Strains, functions and dynamics in the expanded Human Microbiome Project

Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle G. Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White and Curtis Huttenhower ()
Additional contact information
Jason Lloyd-Price: Harvard T. H. Chan School of Public Health
Anup Mahurkar: Institute for Genome Sciences, University of Maryland School of Medicine
Gholamali Rahnavard: Harvard T. H. Chan School of Public Health
Jonathan Crabtree: Institute for Genome Sciences, University of Maryland School of Medicine
Joshua Orvis: Institute for Genome Sciences, University of Maryland School of Medicine
A. Brantley Hall: The Broad Institute
Arthur Brady: Institute for Genome Sciences, University of Maryland School of Medicine
Heather H. Creasy: Institute for Genome Sciences, University of Maryland School of Medicine
Carrie McCracken: Institute for Genome Sciences, University of Maryland School of Medicine
Michelle G. Giglio: Institute for Genome Sciences, University of Maryland School of Medicine
Daniel McDonald: University of California San Diego
Eric A. Franzosa: Harvard T. H. Chan School of Public Health
Rob Knight: University of California San Diego
Owen White: Institute for Genome Sciences, University of Maryland School of Medicine
Curtis Huttenhower: Harvard T. H. Chan School of Public Health

Nature, 2017, vol. 550, issue 7674, 61-66

Abstract: Abstract The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.

Date: 2017
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DOI: 10.1038/nature23889

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