Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle

David K. Jacobson, Tanvi P. Honap, Andrew T. Ozga, Nicolas Meda, Thérèse S. Kagoné, Hélène Carabin, Paul Spicer, Raul Y. Tito, Alexandra J. Obregon-Tito, Luis Marin Reyes, Luzmila Troncoso-Corzo, Emilio Guija-Poma, Krithivasan Sankaranarayanan, Cecil M. Lewis

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Article number1724
JournalScientific Reports
Volume11
Issue number1
DOIs
StatePublished - Dec 2021

Bibliographical note

Funding Information:
Funding for this manuscript came from NSF Doctoral Dissertation Improvement Grant (1925579) and NIH R01 Grant (GM089886).

Publisher Copyright:
© 2021, The Author(s).

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