Timescales of gut microbiome dynamics

Abstract

Vast communities of microorganisms inhabit the gastrointestinal tracts of humans and other animals. Understanding their initial development, fluctuations in composition, stability over long times, and responses to transient perturbations - in other words their dynamics - is important both for gaining basic insights into these ecosystems and for rationally manipulating them for therapeutic ends. Gut microbiome dynamics, however, remain poorly understood. We review here studies of gut microbiome dynamics in the presence and absence of external perturbations, noting especially the long timescales associated with overall stability and the short timescales associated with various underlying biological processes. Integrating these disparate timescales, we suggest, is an important goal for future work and is necessary for developing a predictive understanding of microbiome dynamics.

Figure 1:. Diversity of sampling schemes in selected longitudinal studies of human gut microbiomes.

Each marker corresponds to a study in Table 1. We plot here the median sampling interval (frequency of microbiome sequencing; logarithmic scale) and sampling duration (length of study) for each study. Values were estimated from publications and should be considered approximate. Circles represent studies that used 16s amplicon sequencing to identify microbial taxa; diamonds represents studies that included shotgun metagenomic sequencing. Large markers represent studies that examined more than 10 subjects; small markers, 10 or fewer.