In situ growth rates from snapshot metagenomics

Ever wondered if probiotics survived through the stomach acid?

The species abundances derived from classical metagenomics analysis is the product of previous growth and immigration in and out of the system. In contrast, in situ grown rates provides information about the activities of the microorganisms at the time of sampling. We have developed a method for measuring microbial growth rates directly from shotgun metagenomics. The method uses the relative abundance between the origin of replication and the terminus (see figure) of prokaryote chromosomes as a measure of the average replication rate in the population. Hence, the method generates an overview of which species in a community that are growing and how much.

Figure: Showing the local chromosome abundance of E. coli measured across 171 human stool samples