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.

Abstract

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.

The cellular lipids of Romboutsia

“…As described previously, 2DTLC revealed the presence of several phospholipids and glycolipids in R. ilealis and R. lituseburensis , but some differences between species were noted [1]. We have now analyzed the polar lipids of three species, R. lituseburensis, R. ilealis and strain FRIFI, by 2D-TLC using solvent systems that differ from those used in the previous study.…”

“…On the basis of 16S rRNA gene sequencing and its low G + C content, 28.1 mol%, the new strain, named Romboutsia ilealis , was considered to be closely related to several species of the genus Clostridium , including Clostridium lituseburense (97.2%), Clostridium glycolicum (96.2%), Clostridium irregulare (95.5%) and two other species of clostridia. It was therefore decided to transfer C. lituseburense to this new genus and to reclassify C. glycolicum and C. irregulare into new genera [1]. Furthermore, strain FRIFI was recently isolated from human ileostoma effluent and was shown to represent a new species within the genus Romboutsia [2].…”

Comparisons of gut microbiota profiles in wild-type and gelatinase B/matrix metalloproteinase-9-deficient mice in acute DSS-induced colitis

“…Furthermore, we observed that DSS-supplemented mice had lower relative abundances of Alistipes , Alloprevotella , Prevotella , Odoribacter , Lactobacillus , and Helicobactor ; and higher relative abundances of Romboutsia , Akkermansia , Escherichia , Shigella , and Clostridium sensu stricto compared to control mice. The genus Romboutsia is a newly described bacterial genus, first described in 2014, 29 which may explain the lack of evidence about this genus in the literature. Moreover, the family Enterobacteriaceae was significantly increased in mice that received DSS ( p  < 0.001) and a linear relationship was found between DAI and the incidence of Enterobacteriaceae (Spearman’s rho = 0.82, p  < 0.001) (data not shown).…”

Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species

“…Successive studies supported and expanded this framework (Finegold et al, 2002;Stackebrandt et al, 1999;Wiegel et al, 2006) (Fig. 1) with many organisms formally recognized as species of the genus Clostridium being transferred to new or established genera (Breitenstein et al, 2002;Cai & Dong, 2010;Gerritsen et al, 2014;Kaur et al, 2014;Lee et al, 1993;Liu et al, 2008;Moon et al, 2008;Rainey et al, 2009;Strömpl et al, 2000) -see Table S1 (available in the online Supplementary Material). However, the reclassification of organisms that fall outside the Clostridium cluster I continues, and the reader should consult List of Prokaryotic Names with Standing in Nomenclature (Parte, 2014; http://www.bacterio.net), which is updated regularly on publication of the International Journal of Systematic and Evolutionary Microbiology (IJSEM).…”