Timescales of gut microbiome dynamics

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.

Introduction

It is nowadays well appreciated that the legions of microbes resident in the gastrointestinal tracts of humans and other animals play major roles in development, health, and disease. Because a wide range of disorders are correlated with differences in gut microbial community composition, intentionally altering the composition of the intestinal flora is a major aim of many research strategies that share the ultimate goal of developing effective therapies. So far, progress toward this end has been quite limited. Treatments such as fecal microbiome transplantation ameliorate Clostridium difficile infection [1], but the underlying mechanisms remain largely mysterious and hard to generalize to other diseases. Similarly, microbiome perturbation using probiotic supplementation or diet changes remains inconsistently effective, hard to predict, and contentious [2,3^••].

Understanding how to alter the composition of the gut microbiota requires, almost tautologically, an understanding of how the gut microbiota changes over time. Natural timescales for fluctuations should give a sense of the stability or instability of the microbiome, and timescales for responses to perturbations should inform strategies to maximize or minimize the system’s adoption of new steady-state dynamics. In contrast to characterizations of community membership in different hosts at a given time, however, characterizations within a single host over a range of times are relatively few. Nonetheless, recent studies have provided some sense of the stability and response times of the gut microbiome in humans and other animals. In this review we summarize existing data on the dynamics of vertebrate gut microbiomes, discuss likely mechanisms governing dynamical timescales, and provide suggestions to guide future work.