title: 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.
authors.affiliation: Environmental Microbiology Laboratory, Helmholtz Centre for Infection Research, Braunschweig, Germany. andrew.oxley@helmholtz-hzi.de
authors.forename: Andrew P A
authors.initials: AP
authors.lastname: Oxley
authors.forename: Mariana P
authors.initials: MP
authors.lastname: Lanfranconi
authors.forename: Dieco
authors.initials: D
authors.lastname: Würdemann
authors.forename: Stephan
authors.initials: S
authors.lastname: Ott
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Terry J
authors.initials: TJ
authors.lastname: McGenity
authors.forename: Kenneth N
authors.initials: KN
authors.lastname: Timmis
authors.forename: Balbina
authors.initials: B
authors.lastname: Nogales
mesh_terms: D000328:Adult; D000368:Aged; D019641:DNA, Archaeal / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D006216:Halobacteriaceae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D007413:Intestinal Mucosa / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D054712:Salinity; D017422:Sequence Analysis, DNA; D012965:Sodium Chloride / Q000032:analysis
chemical_list: D019641:DNA, Archaeal; D012336:RNA, Ribosomal, 16S; D012965:Sodium Chloride