Saturday, April 27, 2013

[Microbiota • 2013] Biodiversity and functional genomics in the Human Microbiome

Figure 2. A map of diversity in the human microbiome. The human microbiome is dominated by four phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria.
In the center is a phylogenetic tree of organisms abundant in the human microbiome. Commensal microbes are indicated by circles, and potential pathogens are indicated by stars. The middle ring corresponds to body sites at which the various taxa are abundant and is color-coded by site [e.g., Ruminococcus (blue) is found mostly in the gut, whereas Lactobacillus (purple) is found mostly in the vagina]. The bar heights on the outside of the circle are proportional to taxa abundance at the body site of greatest prevalence [e.g., Streptococcus mitis (yellow) dominates the inside of the cheek, whereas the gut is abundant in a variety of Bacteroides]. The intensity of external colors corresponds to species prevalence in each body site.

Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host–microbe and microbe–microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools.

Keywords: Human Microbiome Project; microbiota; metagenomics

Xochitl C. Morgan, Nicola Segata and Curtis Huttenhower. 2013. Biodiversity and functional genomics in the human microbiome. Trends in Genetics. 29(1), 51–58.