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PLoS One DOI:10.1371/journal.pone.0041294

The "most wanted" taxa from the human microbiome for whole genome sequencing.

Publication TypeJournal Article
Year of Publication2012
AuthorsFodor, AA, DeSantis, TZ, Wylie, KM, Badger, JH, Ye, Y, Hepburn, T, Hu, P, Sodergren, E, Liolios, K, Huot-Creasy, H, Birren, BW, Earl, AM
JournalPLoS One
Date Published2012
KeywordsBacteria, Cohort Studies, Female, Genes, Bacterial, Genes, rRNA, Humans, Male, Metagenome, RNA, Bacterial, RNA, Ribosomal, 16S, Sequence Analysis, DNA

The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.


Alternate JournalPLoS ONE
PubMed ID22848458
PubMed Central IDPMC3406062
Grant ListU54 HG004968 / HG / NHGRI NIH HHS / United States
HHSN2722009000018C / / PHS HHS / United States
U54HG004968 / HG / NHGRI NIH HHS / United States
U54HG004969 / HG / NHGRI NIH HHS / United States