Exploring host-microbiota interactions in animal models and humans

Abstract

The animal and bacterial kingdoms have coevolved and coadapted in response to environmental selective pressures over hundreds of millions of years. The meta'omics revolution in both sequencing and its analytic pipelines is fostering an explosion of interest in how the gut microbiome impacts physiology and propensity to disease. Gut microbiome studies are inherently interdisciplinary, drawing on approaches and technical skill sets from the biomedical sciences, ecology, and computational biology. Central to unraveling the complex biology of environment, genetics, and microbiome interaction in human health and disease is a deeper understanding of the symbiosis between animals and bacteria. Experimental model systems, including mice, fish, insects, and the Hawaiian bobtail squid, continue to provide critical insight into how host-microbiota homeostasis is constructed and maintained. Here we consider how model systems are influencing current understanding of host-microbiota interactions and explore recent human microbiome studies.

Figure 1.

The structure of the microbiota across species. Although there can be significant interindividual variation in the composition of the microbiota, broad trends exist within a given species, particularly at the phylum level. Phyla are represented by color, and the relative abundance of the lower taxonomic levels is indicated by font size. This figure was produced with data adapted from Arumugam et al. (2011), Brinkman et al. (2011), Chandler et al. (2011), and Roeselers et al. (2011).

Figure 2.

The structure of the human intestinal microbiota across the life cycle. The composition of the gut microbiome changes throughout the course of life. The infant microbiome shows great interindividual variability and relatively low diversity but becomes more diverse and converges into an “adult-like” structure by 3 yr after birth. Pregnancy is associated with an increase in Actinobacteria and Proteobacteria and increased diversity, but the gut microbiota returns to its original structure sometime after delivery. Old age (>65 yr) is associated with a number of changes in the microbiota, including an increase in the abundance of Bacteroidetes.