A meta-analysis compared fecal samples collected from healthy individuals who were 3 years of age or older and included in the AGP data set to a previously published 16S rRNA V4 region data set that included healthy people living an industrialized, remote agrarian, or hunter-gatherer lifestyle (6 (link), 11 (link), 12 (link)). The AGP subset of healthy individuals was determined by filtering by the metadata columns “subset_antibiotic,” “subset_ibd,” and “subset_diabetes” and, for individuals over the age of 16 years, “subset_bmi.” All data sets were processed using the Deblur pipeline as noted above, with the exception that all reads in the meta-analysis, including AGP data, were trimmed to 100 nt to accommodate the read length in the work of Yatsunenko et al. (6 (link)). Bloom reads as described above were removed from all samples. We used Striped UniFrac as noted above to estimate beta-diversity (unweighted UniFrac) and EMPeror software (66 (link)) version 0.9 to visualize principal coordinates. We used a nonparametric PERMANOVA with 999 permutations to test for significant differences in fecal microbiomes associated with industrialized, remote agrarian, and hunter-gatherer lifestyles. All AGP samples were considered to be from people living an industrialized lifestyle. Balances were constructed from partial least-squares to assess the differences between the hunter-gatherer and industrialized populations and between the remote farmers and industrialized populations.
Other organizations :
University of California, San Diego, San Diego State University, North Carolina State University, University of Oregon, University of Chicago, Argonne National Laboratory, University of Queensland, Broad Institute, Harvard University, King's College London, Institute on Aging, University of Minnesota, Biotechnology Institute, Gladstone Institutes, University of California, San Francisco, St Petersburg University, Colorado State University, Carnegie Mellon University, Nantes Université, University of Pittsburgh, University of Colorado Boulder, California Institute for Biomedical Research, NOAA Atlantic Oceanographic and Meteorological Laboratories, NOAA National Marine Fisheries Service Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Northern Gulf Institute, University of Southern Mississippi, Duke University, Clinical Research Institute
Fecal microbiome composition (based on 16S rRNA V4 region sequencing)
control variables
Age (3 years or older)
Health status (healthy individuals)
controls
Positive control: None specified.
Negative control: None specified.
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