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Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20.

Strains, functions and dynamics in the expanded Human Microbiome Project.

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Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA.
The Broad Institute, Cambridge, Massachusetts 02142, USA.
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.
Department of Computer Science & Engineering, University of California San Diego, La Jolla, California 92093, USA.


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.

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