The prevalence of species and strains in the human microbiome: a resource for experimental efforts.
Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America.
Laurens
L
Kraal
The Genome Institute, Washington University School of Medicine, Saint Louis, Missouri, United States of America.
Sahar
S
Abubucker
The Genome Institute, Washington University School of Medicine, Saint Louis, Missouri, United States of America.
Karthik
K
Kota
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America.
Michael A
MA
Fischbach
The Genome Institute, Washington University School of Medicine, Saint Louis, Missouri, United States of America; Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States of America; Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, United States of America.
Makedonka
M
Mitreva
D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D064307:Microbiota / Q000235:genetics*; D010802:Phylogeny; D015995:Prevalence; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods
D012336:RNA, Ribosomal, 16S