Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.

ABSTRACT: Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochast

SUBMITTER: Lim JJ 

PROVIDER: S-EPMC10502120 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature