Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov.
ABSTRACT: Five strains of anaerobic, gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that these strains represented a novel group within the family Prevotellaceae, and the most closely related species was Prevotella tannerae. P. tannerae and the novel taxon are deeply branched from the genus Prevotella, with sequence identities to the type strain of the type species of Prevotella, Prevotella melaninogenica, of 82.2 and 85.6?%, respectively. The novel genus Alloprevotella gen. nov. is proposed to accommodate the novel species Alloprevotella rava gen. nov., sp. nov. and the previously named Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. The type species is Alloprevotella tannerae. The type strain of Alloprevotella rava is 81/4-12(T) (?=?DSM 22548(T) ?=?CCUG 58091(T)) and the type strain of Alloprevotella tannerae is ATCC 51259(T) ?=?CCUG 34292(T) ?=?CIP 104476(T) ?=?NCTC 13073(T). Alloprevotella rava is weakly to moderately saccharolytic and produces moderate amounts of acetic acid and major amounts of succinic acid as end products of fermentation. Strains are sensitive to 20?% bile and hydrolyse gelatin. The principal cellular long-chain fatty acids are anteiso-C15?:?0, iso-C15?:?0, C16?:?0, iso-C17?:?0 and iso-C17?:?0 3-OH. The G+C content of the DNA of the type strain is 47 mol%.
Project description:A Gram-negative, strictly anaerobic mucin-degrading bacterium, which we designated strain E39T, was isolated from the rumen epithelium of Korean cattle. The cells were non-motile and had a coccus morphology. Growth of strain E39T was observed at 30-45°C (optimum, 39°C), pH 6.5-8.5 (optimum, pH 7.5), and in the presence of 0.0-1.0% (w/v) NaCl (optimum, 0.0-0.5%). Strain E39T contained C16:0, C18:0, C18:1 ω9c, iso-C15:0, and anteiso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, and unidentified lipids. The major respiratory isoprenoid quinones were MK-8 and MK-9. The major fermented end-products of mucin were acetate and succinate. The G+C content of the genomic DNA was 46.4 mol%. Strain E39T was most closely related to Alloprevotella rava 81/4-12T with an 87.3% 16S rRNA gene sequence similarity. On the basis of phenotypic, chemotaxonomic, and molecular properties, strain E39T represents a novel genus of the family Prevotellaceae; as such, the name Pseudoprevotella muciniphila gen. nov., sp. nov. is proposed. A functional annotation of the whole genome sequences of P. muciniphila E39T revealed that this bacterium has a putative mucin-degrading pathway and biosynthetic pathways of extracellular polymeric substances and virulence factors which enable bacteria to adhere to the epithelial cells and avoid the host's immune responses.
Project description:Two strains of anaerobic, Gram-stain-negative bacilli isolated from the human oral cavity (D033B-12-2(T) and D080A-01) were subjected to a comprehensive range of phenotypic and genotypic tests and were found to be distinct from any previously described species. 16S rRNA gene sequence analysis revealed that the strains were related most closely to the type strain of Prevotella marshii (93.5?% sequence identity). The novel strains were saccharolytic and produced acetic acid and succinic acid as end products of fermentation. The principal cellular long-chain fatty acids were C???:?), iso-C??:?, C??:?, anteiso-C??:?, iso-C???:? and C??:?) 3-OH. The G+C content of the DNA of strain D033B-12-2(T) was 44 mol%. Strains D033B-12-2(T) and D080A-01 are considered to represent a single novel species of the genus Prevotella, for which the name Prevotella saccharolytica sp. nov. is proposed. The type strain is D033B-12-2(T) (=DSM 22473(T) =CCUG 57944(T)).
Project description:Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3:22(T) and N1(T)) are described. Strain CD3:22(T) was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1(T) from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H(2)S, NH(3), butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98% sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/E. saburreum-like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae. While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089(T) confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3:22(T) and N1(T) represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales, class Clostridia, phylum Firmicutes]. Strain CD3:22(T) (=CCUG 58757(T) =DSM 23576(T)) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1(T) (=CCUG 60305(T)=DSM 24553(T)) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089(T) =ATCC 33271(T) =CIP 105341(T) =DSM 3986(T) =JCM 11021(T) =VPI 11763(T)).
Project description:A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199<sup>T</sup>) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were <i>iso-</i>C<sub>15:0</sub>, <i>iso-</i>C<sub>16:0</sub>, <i>anteiso-</i>C<sub>15:0</sub>, and <i>iso-</i>C<sub>17:0</sub>. The peptidoglycan contained <i>meso</i>-diaminopimelic acid (<i>meso</i>-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199<sup>T</sup>. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199<sup>T</sup> belonged to the family <i>Bacillaceae</i> and exhibited a distinctive position among the members of the genus <i>Alkalihalobacillus (Ahb.)</i>. Strain MEB199<sup>T</sup> shared the highest 16S rRNA gene sequence similarity with <i>Alkalihalobacillus alkalinitrilicus</i> ANL-iso4<sup>T</sup> (98.36%), whereas with type species <i>Ahb. alcalophilus</i> DSM 485<sup>T</sup>, it is 94.91%, indicating that strain MEB199<sup>T</sup> is distinctly related to the genus <i>Alkalihalobacillus</i>. The G + C content of genomic DNA was 36.47 mol%. The digital DNA-DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199<sup>T</sup> and <i>Ahb. alkalinitrilicus</i> ANL-iso4<sup>T</sup> confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus <i>Alkalihalobacillus</i> ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus <i>Alkalihalobacillus</i> separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus <i>Alkalihalobacillus</i>. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus <i>Alkalihalobacillus</i> into seven new genera for which the names <i>Alkalihalobacterium</i> gen. nov., <i>Halalkalibacterium</i> gen. nov., <i>Halalkalibacter</i> gen. nov., <i>Shouchella</i> gen. nov., <i>Pseudalkalibacillus</i> gen. nov., <i>Alkalicoccobacillus</i> gen. nov., and <i>Alkalihalophilus</i> gen. nov. are proposed and provide an emended description of <i>Alkalihalobacillus sensu stricto</i>. Also, we propose the <i>Ahb. okuhidensis</i> as a heterotypic synonym of <i>Alkalihalobacillus halodurans</i>. Based on the polyphasic taxonomic analysis, strain MEB199<sup>T</sup> represents a novel species of newly proposed genus for which the name <i>Alkalihalobacterium elongatum</i> gen. nov. sp. nov. is proposed. The type strain is MEB199<sup>T</sup> (= MCC 2982<sup>T</sup>, = JCM 33704<sup>T</sup>, = NBRC 114256<sup>T</sup>, = CGMCC 1.17254<sup>T</sup>).
Project description:Three isolates of a bacterium recovered from human endometrium using conventional culture methods were characterized biochemically and subjected to 16S rRNA gene sequencing and phylogenetic analysis. Isolates were non-motile, obligately anaerobic, non-spore forming, asaccharolytic, non-cellulolytic, indole positive, Gram positive rods. Cell wall fatty acid profiling revealed C14:0, C16:0, C18:2 ?6, 9c, C18:1 ?9c and C18:0 to be the major fatty acid composition. The DNA mol % G+C was determined to be 44.2%. 16S rRNA gene sequence analysis revealed only 91% sequence similarity with the closest cultivated bacterial isolate, Saccharofermentans acetigenes. Based on genotypic and phenotypic data, all three isolates are considered to be members of the same species and data suggest it represents a novel genus and species in the order Clostridiales with an association with Clostridium rRNA cluster III within the family Ruminococcaceae. We propose the name, Mageeibacillus indolicus gen. nov., sp. nov. The type strain is BAA-2120(T) and CCUG 59143(T).
Project description:Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15?:?0, iso-C17?:?0 3-OH, C16?:?0 and C16?:?0 3-OH. The DNA G+C content was 29-31?mol%. They had ?87?% 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T (?=?NRRL B-65307T?=?NCIMB 14986T).
Project description:A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191F<sup>T</sup>, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family <i>Chitinophagaceae</i> that was distinct from members of the genus <i>Pseudoflavitalea</i> (95.1-95.2 % sequence similarity) and <i>Pseudobacter ginsenosidimutans</i> (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191F<sup>T</sup> and <i>Pseudoflavitalea rhizosphaerae</i> T16R-265<sup>T</sup> and <i>Pseudobacter ginsenosidimutans</i> Gsoil 221<sup>T</sup> was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191F<sup>T</sup> was MK-7 and the major fatty acids were iso-C<sub>15 : 0</sub>, iso-C<sub>15 : 1</sub> G and summed feature 3 (C<sub>16:1</sub> ω7<i>c</i> and/or C<sub>16:1</sub> ω6<i>c</i>). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191F<sup>T</sup> calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191F<sup>T</sup> represents a novel species and genus for which the name <i>Parapseudoflavitalea muciniphila</i> gen. nov., sp. nov. is proposed. The type strain is PMP191F<sup>T</sup> (=DSM 104999<sup>T</sup>=ATCC BAA-2857<sup>T</sup> = CCUG 72691<sup>T</sup>). The phylogenetic analyses also revealed that <i>Pseudobacter ginsenosidimutans</i> shared over 98 % sequence similarly to members of the genus <i>Pseudoflavitalea</i>. However, the average nucleotide identity value between <i>Pseudoflavitalea rhizosphaerae</i> T16R-265<sup>T</sup>, the type species of the genus and <i>Pseudobacter ginsenosidimutans</i> Gsoil 221<sup>T</sup> was 86.8 %. Therefore, we also propose that <i>Pseudobacter ginsenosidimutans</i> be reclassified as <i>Pseudoflavitalea ginsenosidimutans</i> comb. nov.
Project description:An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50?°C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85?%. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso-C15:0, iso-C15?:?0 2-OH and iso-C17?:?0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C?content of strain SPSPC-11T was 37.6?mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species.
Project description:A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3?%), Telmatocola sphagniphila (93.3?%) and Gemmata obscuriglobus (91.9?%). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1T displays modest salt tolerance and grows optimally at pH values of 7.5-8.0 and at temperatures of 32-36?°C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16?:?1??5c, 16?:?0 and 18?:?0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1T (=CCUG 69661T=DSM 105045T).
Project description:A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1?9c (39.8%), C18:2?6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4? (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)).