SRX18249652 GSM6729945_r1 SRP407756 PRJNA901390 SRS15744431 GSM6729945 GSM6729945 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249653 GSM6729946_r1 SRP407756 PRJNA901390 SRS15744432 GSM6729946 GSM6729946 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249654 GSM6729947_r1 SRP407756 PRJNA901390 SRS15744433 GSM6729947 GSM6729947 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249655 GSM6729948_r1 SRP407756 PRJNA901390 SRS15744434 GSM6729948 GSM6729948 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249656 GSM6729949_r1 SRP407756 PRJNA901390 SRS15744435 GSM6729949 GSM6729949 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249657 GSM6729950_r1 SRP407756 PRJNA901390 SRS15744436 GSM6729950 GSM6729950 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249658 GSM6729951_r1 SRP407756 PRJNA901390 SRS15744437 GSM6729951 GSM6729951 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550 SRX18249659 GSM6729952_r1 SRP407756 PRJNA901390 SRS15744438 GSM6729952 GSM6729952 RNA-Seq TRANSCRIPTOMIC cDNA Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA. Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol. NextSeq 550