Most metagenomic analysis methods are based on the relative abundance of a marker gene or of sets of genes in functional pathways. However, these methods offer a static view of microbial composition and provide no information on growth dynamics. Korem et al. devised a new approach that measures the number of copies of a sequence at each genomic site for each species in a metagenome. For most bacterial species, a single peak and a single trough are produced, corresponding to the replication fork and replication terminus; the ratio of the two is a proxy for growth rate, as confirmed by a wide range of in vitro and in vivo measurements. Remarkably, application of the method to human faecal datasets revealed new links between bacterial growth rates, rather than composition, and type 2 diabetes, Crohn disease and ulcerative colitis.
Korem, T. et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science http://dx.doi.org/10.1126/science.aac4812 (2015)
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Attar, N. An encrypted growth signature. Nat Rev Microbiol 13, 527 (2015). https://doi.org/10.1038/nrmicro3544