Enterococcus faecalis lives in the human gut.

Extending Our View of Self: The Human Gut Microbiome Initiative (HGMI)

The total number of genes in the various species represented in our internal microbial communities (microbiome) likely exceeds the number of our human genes by at least two orders of magnitude. Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgam of human genes and the genes of our microbial ‘selves’.

Without understanding the interactions between our human and microbial genomes, it is impossible to obtain a complete picture of our biology. Our microbiome is largely unexplored.

The Human Gut Microbiome Initiative (HGMI) (a precursor to the Human Microbiome Project) represents a logical, timely, and cost-effective extension of the Human Genome Project. It promises to improve our understanding of the foundations of human health, and of many common diseases that are the subject of basic and clinical research sponsored by the NIH. The human gut microbiome endows us with physiologic capabilities that we have not had to evolve on our own. It is essentially a bacterial ecosystem residing in the human GI tract; an efficient bioreactor, programmed to break down food and supply us with the extracted energy and nutrients. The HGMI seeks to deliver a more comprehensive view of our biology by providing deep draft whole genome sequences for 100 species representing the bacterial divisions known to reside in the distal gut. Fifteen of these genomes will be selected for finishing. The deposited, curated genome sequences will provide another phase of understanding the “human” genome sequencing project and will serve as a model for sequencing other human microbial communities.

The human GI tract is predominantly a bacterial ecosystem. Cell densities in the colon (10¹¹-10¹²/ml contents) are the highest recorded for any known ecosystem. The vast majority belong to two divisions (superkingdoms) of Bacteria - the Bacteroidetes (48%) and the Firmicutes (51%). The remaining phylotypes are distributed among 6 other common groups and several rare groups. The sequenced organisms were chosen from the 11,831-member 16S rRNA sequence dataset generated from the human colonic microbiota of three healthy adults.

-- Adapted from the human gut microbiome white paper (pdf).