Evolution of Symbiotic Bacteria in the Distal Human Intestine

Abstract

The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies. Little is known about the selective pressures that have shaped and are shaping this community's component species, which are dominated by members of the Bacteroidetes and Firmicutes divisions. To examine how the intestinal environment affects microbial genome evolution, we have sequenced the genomes of two members of the normal distal human gut microbiota, Bacteroides vulgatus and Bacteroides distasonis, and by comparison with the few other sequenced gut and non-gut Bacteroidetes, analyzed their niche and habitat adaptations. The results show that lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine. Our findings show that these processes have been a driving force in the adaptation of Bacteroidetes to the distal gut environment, and emphasize the importance of considering the evolution of humans from an additional perspective, namely the evolution of our microbiomes.

Author Summary

The total number of microbes that colonize the surfaces of our adult bodies is thought to be ten times greater than the total number of our human cells. Our microbial partners provide us with certain features that we have not had to evolve on our own. In this sense, we should consider ourselves to be a supraorganism whose genetic landscape includes both our own genome as well as the genomes of our resident microbes, and whose physiologic features are a synthesis of human and microbial metabolic traits. The largest collection of microbes resides in our gut, which harbors trillions of bacteria, representing hundreds of species, most falling into two groups—the Bacteroidetes and the Firmicutes. We have sequenced the genomes of two human gut-dwelling Bacteroidetes, and compared their genomes to the genomes of other bacteria that live both inside and outside of our bodies. Our results illustrate that adaptation to the gut habitat is a dynamic process that includes acquisition of genes from other microorganisms. These findings emphasize the importance of including the evolution of “our” microbial genomes when considering the evolution of humans.

Abstract

Human microbiome evolution was explored by comparing human gut Bacteroidete genomic sequences to available data; common modes of evolution were revealed that have enabled these gut-dwelling microbes to adapt to their environments.