503 1019aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729737 1019aArc1 1019aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798504 1018aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729738 1018aEub1 1018aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798505 1018aArc1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729739 1018aArc1 1018aArc1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium SRX5798506 1017aEub1 SRP195650 bp0 Eight bull calves (Friesian Jersey cross) had access to colostrum for four days post-partum to ensure a good immune status before being fed a standard diet. Methane measurements and rumen content collections were carried out every two weeks until weaning (at 10 weeks of age), and every four weeks after weaning, until week 24. In total, eight methane 24 h measurements were carried out over the 23-week period. Live weights of the animals were determined weekly, and dry matter intake (DMI) was determined on a daily basis until week 10, and then every four weeks during methane measurements in respiration chambers. Rumen fluid sampling was carried out via stomach tubing after the calves were released from the respiration chambers. Rumen samples were subsampled for microbial community analysis via DNA extraction (0.9 ml). Subsamples for microbial community analysis were snap-frozen and stored at -20 C. The samples for DNA extraction were thawed in a 25 C water bath and an aliquot of 200 l of the rumen contents were collected into the pH 8 phenol-chloroform solution (Sigma-Aldrich, St. Louis, MO, USA) using a wide bore tip. The nucleic acids were then extracted following the combined phenol-chloroform and bead-beating method (Rius et al., 2012). DNA was normalized, amplified using barcoded primers targeting variable regions V1-V3 of the bacterial and V6-V8 of the archaeal 16S rRNA gene, or variable regions V5-V8 of the eukaryote 18S rRNA gene and amplicons were pooled and sent to Eurofins Genomics (Ebersberg, Germany) for 454 Titanium pyrosequencing. SRS4729740 1017aEub1 1017aEub1 AMPLICON METAGENOMIC PCR 454 GS FLX Titanium