The dynamic microbiome

Abstract

a b s t r a c t While our genomes are essentially static, our microbiomes are inherently dynamic. The microbial communities we harbor in our bodies change throughout our lives due to many factors, including maturation during childhood, alterations in our diets, travel, illnesses, and medical treatments. Moreover, there is mounting evidence that our microbiomes change us, by promoting health through their beneficial actions or by increasing our susceptibility to diseases through a process termed dysbiosis. Recent technological advances are enabling unprecedentedly detailed studies of the dynamics of the microbiota in animal models and human populations. This review will highlight key areas of investigation in the field, including establishment of the microbiota during early childhood, temporal variability of the microbiome in healthy adults, responses of the microbiota to intentional perturbations such as antibiotics and dietary changes, and prospective analyses linking changes in the microbiota to host disease status. Given the importance of computational methods in the field, this review will also discuss issues and pitfalls in the analysis of microbiome time-series data, and explore several promising new directions for mathematical model and algorithm development.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

“…Evidence is emerging for their applicability at the micro scale as well-for example, in describing the microbial dynamics in a cheese model community (Mounier et al, 2008) and within individuals (Gerber 2014), as well as their shifts in response to environmental perturbations (Pepper and Rosenfeld, 2012). Previous investigation in this area mostly tested standard correlation metrics not developed for microbiome data (Berry and Widder, 2014).…”

Engineering Microbiomes to Improve Plant and Animal Health

“…Microbiomes of animals and plants are often dominated by eubacteria, but fungi, protozoa, archaea, and viruses also can play important roles in these communities [1][2][3][4][5]. Microbiomes are not passive players [6,7]; rather, microbes can alter host development, physiology, and systemic defenses [2,8,9], enable toxin production and disease resistance [10,11], increase host tolerance to stress and drought [12][13][14], modulate niche breadth [15], and change fitness outcomes in host interactions with competitors, predators, and pathogens [6]. Because microbiomes can encompass a hundred-fold more genes than host genomes [16], and because this 'hologenome' of a hostmicrobiome association can vary over space and time [17,18], microbiomes can function as a phenotypically plastic buffer between the host-genotype's effects and the environmental effects that interact to shape host phenotypes.…”

Recurrent Clostridium difficile infection and the microbiome

“…The indigenous intestinal microbiota is a highly dynamic ecosystem that is perturbed by environmental factors [38,43,44]. While the altered ecosystem seems to restore itself to homeostasis after CDI clearance with antibiotics, in the remaining 20 % of CDI cases, the microbiome has likely been altered beyond the point of spontaneous recovery, rendering the host susceptible to recurrent infection (Fig.…”