Genomics and metagenomics of trimethylamine-utilizing Archaea in the human gut microbiome

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.

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

“…The same finding was reported for M. luminyensis [129]. In fact, M. luminyensis was shown to be able to degrade trimethylamine (TMA), a compound associated with metabolic disorders such as trimethylaminuria [130], as well as reducing trimethylamine-N-oxide (TMAO) plasma levels, preventing the development of cardiovascular and chronic kidney diseases [131,132]. Thus, a potential use of M. luminyensis as an archaeal probiotic, or "archaebiotic", was proposed to promote a positive effect of archaea on human health [133].…”

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders

“…4,20,[21][22][23][24][25] Furthermore, disappearance of methane from a breath test correlates strongly with a reduction of M. smithii levels in stool. Emerging evidence suggests patients with FGID may have a different microbiome compared to asymptomatic controls, but methanogens appear to be equally prevalent in IBS and in controls, although associated with a Clostridiales-enriched enterotype.…”

Lysogeny is prevalent and widely distributed in the murine gut microbiota

“…The gut microbiota is recognized as a hidden modifier of host physiology and metabolism [1]. Although the microbiome-mediated host phenotypes are attributed to the interplay between different types of microorganisms [2,3], most microbiome studies have focused on bacteria. Viruses are central members of the gut microbiota; most of them are bacterial viruses (bacteriophages or phages) [1].…”