title: Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.
abstract: BACKGROUND
  The incidence and diversity of human methanogens are insufficiently characterised in the gastrointestinal tract of both health and disease. A PCR and clone library methodology targeting the mcrA gene was adopted to facilitate the two-fold aim of surveying the relative incidence of methanogens in health and disease groups and also to provide an overview of methanogen diversity in the human gastrointestinal tract.
  
  
  RESULTS
  DNA faecal extracts (207 in total) from a group of healthy controls and five gastrointestinal disease groups were investigated. Colorectal cancer, polypectomised, irritable bowel syndrome and the control group had largely equivalent numbers of individuals positive for methanogens (range 45-50%). Methanogen incidence in the inflammatory bowel disease groups was reduced, 24% for ulcerative colitis and 30% for Crohn's disease. Four unique mcrA gene restriction fragment length polymorphism profiles were identified and bioinformatic analyses revealed that the majority of all sequences (94%) retrieved from libraries were 100% identical to Methanobrevibacter smithii mcrA gene. In addition, mcrA gene sequences most closely related to Methanobrevibacter oralis and members of the order Methanosarcinales were also recovered.
  
  
  CONCLUSIONS
  The mcrA gene serves as a useful biomarker for methanogen detection in the human gut and the varying trends of methanogen incidence in the human gut could serve as important indicators of intestinal function. Although Methanobrevibacter smithii is the dominant methanogen in both the distal colon of individuals in health and disease, the diversity of methanogens is greater than previously reported. In conclusion, the low incidence of methanogens in Inflammatory Bowel Disease, the functionality of the methanogens and impact of methane production in addition to competitive interactions between methanogens and other microbial groups in the human gastrointestinal tract warrants further investigation.
authors.affiliation: Alimentary Pharmabiotic Centre, National University of Ireland, University College Cork, Cork, Ireland. paulinescanlan@yahoo.co.uk
authors.forename: Pauline D
authors.initials: PD
authors.lastname: Scanlan
authors.forename: Fergus
authors.initials: F
authors.lastname: Shanahan
authors.forename: Julian R
authors.initials: JR
authors.lastname: Marchesi
mesh_terms: D000328:Adult; D000368:Aged; D044822:Biodiversity; D003001:Cloning, Molecular; D015179:Colorectal Neoplasms / Q000382:microbiology*; D019641:DNA, Archaeal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D007410:Intestinal Diseases / Q000382:microbiology*; D008297:Male; D017012:Methanobacteriales / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D041581:Methanobrevibacter / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D019640:Methanosarcinales / Q000235:genetics / Q000302:isolation & purification; D008875:Middle Aged; D008969:Molecular Sequence Data; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase