Bioenergetic diversity of the human gut microbiome

Abstract

The human microbiome has lately emerged as an important factor in health and disease. The general patterns that emerge from metagenomics studies of the microbial diversity in the human gut of healthy adults, children and infants, are that (a) the microbiome is less diverse early in life, and gets enriched after infancy, and (b) that it is dominated by organisms from two bacterial phyla: bacteroidetes and firmicutes. However, there is still considerable diversity between individuals, based on age, habitat and health status, while a lot of questions on how the diversity of the microbiome affects our health still remain unanswered. One aspect that has been largely overlooked is the diversity of the microbiome with regards to bioenergetic pathways. We therefore set out to address this by re-examining freely available data from three major studies of human gut microbiota, as deposited on MG-RAST, based on the available complete genome sequences of a set of species which represent the full bioenergetic diversity of prokaryotes across all the major bacterial and archaeal lineages. Our results indicate that a number of species are present in the human gut of both adults and infants which normally derive their energy from methanogenesis, iron oxidation, iron reduction, sulfate and arsenate reduction, and even anoxygenic photosynthesis. We discuss the meaning of the presence of these bioenergetic pathways to the dynamics of the human gut microbial community, as well as future directions to better characterize this previously unsuspected diversity.