Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or…

• RF
  Rockefeller Foundation
• MD
  Ministero dell’Istruzione, dell’Università e della Ricerca

  Award: RBFR13EWWI
• MR
  Medical Research Council

  Awards: MR/M50161X/1, MR/L015080/1
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/L027801/1, BB/R015171/1
• NI
  National Institute of Diabetes and Digestive and Kidney Diseases

  Awards: R24DK110499, U54DE023798