Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Microbiome proliferation

Metagenomic sequencing has revolutionized our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different bacterial microbial genomes contains a single trough and a single peak, thate latter coincidinges with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species’ growth rate. We demonstrate this in vitro and in vivo, under different growth conditions and in complex bacterial communities. For several bacterial species, peak to trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes