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.
Highlights
Our distal gut is one of the most densely populated and most thoroughly surveyed bacterial ecosystems in nature
Our results illustrate that adaptation to the gut habitat is a dynamic process that includes acquisition of genes from other microorganisms
The 5,163,189–base pair genome of the human gutderived B. vulgatus type strain ATCC 8482 encodes a predicted 4,088-member proteome, whereas the 4,811,369bp genome of B. distasonis type strain ATCC 8503 possesses 3,867 predicted protein-coding genes (Figure S1 and Table S1). These genomes were initially compared to the genomes of two other Bacteroidetes that live in the distal human gut: B. thetaiotaomicron
Summary
Our distal gut is one of the most densely populated and most thoroughly surveyed bacterial ecosystems in nature. This microbiota contains more bacterial cells than all of our body’s other microbial communities combined. With an estimated 500–1,000 species, and over 7,000 strains [4], the evolutionary tree of our distal intestinal microbiota can be visualized as a grove of ten palm trees (divisions), each topped by fronds representing divergent lineages, and with each frond composed of many leaves representing closely related bacteria [1]. Soil, Earth’s terrestrial ‘‘gut’’ for degrading organic matter, can be viewed as a bush, composed of many more intermediate and deeply diverging lineages [5]
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