Archaea and the human gut: new beginning of an old story

World J Gastroenterol. 2014 Nov 21;20(43):16062-78. doi: 10.3748/wjg.v20.i43.16062.


Methanogenic archaea are known as human gut inhabitants since more than 30 years ago through the detection of methane in the breath and isolation of two methanogenic species belonging to the order Methanobacteriales, Methanobrevibacter smithii and Methanosphaera stadtmanae. During the last decade, diversity of archaea encountered in the human gastrointestinal tract (GIT) has been extended by sequence identification and culturing of new strains. Here we provide an updated census of the archaeal diversity associated with the human GIT and their possible role in the gut physiology and health. We particularly focus on the still poorly characterized 7th order of methanogens, the Methanomassiliicoccales, associated to aged population. While also largely distributed in non-GIT environments, our actual knowledge on this novel order of methanogens has been mainly revealed through GIT inhabitants. They enlarge the number of final electron acceptors of the gut metabolites to mono- di- and trimethylamine. Trimethylamine is exclusively a microbiota-derived product of nutrients (lecithin, choline, TMAO, L-carnitine) from normal diet, from which seems originate two diseases, trimethylaminuria (or Fish-Odor Syndrome) and cardiovascular disease through the proatherogenic property of its oxidized liver-derived form. This therefore supports interest on these methanogenic species and its use as archaebiotics, a term coined from the notion of archaea-derived probiotics.

Keywords: Archaebiotics; Cardiovascular disease; Human gut microbiota; Methane; Methanogens; Methanomassiliicoccus; Methanomethylophilus; Probiotics; Trimethylamine; Trimethylaminuria.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Breath Tests
  • Disease
  • Euryarchaeota / classification
  • Euryarchaeota / genetics
  • Euryarchaeota / growth & development
  • Euryarchaeota / metabolism*
  • Evolution, Molecular
  • Gastrointestinal Tract / metabolism
  • Gastrointestinal Tract / physiology*
  • Host-Pathogen Interactions
  • Humans
  • Methane / metabolism*
  • Microbiota*
  • Phylogeny


  • Methane