scholarly journals Reclassification of [Pasteurella] trehalosi as Bibersteinia trehalosi gen. nov., comb. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 666-674 ◽  
Author(s):  
P. J. Blackall ◽  
Anders Miki Bojesen ◽  
Henrik Christensen ◽  
Magne Bisgaard

[Pasteurella] trehalosi is an important pathogen of sheep, being primarily associated with serious systemic infections in lambs but also having an association with pneumonia. The aim of the present investigation was to characterize a broad collection of strains tentatively identified as [P.] trehalosi in order to reclassify and rename this taxon to support improvements in our understanding of the pathogenesis and epidemiology of this important organism. The type strain for [P.] trehalosi, strain NCTC 10370T, was included along with 42 field isolates from sheep (21), cattle (14), goats (1), roe deer (3) and unknown sources (3). An extended phenotypic characterization was performed on all 43 strains. Amplified fragment length polymorphism (AFLP) was also performed on the isolates. Two of the field isolates were subjected to 16S rRNA gene sequencing. These sequences, along with five existing sequences for [P.] trehalosi strains and 12 sequences for other taxa in the family Pasteurellaceae, were subjected to a phylogenetic analysis. All the isolates and the reference strains were identified as [P.] trehalosi. A total of 17 out of 22 ovine isolates produced acid from all glycosides, while only four out of 14 bovine isolates produced acid from all glycosides. All 22 ovine isolates were haemolytic and CAMP-positive, while no other isolate was haemolytic and only two bovine isolates were CAMP-positive. Nineteen AFLP types were found within the [P.] trehalosi isolates. All [P.] trehalosi isolates shared at least 70 % similarity in AFLP patterns. The largest AFLP type included the type strain and 7 ovine field isolates. Phylogenetic analysis indicated that the seven strains studied (two field isolates and the five serovar reference strains) are closely related, with 98.6 % or higher 16S rRNA gene sequence similarity. As both genotypic and phenotypic testing support the separate and distinct nature of these organisms, we propose the transfer of [P.] trehalosi to a new genus, Bibersteinia, as Bibersteinia trehalosi comb. nov. The type strain is NCTC 10370T (=ATCC 29703T). Bibersteinia trehalosi can be distinguished from the existing genera of the family by the observation of only nine characteristics; catalase, porphyrin, urease, indole, phosphatase, acid from dulcitol, (+)-d-galactose, (+)-d-mannose and (+)-d-trehalose.

2011 ◽  
Vol 61 (12) ◽  
pp. 2974-2978 ◽  
Author(s):  
Jinxing Zhu ◽  
Xiaoli Liu ◽  
Xiuzhu Dong

Two mesophilic methanogenic strains, designated TS-2T and GHT, were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3–0.5×2–5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2T was motile with one or two polar flagella and used only H2/CO2 for growth and methanogenesis. Strain GHT was non-motile, used both H2/CO2 and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H2 and single cells under low pressure H2. Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2T was most closely related to Methanobacterium alcaliphilum NBRC 105226T (96 % 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA–DNA relatedness between the isolates and M. alcaliphilum DSM 3387T was 39–53 %. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2T = AS 1.5093T = JCM 15415T) and Methanobacterium flexile sp. nov. (type strain GHT = AS 1.5092T = JCM 15416T).


2004 ◽  
Vol 54 (5) ◽  
pp. 1669-1676 ◽  
Author(s):  
Yi-Chueh Lin ◽  
Kazunori Uemori ◽  
Dominique A. de Briel ◽  
Vallapa Arunpairojana ◽  
Akira Yokota

Seven strains of actinobacteria, isolated from soil, wounds, urine, cow faeces, human blood and butter, were characterized by a polyphasic approach to clarify their taxonomic position. On the basis of chemotaxonomy, 16S rRNA gene analysis and DNA relatedness, strain IAM 14851T can be classified within the cluster of the genus Leucobacter and is proposed as a novel species, Leucobacter albus sp. nov., with strain IAM 14851T (=TISTR 1515T) as the type strain. The other six strains formed a phylogenetically separate branch in the family Microbacteriaceae, having the following characteristics: the major menaquinones are MK-8 to MK-10, the DNA G+C content ranges from 62 to 68 mol%, the diamino acid in the cell wall is diaminobutyric acid and the muramic acid in the peptidoglycan is of the acetyl type. The major fatty acids are 12-methyltetradecanoic acid (anteiso-C15 : 0), hexadecanoic acid (C16 : 0), 14-methyl-pentadecanoic acid (iso-C16 : 0) and 14-methyl-hexadecanoic acid (anteiso-C17 : 0). On the basis of morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA hybridization and 16S rRNA gene sequence comparison, the novel genus Zimmermannella gen. nov. is proposed for these six strains. Four novel species are proposed: Zimmermannella helvola sp. nov. (type species; type strain IAM 14726T=NBRC 15775T=DSM 20419T=TISTR 1509T), Zimmermannella alba sp. nov. (type strain IAM 14724T=NBRC 15616T=TISTR 1510T), Zimmermannella bifida sp. nov. (type strain IAM 14848T=TISTR 1511T) and Zimmermannella faecalis sp. nov. (type strain IAM 15030T=NBRC 15706T=ATCC 13722T=TISTR 1514T).


2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2357-2364 ◽  
Author(s):  
Nupur ◽  
Naga Radha Srinivas Tanuku ◽  
Takaichi Shinichi ◽  
Anil Kumar Pinnaka

A novel brown-coloured, Gram-negative-staining, rod-shaped, motile, phototrophic, purple sulfur bacterium, designated strain AK40T, was isolated in pure culture from a sediment sample collected from Coringa mangrove forest, India. Strain AK40T contained bacteriochlorophyll a and carotenoids of the rhodopin series as major photosynthetic pigments. Strain AK40T was able to grow photoheterotrophically and could utilize a number of organic substrates. It was unable to grow photoautotrophically and did not utilize sulfide or thiosulfate as electron donors. Thiamine and riboflavin were required for growth. The dominant fatty acids were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile of strain AK40T was found to contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and eight unidentified lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK40T was 65.5 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represented a member of the family Chromatiaceae within the class Gammaproteobacteria. 16S rRNA gene sequence analysis indicated that strain AK40T was closely related to Phaeochromatium fluminis, with 95.2 % pairwise sequence similarity to the type strain; sequence similarity to strains of other species of the family was 90.8–94.8 %. Based on the sequence comparison data, strain AK40T was positioned distinctly outside the group formed by the genera Phaeochromatium, Marichromatium, Halochromatium, Thiohalocapsa, Rhabdochromatium and Thiorhodovibrio. Distinct morphological, physiological and genotypic differences from previously described taxa supported the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeobacterium nitratireducens gen. nov., sp. nov. is proposed. The type strain of Phaeobacterium nitratireducens is AK40T ( = JCM 19219T = MTCC 11824T).


2011 ◽  
Vol 61 (9) ◽  
pp. 2238-2246 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Vânia Figueira ◽  
Ana R. Lopes ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
...  

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).


2010 ◽  
Vol 60 (12) ◽  
pp. 2724-2728 ◽  
Author(s):  
Qiu-Xiang Yan ◽  
Yong-Xia Wang ◽  
Shun-Peng Li ◽  
Wen-Jun Li ◽  
Qing Hong

A Gram-staining-negative, catalase-positive, carbaryl-degrading, non-spore-forming, non-motile, rod-shaped bacterium, designated strain X23T, was isolated from a wastewater treatment system. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain belongs to the genus Sphingobium. The highest 16S rRNA gene sequence similarity observed for the isolate was 96.6 % with the type strain of Sphingobium amiense. Chemotaxonomic data [major ubiquinone: Q-10; major polar lipids: diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine and unknown aminolipids and phospholipids; major fatty acids: summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t), C16 : 1 ω5c, C14 : 0 2-OH and C16 : 0 2-OH] as well as the inability to reduce nitrate and the presence of spermidine as the major polyamine supported the affiliation of the strain to the genus Sphingobium. Based on the phylogenetic analysis, whole-cell fatty acid composition and biochemical characteristics, the strain could be separated from all recognized species of the genus Sphingobium. Strain X23T should be classified as a novel species of the genus Sphingobium, for which the name Sphingobium qiguonii sp. nov. is proposed, with strain X23T (=CCTCC AB 208221T =DSM 21541T) as the type strain.


2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 870-878 ◽  
Author(s):  
Karoline Kläring ◽  
Sarah Just ◽  
Ilias Lagkouvardos ◽  
Laura Hanske ◽  
Dirk Haller ◽  
...  

Three strains of an anaerobic, Gram-stain-positive coccobacillus were isolated from the intestines of mice. These strains shared 100 % similarity in their 16S rRNA gene sequences, but were distantly related to any described members of the family Lachnospiraceae (<94 %). The most closely related species with names that have standing in nomenclature were Robinsoniella peoriensis , Ruminococcus gnavus , Blautia producta and Clostridium xylanolyticum . Phylogenetic relationships based on 16S rRNA gene sequence analysis were confirmed by partial sequencing of hsp60 genes. The use of an in-house database search pipeline revealed that the new isolates are most prevalent in bovine gut samples when compared with human and mouse samples for Ruminococcus gnavus and B. producta . All three isolated strains shared similar cellular fatty acid patterns dominated by C16 : 0 methyl ester. Differences in the proportions of C12 : 0 methyl ester, C14 : 0 methyl ester and C18 : 1 cis-11 dimethyl acetal were observed when compared with phylogenetically neighbouring species. The major short-chain fatty acid produced by strain SRB-530-5-HT was acetic acid. This strain tested positive for utilization of d-fructose, d-galacturonic acid, d-malic acid, l-alanyl l-threonine and l-glutamic acid but was negative for utilization of amygdalin, arbutin, α-d-glucose, 3-methyl d-glucose and salicin, in contrast to the type strain of the closest related species Robinsoniella peoriensis . The isolates were not able to use mannitol for growth. Based on genotypic, phenotypic and chemotaxonomic characteristics, we propose to create the new genus and species Murimonas intestini gen. nov., sp. nov. to accommodate the three strains SRB-530-5-HT ( = DSM 26524T = CCUG 63391T) (the type strain of Murimonas intestini), SRB-509-4-S-H ( = DSM 27577 = CCUG 64595) and SRB-524-4-S-H ( = DSM 27578 = CCUG 64594).


2006 ◽  
Vol 56 (3) ◽  
pp. 569-576 ◽  
Author(s):  
Margarita Grabovich ◽  
Ekaterina Gavrish ◽  
Jan Kuever ◽  
Anatoly M. Lysenko ◽  
Daria Podkopaeva ◽  
...  

Five Gram-negative, motile, spiral-shaped strains were isolated from a sulfide spring (D-412T), active sludge of wastewater (D-419T, D-420, D-424) and industrial wastewater (D-416). Comparative 16S rRNA gene sequence analysis showed that the isolates belong to the family Comamonadaceae, within the class Betaproteobacteria, but fall into a distinct cluster. On the basis of phenotypic, chemotaxonomic and phylogenetic data, a new genus, Giesbergeria gen. nov., is proposed, including five species. The type species of the genus is Giesbergeria voronezhensis sp. nov. (type strain D-419T=DSM 12825T=CIP 107340T=VKM B-2350T) and other novel members of the genus are Giesbergeria kuznetsovii sp. nov. (type strain D-412T=DSM 12827T=VKM B-2352T), Giesbergeria giesbergeri comb. nov. (basonym Aquaspirillum giesbergeri), Giesbergeria sinuosa comb. nov. (basonym Aquaspirillum sinuosum) and Giesbergeria anulus comb. nov. (basonym Aquaspirillum anulus). Using the same criteria, isolate D-416 (=DSM 12826) was identified as a strain of [Aquaspirillum] metamorphum. Strain D-416, the type strain of [A.] metamorphum and the type strain of [Aquaspirillum] psychrophilum form a distinct cluster within the family Comamonadaceae (97–97·2 % 16S rRNA gene sequence similarity) and share phenotypic and chemotaxonomic properties. Therefore, it is proposed that these strains are reclassified as members of a new genus, Simplicispira gen. nov., as Simplicispira metamorpha comb. nov. (the type species) and Simplicispira psychrophila comb. nov., respectively.


2005 ◽  
Vol 55 (5) ◽  
pp. 1979-1983 ◽  
Author(s):  
Michael Goodfellow ◽  
Luis A. Maldonado ◽  
Erika T. Quintana

A polyphasic study was undertaken to clarify the taxonomic position of Nonomuraea flexuosa DSM 41386T. The distinct 16S rRNA gene sequence phyletic branch formed by this strain was equated with nine related monophyletic clades composed of representatives of the genera classified in the family Streptosporangiaceae. The organism produced a PCR product characteristic of this taxon when examined using a set of oligonucleotide primers specific for members of the family Streptosporangiaceae. Strain DSM 41386T could also be distinguished from representatives of the nine genera assigned to this family using a combination of chemotaxonomic, morphological and physiological properties. It is evident from the genotypic and phenotypic data that strain DSM 41386T is misclassified in the genus Nonomuraea and merits recognition as a monospecific genus within the family Streptosporangiaceae. It is proposed that the name Thermopolyspora flexuosa gen. nov., comb. nov., nom. rev. be used for this purpose, with the type strain DSM 41386T (=NRRL B-24348T).


2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1296-1303 ◽  
Author(s):  
Haruka Horino ◽  
Takashi Fujita ◽  
Akio Tonouchi

An obligately anaerobic bacterial strain designated T-1-35T was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35T stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8–1.0×3.5–15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35T exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15–40 °C, with an optimum at 35 °C. The pH range for growth was 5.5–9.0, with an optimum at pH 8.0–8.5 (slightly alkaliphilic). Strain T-1-35T fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35T belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35T was Bacteroides cellulosolvens WM2T, with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35T was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35T is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35T ( = DSM 27016T = NBRC 109520T). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2T ( = ATCC 35603T = DSM 2933T = NRCC 2944T).


2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).


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