Strains, functions and dynamics in the expanded Human Microbiome Project.
Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C
Nature. 10 2017. doi: 10.1038/nature23889
COMMENT: In this article The Human Microbiome Project provides a second wave of data from the human microbiome studies, comprising 1,631 new metagenomes from diverse body sites and studies analyzing multiple time points in the same individual (265 individuals). New data and updated methods for analyzing human microbiomes with a special focus on personal microbiome dynamics.
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.