- Volume 57, Issue 4, 2007

[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.

A total of 34 Halomonas strains were isolated from saline water in Anmyeondo, Korea. Ten of these strains, considered to belong to novel species, were subjected to a polyphasic taxonomic investigation. The strains were Gram-negative, moderately halophilic, motile and non-spore-forming rods that contained Q-9 as the predominant ubiquinone and C18 : 1 ω7c, C16 : 0 and either summed feature 4 (C16 : 1 ω7c/C15 : 0 iso 2-OH) or C19 : 0 cyclo ω8c as the major fatty acids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the ten isolates formed four separate lineages in the genus Halomonas. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that they represent four novel species in the genus Halomonas, for which the names Halomonas gomseomensis sp. nov. (type strain M12T=KCTC 12662T=DSM 18042T), Halomonas janggokensis sp. nov. (type strain M24T=KCTC 12663T=DSM 18043T), Halomonas salaria sp. nov. (type strain M27T=KCTC 12664T=DSM 18044T) and Halomonas denitrificans sp. nov. (type strain M29T=KCTC 12665T=DSM 18045T) are proposed.

A Gram-negative, aerobic, halophilic bacterium, designated strain Iso 3T, was isolated from the East Sea in Korea. Strain Iso 3T was motile by means of polar flagella, occasionally formed rosette-like aggregates and contained 18 : 1ω7c as the dominant cellular fatty acid. Strain Iso 3T grew at NaCl concentrations of 1–10 % and temperatures of 4–30 °C. The optimal growth temperature was 20 °C. Analysis of the 16S rRNA gene sequence revealed that this strain is affiliated with a subcluster of the Alphaproteobacteria. However, strain Iso 3T generated metabolic energy by sulfide oxidation. The 16S rRNA gene sequence similarity between strain Iso 3T and the type strain of the most closely related species, Sulfitobacter pontiacus, was 97.7 %. DNA–DNA relatedness between strain Iso 3T and Sulfitobacter pontiacus DSM 10014T was 24.1 %. On the basis of phenotypic properties and phylogenetic distinctiveness, strain Iso 3T is classified within a novel Sulfitobacter species, for which the name Sulfitobacter litoralis sp. nov. is proposed, with the type strain Iso 3T (=KCTC 12521T=DSM 17584T).

Bacterial strains Eant 3-9T and Eant 3-3, isolated from the gut of the termite Odontotermes formosanus, were characterized using a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, non-pigmented, rod-shaped, non-endospore-forming and facultatively anaerobic. Phenotypic, physiological and genetic characteristics of the two strains were highly similar. Phylogenetic analyses using 16S rRNA gene sequences showed that strain Eant 3-9T formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Trabulsiella; its closest neighbour was Trabulsiella guamensis DSM 16940T (98.1 % similarity). Genomic DNA–DNA relatedness between strains Eant 3-9T and Eant 3-3 was 96±4 %, indicating that they belong to a single species. Eant 3-9T displayed DNA–DNA relatedness values of 48±5 and 14±3 % with T. guamensis DSM 16940T and Salmonella typhimurium ATCC 13311T, respectively, indicating that Eant 3-9T warrants novel species status in the genus Trabulsiella. Eant 3-9T and Eant 3-3 could be further distinguished from T. guamensis DSM 16940T using whole-cell protein profiles and a range of physiological and biochemical characteristics. It is evident from genotypic and phenotypic data that Eant 3-9T represents a novel species in the genus Trabulsiella, for which the name Trabulsiella odontotermitis sp. nov. is proposed. The type strain is Eant 3-9T (=BCRC 17577T=LMG 23580T); Eant 3-3 is a reference strain.

A yellow-pigmented, Gram-negative, rod-shaped bacterium (strain CC-YY255T) was isolated from compost generated from food waste collected from Kinmen County, Taiwan. 16S rRNA gene sequence analysis indicated that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Luteimonas; its closest neighbour was the type strain of Luteimonas mephitis (94.4 % sequence similarity). The isolate was distinguished from Luteimonas mephitis on the basis of several phenotypic properties. The organism utilized glucose, maltose, gentiobiose, melibiose and turanose and only a few organic acids (acetate, propionate) and amino acids (l-alanyl glycine, glycyl l-aspartic acid and glycyl l-glutamic acid) as substrates. The fatty acid profile was slightly different from that reported for Luteimonas mephitis. It is evident from the genotypic, chemotaxonomic and physiological data presented that strain CC-YY255T represents a novel species of the genus Luteimonas, for which the name Luteimonas composti sp. nov. is proposed. The type strain is CC-YY255T (=CCUG 53595T=CIP 109311T=BCRC 17598T).

A Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (strain CCUG 49584T), isolated from a seafood processing plant sample in New Zealand, was subjected to a polyphasic taxonomic study. On the basis of 16S rRNA and recA gene sequence similarities, the isolate was allocated to the genus Pseudochrobactrum. This was confirmed by fatty acid data (major fatty acids: C18 : 1 ω7c and C19 : 0 cyclo ω8c), a polar lipid profile exhibiting major characteristics of Pseudochrobactrum (phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine), quinone system Q-10 and a polyamine pattern with the predominant compounds spermidine and putrescine. DNA–DNA hybridization with the type strains of the two established species of Pseudochrobactrum and physiological and biochemical data clearly differentiated the isolate from established Pseudochrobactrum species. As a consequence, this organism represents a novel species, for which the name Pseudochrobactrum kiredjianiae sp. nov. is proposed, with the type strain CCUG 49584T (=CIP 109227T).

Two strains named ESC1T and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA–DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21T, O. anthropi DSM 6882T and Ochrobactrum tritici DSM 13340T. The predominant fatty acids were C18 : 1 ω7c and C18 : 1 2-OH. Strains ESC1T and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced β-galactosidase and β-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1T was 56.4 mol%. Both strains ESC1T and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1T (=LMG 22713T=CECT 7172T).

Eighteen isolates of a Gram-negative coccus (strain 237T) were cultured from the eyes of dairy and beef calves affected with infectious bovine keratoconjunctivitis (IBK; ‘pinkeye’) in northern California, USA, during summer 2002. These isolates had near full-length (1397 bp) 16S rRNA gene sequences that clustered into three groups with 99.9 % sequence similarity. On the basis of 16S rRNA gene sequence, the isolates were most closely associated with Moraxella bovis and Moraxella ovis in clade I of the classical moraxellae. Biochemically, the novel isolates could be distinguished from the other members of the genus Moraxella isolated from animals on the basis of phenylalanine deaminase activity. The results of partial sequence analysis of six housekeeping genes, the 16S–23S rRNA gene interspacer region and partial 23S rRNA gene provide strong support for the inclusion of these isolates in a novel taxon, for which the name Moraxella bovoculi sp. nov. is proposed. The type strain is strain 237T (=ATCC BAA-1259T=CCUG 52049T).

The taxonomic positions of the genera Ruegeria and Silicibacter were evaluated by a polyphasic investigation. It was evident from 16S rRNA gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9–98.2 %). Several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. Further, a comparative study based on DNA–DNA hybridization, phenotypic characterization and chemotaxonomic analysis indicated that the members of this clade, namely Ruegeria atlantica, Silicibacter lacuscaerulensis and Silicibacter pomeroyi, can be readily differentiated from each other. On the basis of the polyphasic data obtained in this study, all species of the genus Silicibacter should be transferred to the genus Ruegeria, since the latter has nomenclatural priority. It is therefore proposed that Silicibacter lacuscaerulensis and Silicibacter pomeroyi are transferred to the genus Ruegeria as Ruegeria lacuscaerulensis comb. nov. and Ruegeria pomeroyi comb. nov.

Four Gram-negative, facultatively anaerobic, non-spore-forming isolates of coccoid rods were obtained from fruit powder and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis allocated the isolates to the family Enterobacteriaceae. Their phylogenetic position within the family Enterobacteriaceae was confirmed by rpoB sequence analysis and as the highest rpoB sequence similarities were obtained with Enterobacter radicincitans, Enterobacter cowanii and Enterobacter sakazakii, the isolates clearly belong to the genus Enterobacter. Biochemical data revealed that the isolates can be separated into two distinct groups that represent two novel species, as confirmed by DNA–DNA hybridizations. The two novel species can be differentiated from their nearest neighbours by the following characteristics: the utilization of sucrose, d-sorbitol, putrescine and mucate, the hydrolysis of aesculin and a negative result in the Voges–Proskauer reaction. It is therefore proposed that these novel isolates are classified as Enterobacter turicensis sp. nov. (type strain 508/05T=LMG 23730T=DSM 18397T) and Enterobacter helveticus sp. nov. (type strain 513/05T=LMG 23732T=DSM 18396T).

A novel facultatively anaerobic sulfur-reducing bacterium, designated strain Phe91T, was isolated from petroleum-contaminated groundwater in an underground crude oil storage cavity at Kuji in Iwate, Japan. Cells of strain Phe91T were slightly curved rods with single polar flagella. Optimum growth was observed at pH 7.0 and 30 °C. The novel strain utilized elemental sulfur, thiosulfate, sulfite, dithionite, arsenate, nitrate and DMSO as electron acceptors with lactate as an energy and carbon source, but nitrite was not utilized. Microaerophilic growth was also observed. Fumarate, pyruvate, lactate, malate, succinate, hydrogen (with acetate as a carbon source) and formate (with acetate) could serve as electron donors. Fumarate, pyruvate and malate were fermented. The DNA G+C content was 42.7 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain Phe91T was affiliated with the genus Sulfurospirillum in the class Epsilonproteobacteria and was most closely related to Sulfurospirillum deleyianum (sequence similarity 97 %). However, the DNA–DNA hybridization value between strain Phe91T and S. deleyianum was only 14 %. Based on the physiological and phylogenetic data, Phe91T should be classified as a representative of a novel species in the genus Sulfurospirillum; the name Sulfurospirillum cavolei sp. nov. is proposed, with Phe91T (=JCM 13918T=DSM 18149T) as the type strain.

During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).

Two strictly anaerobic, mesophilic, sulfate-reducing bacterial strains, Pro1T and Pro16, were isolated from an estuarine sediment in the Sea of Japan of the Japanese islands and were characterized by phenotypic and phylogenetic methods. Strains Pro1T and Pro16 had almost the same physiological and chemotaxonomic characteristics. Cells of both strains were Gram-negative, motile, non-spore-forming rods. Catalase activity was not detected. The optimum NaCl concentration for growth was 3.0 % (w/v). The optimum temperature for growth was 35 °C and the optimum pH was 6.7. Both strains used formate, propionate, pyruvate, lactate, fumarate, malate, ethanol, propanol, butanol, glycerol, alanine, glucose, fructose and H2 as electron donors for sulfate reduction and did not use acetate, butyrate, succinate, methanol, glycine, serine, aspartate, glutamate, cellobiose or sucrose. Organic electron donors were incompletely oxidized mainly to acetate. Both strains also used thiosulfate as an electron acceptor. Without electron acceptors, both strains fermented pyruvate and lactate. The genomic DNA G+C contents of strains Pro1T and Pro16 were 48.6 and 46.0 mol%, respectively. The major respiratory quinone of both strains was menaquinone MK-5(H2). Major cellular fatty acids of both strains were C15 : 0, C16 : 0, C17 : 1 ω6 and C18 : 1 ω7. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the class Deltaproteobacteria. The closest recognized relative of strains Pro1T and Pro16 was Desulfobulbus mediterraneus with sequence similarities of 95.2 and 94.8 %, respectively. Based on phylogenetic, physiological and chemotaxonomic characteristics, strains Pro1T and Pro16 represent a novel species of the genus Desulfobulbus, for which the name Desulfobulbus japonicus is proposed. The type strain is Pro1T(=JCM 14043T=DSM 18378T) and strain Pro16 (=JCM 14044=DSM 18379) is a reference strain.

A Gram-negative, motile and egg-shaped bacterium, strain TF-218T, was isolated from a tidal flat at Daepo Beach (Yellow Sea), Korea, and subjected to a polyphasic taxonomic analysis. Strain TF-218T grew optimally at pH 7.0–8.0 and 37 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and 11-methyl C18 : 1 ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and an aminolipid. The DNA G+C content was 64.9 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain TF-218T is phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum of the Alphaproteobacteria. The phylogenetic and chemotaxonomic similarities suggest that strain TF-218T represents a member of the genus Phaeobacter. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain TF-218T differs from the recognized Phaeobacter species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain TF-218T represents a novel species of the genus Phaeobacter, for which the name Phaeobacter daeponensis sp. nov. is proposed. The type strain is TF-218T (=KCTC 12794T=JCM 13606T).

Polyphasic characterization of strain DSM 9128, described as ‘Pseudomonas azelaica’ by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143–153 (1971) ], and four biochemically similar isolates was performed with the aim of validly publishing the name ‘Pseudomonas azelaica’. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization, fatty acid patterns and extensive biochemical testing, it was concluded that DSM 9128, two further strains and the type strains of Pseudomonas nitroreducens and Pseudomonas multiresinivorans form a highly related cluster. However, DNA–DNA binding did not conclusively resolve whether these strains should be regarded as members of one species. Based on results gained with the above-mentioned methods, two other isolates were assigned to the species Pseudomonas citronellolis, a species very close to P. nitroreducens. Based on genetic and biochemical similarities, it is suggested that Pseudomonas multiresinivorans should be considered as a later heterotypic synonym of Pseudomonas nitroreducens. The species descriptions of P. nitroreducens and P. citronellolis are emended.

A bacterial strain, designated Dant 3-8T, isolated from the gut of the termite Odontotermes formosanus, was investigated by a polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbours being Comamonas testosteroni DSM 50244T (96.4 % sequence similarity), Comamonas koreensis KCTC 12005T (96.0 %) and Comamonas terrigena DSM 7099T (96.2 %). Strain Dant 3-8T was clearly distinguished from all of these strains by using phylogenetic analysis, DNA–DNA hybridization, whole-cell protein profiles, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that Dant 3-8T represents a novel species in the genus Comamonas, for which the name Comamonas odontotermitis sp. nov. is proposed. The type strain is Dant 3-8T (=BCRC 17576T=LMG 23579T).

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.

Three Gram-positive, anaerobic, non-spore-forming, rod-shaped bacteria with pointed ends were isolated from clinical specimens. The organisms were weakly saccharolytic and produced indole, acetate, butyrate and lactate as major metabolic end products. 16S rRNA gene sequence analysis indicated that the isolates had no known close relatives among recognized bacteria but that they exhibited a phylogenetic association with Clostridium rRNA cluster XIVa [as defined by Collins, M. D. et al. (1994) . Int J Syst Bacteriol 44, 812–826]. The closest recognized relatives were the type strains of Clostridium clostridioforme, Clostridium bolteae and Clostridium asparagiforme (16S rRNA gene sequence similarity values of 90.2–91.4 %). These results suggest that these three clinical isolates represent a novel species of a new genus, for which the name Moryella indoligenes gen. nov., sp. nov. is proposed. The type strain of Moryella indoligenes is AIP 220.04T (=CIP 109174T=CCUG 52648T).

Two strains of Gram-positive, catalase-negative, lactic acid bacteria, strains TMW 1.1309T and TMW 1.1313, were isolated at an interval of several years from an industrial type II sourdough. They occurred at cell numbers of 8×108 c.f.u. g−1 and therefore were considered to be one of the dominant members of the microbiota in this type of fermentation. Cells of both strains grow exclusively on modified MRS containing trypsin-digested rye-bran extract. Both strains possessed identical 16S rRNA gene sequences, but could be discriminated by RAPD fingerprints. Comparative 16S rRNA and tuf gene sequence analyses positioned strain TMW 1.1309T as part of the Lactobacillus reuteri phylogenetic group within the genus Lactobacillus. The 16S rRNA gene sequence similarities to the closest related species, Lactobacillus coleohominis and Lactobacillus ingluviei were 97.1 and 95.4 %, respectively. The DNA G+C content of strain TMW 1.1309T was 48 mol%. Growth characteristics, biochemical features and DNA–DNA hybridization values below 70 % with all the nearest neighbours demonstrated that the isolates represent a novel Lactobacillus species. The name Lactobacillus secaliphilus sp. nov. is proposed for the novel isolates, with the type strain TMW 1.1309T (=DSM 17896T=CCUG 53218T).