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Abstract
High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2–5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.
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1 University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018); University of Oklahoma, Department of Anthropology, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)
2 Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, USA (GRID:grid.261241.2) (ISNI:0000 0001 2168 8324)
3 Ministry of Health, Ouagadougou, Burkina Faso (GRID:grid.261241.2)
4 Centre MURAZ Research Institute, Bobo-Dioulasso, Burkina Faso (GRID:grid.418128.6) (ISNI:0000 0004 0564 1122)
5 University of Oklahoma Health Sciences Center, Department of Biostatistics and Epidemiology, College of Public Health, Oklahoma City, USA (GRID:grid.266902.9) (ISNI:0000 0001 2179 3618); Faculté de médecine vétérinaire, Université de Montréal, Département de Pathologie et Microbiologie, Saint-Hyacinthe, Canada (GRID:grid.14848.31) (ISNI:0000 0001 2292 3357); École de santé publique de l’université de Montréal, Département de médecine sociale et préventive, Montréal, Canada (GRID:grid.14848.31) (ISNI:0000 0001 2292 3357); Centre de Recherche en Santé Publique (CReSP) de l’université de Montréal et du CIUSS du Centre Sud de Montréal, Montréal, Canada (GRID:grid.14848.31) (ISNI:0000 0001 2292 3357)
6 University of Oklahoma, Department of Anthropology, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018); University of Oklahoma, Center for Applied Social Research, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)
7 University of Oklahoma, Department of Anthropology, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)
8 Instituto Nacional de Salud, Centro Nacional de Salud Publica, Lima, Perú (GRID:grid.419228.4) (ISNI:0000 0004 0636 549X)
9 Universidad Nacional Mayor de San Marcos, Facultad de Medicina, Lima, Perú (GRID:grid.10800.39) (ISNI:0000 0001 2107 4576)
10 Universidad de San Martín de Porres, Centro de Investigación de Bioquímica y Nutrición, Facultad de Medicina Humana, Lima, Perú (GRID:grid.441816.e) (ISNI:0000 0001 2182 6061)
11 University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018); University of Oklahoma, Department of Microbiology and Plant Biology, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)