Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
2019/01/01 by Edoardo Pasolli, Francesco Asnicar, Serena Manara +16 · 1,744 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Anthropology #Biology #Computational biology #Diversity (politics) #Evolutionary biology #Gene #Genetics #Genome #Gut microbiota and health #Human microbiome #Metabolomics and Mass Spectrometry Studies #Metagenomics #Microbial Community Ecology and Physiology #Microbiome
paper · pdf · doi:10.1016/j.cell.2019.01.001
published in Cell 176(3), 649-662.e20 (Cell Press)
openalex publication_date 2019/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
Abstract
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 Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.
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