title: Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome.
abstract: In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed.
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: ulla.hynonen@helsinki.fi.
authors.forename: Ulla
authors.initials: U
authors.lastname: Hynönen
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: pia.rasinkangas@helsinki.fi.
authors.forename: Pia
authors.initials: P
authors.lastname: Rasinkangas
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: reetta.satokari@helsinki.fi.
authors.forename: Reetta
authors.initials: R
authors.lastname: Satokari
authors.affiliation: Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland. Electronic address: lars.paulin@helsinki.fi.
authors.forename: Lars
authors.initials: L
authors.lastname: Paulin
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: willem.devos@helsinki.fi.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: taija.pietila@helsinki.fi.
authors.forename: Taija E
authors.initials: TE
authors.lastname: Pietilä
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: ravi.kant@helsinki.fi.
authors.forename: Ravi
authors.initials: R
authors.lastname: Kant
authors.affiliation: Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland. Electronic address: airi.palva@helsinki.fi.
authors.forename: Airi
authors.initials: A
authors.lastname: Palva
mesh_terms: D019342:Acetic Acid / Q000378:metabolism; D001421:Bacteria, Anaerobic / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001482:Base Composition; D001483:Base Sequence; D003967:Diarrhea / Q000175:diagnosis* / Q000382:microbiology; D000431:Ethanol / Q000378:metabolism; D005227:Fatty Acids / Q000378:metabolism; D005561:Formates / Q000378:metabolism; D041981:Gastrointestinal Tract / Q000382:microbiology; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D016908:Gram-Positive Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology; D006801:Humans; D043183:Irritable Bowel Syndrome / Q000175:diagnosis* / Q000382:microbiology; D019344:Lactic Acid / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D045857:Ruminococcus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D019802:Succinic Acid / Q000378:metabolism
chemical_list: D005227:Fatty Acids; D005561:Formates; D012336:RNA, Ribosomal, 16S; C030544:formic acid; D019344:Lactic Acid; D000431:Ethanol; D019802:Succinic Acid; D005947:Glucose; D019342:Acetic Acid
keywords: Genome; IBS; Intestinal microbiota; Ruminococcus