The Human Microbiome Project has improved our understanding of microbial and functional diversity. Lloyd-Price, Mahurkar et al. now report an expanded data set from the study, comprising 1,631 new metagenomes (2,355 total) from diverse body sites at multiple time points in 265 individuals. Strain-level metagenomic profiles revealed body site-specific subspecies clades and the authors were able to quantify species with phylogenetic diversity that were under-represented in isolate genomes. Moreover, species-level taxonomic profiling revealed co-occurrence patterns between bacterial species and several archaea, eukaryotes and viruses. Using functional profiling methods, the authors classified metabolic core pathways into universal, microbiome-enriched and body site-enriched; the latter being indicative of functional adaptation by the microbiota to a particular niche. Finally, the authors characterized microbial and functional variation over time at different body sites.
Lloyd-Price, J., Mahurkar, A. et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature http://dx.doi.org/10.1038/nature23889 (2017)
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Du Toit, A. Diving deeper into the communities. Nat Rev Microbiol 15, 643 (2017). https://doi.org/10.1038/nrmicro.2017.130