Abstract
The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades. Genes for utilizing trimethylamine (TMA), a bacterial precursor to an atherosclerogenic human metabolite, were present in four of the six novel Methanomassiliicoccales genomes assembled from ELDERMET metagenomes. In addition to increased microbiota TMA production capacity in long-term residential care subjects, abundance of TMA-utilizing Methanomassiliicoccales correlated positively with bacterial gene count for TMA production and negatively with fecal TMA concentrations. The two large Methanomassiliicoccales clades have opposite correlations with host health status in the ELDERMET cohort and putative distinct genomic signatures for gut adaptation.
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Acknowledgements
We thank JK Goodrich, RE Ley, JC Clemente and MG Domingo-Bello for sharing their data to identify human-associated Methanomassiliicoccales, as well as J-F Mangot for his early advice with binning. PWO’T was supported by Science Foundation Ireland through a Principal Investigator award, by a CSET award to the APC Microbiome Institute and by an FHRI award to the ELDERMET project by the Department of Agriculture, Fisheries and Marine of the Government of Ireland.
Author contributions
Conceptualization: GB, J-FB, and PWO’T; methodology: GB and PWO’T; investigation: GB, JD, and MCN; formal analysis: GB, AMC, and DBL; writing—original draft: GB; writing—review and editing: AMC, J-FB, and PWO’T.
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Affiliations
School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland
- Guillaume Borrel
- , Angela McCann
- , Jennifer Deane
- , Marta C Neto
- , Denise B Lynch
- & Paul W O'Toole
EA-4678 CIDAM, Clermont Université, Université d’Auvergne, Clermont-Ferrand, France
- Jean- François Brugère
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The authors declare no conflict of interest.
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Correspondence to Paul W O'Toole.
Supplementary information
Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)
