Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)

Carlier, Jean‐Philippe; K'ouas, Guylène; Bonne, Isabelle; Lozniewski, Alain; Mory, F.

doi:10.1099/ijs.0.63060-0

Cited by 54 publications

(43 citation statements)

References 10 publications

(8 reference statements)

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“…Emended description of Oribacterium (Carlier et al, 2004) Elongated ovoid rods, about 1.2-2.2 mm long and 0.45-1 mm wide, usually occurring singly, in pairs or, occasionally, in short chains. Motile with laterally inserted flagella.…”

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confidence: 99%

“…2). The genus Oribacterium comprises, at the time of writing, a single recognized species Oribacterium sinus (Carlier et al, 2004;Rainey, 2009 Table 3). The 16S rRNA gene sequence similarity value of 99.5 % between species within a genus is higher than the reported range of 98.2-99.0 % (Kim et al, 2014;Meier-Kolthoff et al, 2013;Stackebrandt & Ebers, 2006;Yarza et al, 2008).…”

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confidence: 99%

“…The Human Oral Microbiome Database (HOMD) classified the isolated strains as members of oral taxon 108 (Chen et al, 2010). According to preliminary 16S rRNA gene sequence phylogeny, strains ACB1 T , ACB7 T and ACB8 belong to the genus Oribacterium (Carlier et al, 2004) within the family Lachnospiraceae (Rainey, 2009). …”

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confidence: 99%

“…Tables 1-3 summarize physiological and genomic properties that can be used to differentiate strains ACB1 T , ACB7 T and ACB8 from O. sinus and other members of the genus. The type strain of O. sinus (Carlier et al, 2004) was isolated from sinus pus of a 6-year-old child with bilateral maxillary sinusitis, while strains ACB1 T , ACB7 T and ACB8 were enriched from a non-infectious subgingival plaque sampled from a generally healthy 25-year-old adult. Cells of O. sinus were 0.8-1.0 mm wide compared with 0.45-0.5 mm for cells of strains ACB1 T , ACB8 and ACB7 T .…”

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confidence: 99%

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Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

Sizova

Muller

Stancyk

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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Three strictly anaerobic, Gram-positive, non-spore-forming, rod-shaped, motile bacteria, designated strains ACB1 T , ACB7 T and ACB8, were isolated from human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1 T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin and raffinose; strain ACB7 T grew weakly on sucrose only. The growth temperature range was 30-42 6C with optimum growth at 37 6C. Major metabolic fermentation end products of strain ACB1 T were acetate and lactate; the only product of strains ACB7 T and ACB8 was acetate. Major fatty acids of strain ACB1 T were C 14 : 0 , C 16 : 0 , C 16 : 1 v7c dimethyl aldehyde (DMA) and C 18 : 1 v7c DMA. Major fatty acids of strain ACB7 T were C 12 : 0 , C 14 : 0 , C 16 : 0 , C 16 : 1 v7c and C 16 : 1 v7c DMA. The hydrolysate of the peptidoglycan contained meso-diaminopimelic acid, indicating peptidoglycan type A1c. Genomic DNA G+C content varied from 42 to 43.3 % between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1 T , ACB8 and ACB7 T formed two separate branches within the genus Oribacterium, with 98.1-98.6 % sequence similarity to the type strain of the type species, Oribacterium sinus. Predicted DNA-DNA hybridization values between strains ACB1 T , ACB8, ACB7 T and O. sinus F0268 were ,70 %. Based on distinct genotypic and phenotypic characteristics, strains ACB1 T and ACB8, and strain ACB7 T are considered to represent two distinct species of the genus Oribacterium, for which the names Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov. are proposed. The type strains are ACB1 T (5DSM

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confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

Sizova

Muller

Stancyk

et al. 2014

International Journal of Systematic and Evolutionary Microbiology

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“…DNA purification from 24-h TGYH broth bacterial culture was performed with InstaGene matrix (Bio-Rad). The 16S rRNA gene sequences were determined as described previously (28) and compared with sequences available in the GenBank database by using the multisequence advanced BLAST comparison software from the National Center for Biotechnology Information (NCBI) (29).…”

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confidence: 99%

16S rRNA Gene Sequencing, Multilocus Sequence Analysis, and Mass Spectrometry Identification of the Proposed New Species “Clostridium neonatale”

et al. 2014

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In 2002, an outbreak of necrotizing enterocolitis in a Canadian neonatal intensive care unit was associated with a proposed novel species of Clostridium, "Clostridium neonatale." To date, there are no data about the isolation, identification, or clinical significance of this species. Additionally, C. neonatale has not been formally classified as a new species, rendering its identification challenging. Indeed, the C. neonatale 16S rRNA gene sequence shows high similarity to another Clostridium species involved in neonatal necrotizing enterocolitis, Clostridium butyricum. By performing a polyphasic study combining phylogenetic analysis (16S rRNA gene sequencing and multilocus sequence analysis) and phenotypic characterization with mass spectrometry, we demonstrated that C. neonatale is a new species within the Clostridium genus sensu stricto, for which we propose the name Clostridium neonatale sp. nov. Now that the status of C. neonatale has been clarified, matrix-assisted laser desorption ionizationtime of flight mass spectrometry (MALDI-TOF MS) can be used for better differential identification of C. neonatale and C. butyricum clinical isolates. This is necessary to precisely define the role and clinical significance of C. neonatale, a species that may have been misidentified and underrepresented during previous neonatal necrotizing enterocolitis studies.

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Revised Road Map to the Phylum Firmicutes

Ludwig

Schleifer

Whitman

2015

Bergey's Manual of Systematics of Archaea and Bacteria

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The phylum Firmicutes contains three classes, “ Bacilli ”, “ Clostridia ” and “ Erysipelotrichia ”. The Mollicutes were removed from the phylum given the general low support by alternative markers and its unique phenotypic properties, in particular the lack of rigid cell walls. The family Erysipelotrichaceae , which includes wall‐forming Gram‐positive organisms previously classified with the Mollicutes , was retained in the Firmicutes as a novel class, “ Erysipelotrichia ”, and order, “ Erysipelotrichales ”. While the bipartition of the classes “ Clostridia ” and “ Bacilli ” is corroborated by the new analyses, some of the taxa previously assigned to the “ Clostridia ” tend to root outside the Firmicutes and may represent separate phyla. These include taxa previously classified within the “ Thermoanaerobacterales ” and Syntrophomonadaceae , which may contain a number of phylogenetic clades that are distinct at the phylum level. However, given the absence of corroboration by other phylogenetic markers for many of these assignments and a clear consensus on the definition of a phylum, these taxa were retained within the Firmicutes for the present.

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Oribacterium sinus gen. nov., sp. nov., within the family ‘Lachnospiraceae’ (phylum Firmicutes)

Cited by 54 publications

References 10 publications

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium

16S rRNA Gene Sequencing, Multilocus Sequence Analysis, and Mass Spectrometry Identification of the Proposed New Species “Clostridium neonatale”

Revised Road Map to the Phylum Firmicutes

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