Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.
A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight-chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell-wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1σ lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol%. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of species of the genus Clostridium, including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium mayombei (96.2%), Clostridium bartlettii (96.0%) and Clostridium irregulare (95.5%). All these species show very low 16S rRNA gene sequence similarity (<85%) to the type strain of Clostridium butyricum, the type species of the genus Clostridium. DNA-DNA hybridization with closely related reference strains indicated reassociation values below 32%. On the basis of phenotypic and genetic studies, a novel genus, Romboutsia gen. nov., is proposed. The novel isolate CRIBT (=DSM 25109T=NIZO 4048T) is proposed as the type strain of the type species, Romboutsia ilealis gen. nov., sp. nov., of the proposed novel genus. It is proposed that C. lituseburense is transferred to this genus as Romboutsia lituseburensis comb. nov. Furthermore, the reclassification into novel genera is proposed for C. bartlettii, as Intestinibacter bartlettii gen. nov., comb. nov. (type species of the genus), C. glycolicum, as Terrisporobacter glycolicus gen. nov., comb. nov. (type species of the genus), C. mayombei, as Terrisporobacter mayombei gen. nov., comb. nov., and C. irregulare, as Asaccharospora irregularis gen. nov., comb. nov. (type species of the genus), on the basis of additional data collected in this study. In addition, an emendation of the species Peptostreptococcus anaerobius and the order Eubacteriales is provided.
Winclove Probiotics, Hulstweg 11, 1032 LB Amsterdam, The Netherlands.|Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
Jacoline
J
Gerritsen
Winclove Probiotics, Hulstweg 11, 1032 LB Amsterdam, The Netherlands.|Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
Susana
S
Fuentes
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
Wieke
W
Grievink
Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
Laura
L
van Niftrik
Leibniz-Institut DSMZ - Deutsche Sammlung vor Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany.
Brian J
BJ
Tindall
Department of Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 GA Utrecht, The Netherlands.|Winclove Probiotics, Hulstweg 11, 1032 LB Amsterdam, The Netherlands.
Harro M
HM
Timmerman
Department of Operating Rooms, University Medical Center St. Radboud, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.|Laboratory for Medical Microbiology and Immunology, St. Antonius Hospital, P.O. Box 2500, 3430 EM Nieuwegein, The Netherlands.|Department of Surgery, University Medical Center Utrecht, P.O. Box 85500, 3508 GA Utrecht, The Netherlands.
Ger T
GT
Rijkers
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
Hauke
H
Smidt
D000818:Animals; D015373:Bacterial Typing Techniques; D001482:Base Composition; D004269:DNA, Bacterial / Q000235:genetics; D005227:Fatty Acids / Q000737:chemistry; D006017:Glycolipids / Q000737:chemistry; D016937:Gram-Positive Endospore-Forming Rods / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D007082:Ileum / Q000382:microbiology*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010457:Peptidoglycan / Q000737:chemistry; D010743:Phospholipids / Q000737:chemistry; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D051381:Rats; D017207:Rats, Sprague-Dawley / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D024482:Vitamin K 2 / Q000031:analogs & derivatives / Q000737:chemistry
D004269:DNA, Bacterial; D005227:Fatty Acids; D006017:Glycolipids; D010457:Peptidoglycan; D010743:Phospholipids; D012336:RNA, Ribosomal, 16S; D024482:Vitamin K 2; C042455:menaquinone 6