Article

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

International Journal of Systematic and Evolutionary Microbiology (Impact Factor: 2.8). 05/2014; 64. DOI: 10.1099/ijs.0.060988-0
Source: PubMed

ABSTRACT Three strictly anaerobic Gram-positive non-spore-forming rod-shaped motile bacteria designated as Oribacterium sp. ACB1T, ACB7T and ACB8 were isolated from the human subgingival dental plaque. All strains required yeast extract for growth. Strains ACB1T and ACB8 were able to grow on glucose, lactose, maltose, maltodextrin, and raffinose; strain ACB7T grew weakly on sucrose only. The growth temperature range was 30 - 42 oC with optimum at 37 oC. Major metabolic fermentation end products of strain ACB1T were acetate and lactate; the only product of strains ACB7T and ACB8 was acetate. Major fatty acids of strain ACB1T were C14:0, C16:0, C16:1 ω7c DMA (dimethyl aldehyde) and C18:1 ω7c DMA. Major fatty acids of strain ACB7T were C12:0, C14:0, C16:0, C16:1 ω7c and C16:1 ω7c DMA. The hydrolysate of peptidoglycan contained meso-diaminopimelic acid indicating peptidoglycan type A1γ. Genomic DNA G + C content varied from 42 to 43.3% between strains. According to 16S rRNA gene sequence phylogeny, strains ACB1T, ACB8 and ACB7T formed two separate branches within the genus Oribacterium, with sequence similarity to type species of Oribacterium sinus at 98.1-98.6%. Predicted DNA-DNA hybridization values between strains ACB1T, ACB8, ACB7T and O. sinus were <70%. Based on distinct genotypic and phenotypic characteristics, we suggest that strains ACB1T and ACB8, and strain ACB7T 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 strain ACB1T (= DSM 24637T; = HM-481T; =ATCC BAA-2638T) and strain ACB7T (= DSM 24638T; = HM-482T; =ATCC BAA-2639T).

Full-text

Available from: Nicolai S Panikov, May 18, 2014
0 Followers
 · 
86 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).
    Standards in Genomic Sciences 01/2010; 2(1):142-8. DOI:10.4056/sigs.541628 · 3.17 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.
    Standards in Genomic Sciences 01/2010; 2(1):117-34. DOI:10.4056/sigs.531120 · 3.17 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A hitherto unknown anaerobic bacillus isolated from sinus pus in a young child (strain AIP 354.02T) was characterized by using phenotypic and genotypic methods. 16S rRNA gene sequence analysis indicated that this strain was phylogenetically affiliated with several sequences of cloned 16S rRNA gene inserts previously deposited in the public databases. According to their 16S rRNA gene sequence similarities, these uncultivated bacteria, together with strain AIP 354.02T, formed a separate subgroup belonging to the family 'Lachnospiraceae' within the phylum Firmicutes. Oribacterium gen. nov. is proposed for this group of organisms and Oribacterium sinus gen. nov. sp. nov. for strain AIP 354.02T (= CIP 107991T = CCUG 48084T).
    International Journal of Systematic and Evolutionary Microbiology 10/2004; 54(Pt 5):1611-5. DOI:10.1099/ijs.0.63060-0 · 2.80 Impact Factor