| description |
Current gut microbiome studies usually compare the relative abundance of organisms in different specimens. Although this accurately reflects any changes in the microbiome composition, it does not reveal alterations in absolute numbers of specific taxa. Here we suggest to spike exogenous bacteria into crude specimens to quantify ratios of absolute bacterial abundances. We use the read counts of the spike-in bacteria obtained from 454 sequencing to adjust the read counts of endogenous bacteria for changes in the microbial abundance across specimens. With serially diluted stool samples containing defined absolute numbers of spike bacteria we found that spike-in-based calibration to total microbial abundance allows accurate estimation of absolute ratios of endogenous bacteria, however not of absolute quantities of bacteria themselves. In an application to stool specimens of patients undergoing allogeneic stem cell transplantation with concomitant antibiosis we observed that changes in absolute abundances differ strongly from relative shifts, revealing comprehensive insight in the dynamics of the intestinal microbiome in these patients. |