Halophilic archaea in the human intestinal mucosa

Abstract

The human gastrointestinal tract microbiota, despite its key roles in health and disease, remains a diverse, variable and poorly understood entity. Current surveys reveal a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea. In an analysis of the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease we found 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae (haloarchaea), including novel phylotypes. As the human colon is not considered a salty environment and haloarchaea are described as extreme halophiles, we evaluated and further discarded the possibility that these sequences originated from pre-colonoscopy saline lavage solutions. Furthermore, aerobic enrichment cultures prepared from a patient biopsy at low salinity (2.5% NaCl) yielded haloarchaeal sequence types. Microscopic observation after fluorescence in situ hybridization provided evidence of the presence of viable archaeal cells in these cultures. These results prove the survival of haloarchaea in the digestive system and suggest that they may be members of the mucosal microbiota, even if present in low numbers in comparison with methanogenic archaea. Investigation of a potential physiological basis of this association may lead to new insights into gastrointestinal health and disease.

Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon

“…Archaeal diversity (16S rRNA gene TRFs) was greater than MA diversity (mcrA TRFs). This observation indicates significant colonization by non-MA, which is in accordance with previous detection of non-MA from colonic mucosa (Oxley et al, 2010). Alternatively, it is possible that MA harboring the mrtA functional gene, such as Msp.…”

“…Relatively limited MA diversity has been detected, with only Methanobrevibacter smithii and Methanosphaera stadtmanae cultured from stool (Miller et al, 1982;Miller and Wolin, 1985) and also predominant in molecular surveys (Eckburg et al, 2005;Zhang et al, 2009). More recently, Oxley et al (2010) reported the presence of Mb. smithii, Mb.…”

Archaeal Diversity and Their Biotechnological Potential

“…In another study the microbiota in colonic mucosal biopsies from patients with inflammatory bowel disease, 16S rDNA sequences representing a phylogenetically rich diversity of halophilic archaea from the Halobacteriaceae were determined. The study revealed a multitude of undefined bacterial taxa and a low diversity of methanogenic archaea (Oxley et al, 2010). Representatives of Archaea, the third domain of life, were generally thought to be limited to environmental extremes of the earth.…”

“…Like Bacteria, Archaea are commonly mesophilic, and some members are known to be closely associated with eukaryotic hosts, including humans. For instance, high numbers of methane-producing Archaea (methanogens) have been detected in the gastrointestinal tract, vagina, and oral cavity (Belay et al, 1990;Vianna et al, 2006) and recently non-methanogenic Archaea including members of the Crenarchaeota, Thermococcales, Thermoplasmatales and Halobacteriaceae, have been detected in human faeces (Oxley et al, 2010). They are now recognized as a component of human microbiota and it is subjects of debate wheather archaea are cause of any disease in human.…”

“…Archaeal ecology is generally accepted as synonymous with extreme environments in the point of the human being view. Representatives of Archaea, however, occur everywhere: in samples from ocean water, ocean sediments, freshwater lakes, soil, solid gas hydrates, tidal flat sediments, plant roots, peatlands, petroleum-contaminated aquifers, human subgingival area, skin and gastrointestinal tract and as a simbiyont within the sponge (Cavicchioli et al, 2003;Mills et al, 2005;DeLong, 2005;Knittel et al 2005;Fierer et al, 2007;Brochier-Armanet et al 2008;Oxley et al 2010;Kong, 2011).…”