Structure, function and diversity of the healthy human microbiome

Abstract

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Keywords

Affiliated Institutions

• Cleveland Clinic US
• J. Craig Venter Institute US
• University of Maryland, Baltimore US
• Los Alamos National Laboratory US
• University of Guelph CA
• Lawrence Berkeley National Laboratory US
• Massachusetts Institute of Technology US
• University of Baltimore US
• Virginia Commonwealth University US
• Vrije Universiteit Brussel BE
• University of North Carolina at Charlotte US
• United States Department of Energy US
• University of Idaho US
• Saint Louis University US
• New York University US
• University of Colorado Boulder US
• Broad Institute US
• Howard Hughes Medical Institute US
• University of California, San Francisco US
• Washington University in St. Louis US
• Harvard University Press US
• Baylor College of Medicine US
• Procter & Gamble (United States) US
• National Institutes of Health US

Related Publications