The use of chemostat experiments to measure and analyze the growth dynamics of microorganisms: Inferring from in-vitro experiments to the state in the gut microbiota in-vivo

Whole genome sequencing of microorganisms from a complex sample, for example a human microbiome, provides only a snapshot of a dynamic ecosystem. Such a microbiome, which comprises of many distinct microorganisms, can be analyzed to calculate the relative abundance of the various microorganisms, yet it does not permit to calculate the relative growth rates, nor the dynamics within the population. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Using chemostat experiments we show that there is a correlation between peak and trough (PTR) values, and growth rates in a wide range of rates, suggesting that PTR can be used as a quantitative measure of a species’ growth rate. Finally, we show that the use of PTR values can be expanded to other microorganisms both in vitro and in vivo, in simple and in complex bacterial communities.