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Volume 53,
Issue 1,
2003
Volume 53, Issue 1, 2003
- New Taxa
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- Proteobacteria
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Methylophaga alcalica sp. nov., a novel alkaliphilic and moderately halophilic, obligately methylotrophic bacterium from an East Mongolian saline soda lake
More LessA moderately haloalkaliphilic and obligately methylotrophic bacterium (strain M39T) with the ribulose monophosphate pathway of carbon assimilation is described. Cells of this methanol and methylamine utilizer are aerobic, Gram-negative, asporogenous, motile short rods, multiplying by binary fission. It is auxotrophic for vitamin B12 and requires NaHCO3 or NaCl for growth in alkaline medium. Its cellular fatty acid profile consists primarily of straight-chain saturated C16 : 0 and unsaturated C16 : 1 and C18 : 1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25–29 °C, pH 9·0–9·5 and 3–4 % (w/v) NaCl. Cells accumulate the cyclic amino acid ectoine as the main compatible solute. The DNA G+C content is 48·3 mol%. Based on 16S rDNA sequence analysis and DNA–DNA relatedness (25–30 %) with the type strains of marine methylotrophs belonging to the genus Methylophaga, the novel isolate M39T (=VKM B-2251T =ATCC BAA-297T) was classified as the type strain of Methylophaga alcalica sp. nov.
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Paracoccus zeaxanthinifaciens sp. nov., a zeaxanthin-producing bacterium
A comprehensive taxonomic re-evaluation was performed on the marine, zeaxanthin-producing bacterium formerly classified as [Flavobacterium] sp. strain R-1512 (ATCC 21588). This strain, together with two other previously described marine isolates, [Flavobacterium] strain R-1506 and Paracoccus sp. strain MBIC 3966, were found to comprise a new species of the genus Paracoccus. The name Paracoccus zeaxanthinifaciens sp. nov. is proposed, with ATCC 21588T (=R-1512T =LMG 21293T) designated as the type strain.
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Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis
More LessFive Gram-negative bacterial strains, oxidase-positive, motile by means of more than one polar flagella, facultative anaerobe, arginine dihydrolase-negative, lysine- and ornithine decarboxylase-positive, sensitive to the vibriostatic agent O/129, were isolated from a flow-through rotifer culture system in Gent, Belgium, and previously characterized by fluorescent amplified fragment length polymorphism. Comparison of the 16S rDNA sequence of strain LMG 21460T indicated close relationships (∼99 % similarity) to Vibrio campbellii, Vibrio harveyi, Vibrio alginolyticus and Vibrio parahaemolyticus. However, DNA hybridization experiments revealed similarity values below 70 % with its closest species V. campbellii and V. harveyi. Additionally, the analysed strains differ from related Vibrio species by the utilization of melibiose and production of acid from l-arabinose and amygdalin. Among the strains analysed, differences were observed in some phenotypic characters, particularly susceptibility to ampicillin, polymyxin B and amikacin, and urease activity. The major fatty acids identified were 16 : 0, 18 : 1ω7c, 14 : 0, 12 : 0 3-OH and 18 : 0. Vibrio rotiferianus sp. nov. is proposed, with type strain LMG 21460T (=CAIM 577T); it has a DNA G+C content of 44·5±0·01 mol%.
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Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps)
The fluorescent amplified fragment length polymorphism (FAFLP) groups A5 (21 isolates), A8 (6 isolates) and A23 (3 isolates) distinguished in an earlier paper (Thompson et al., Syst Appl Microbiol 24, 520–538, 2001) were examined in more depth. These three groups were phylogenetically related to Vibrio tubiashii, but DNA–DNA hybridization experiments proved that the three AFLP groups are in fact novel species. Chemotaxonomic and phenotypic analyses further revealed several differences among the 30 isolates and known Vibrio species. It is proposed to accommodate these isolates in three novel species, namely Vibrio neptunius (type strain LMG 20536T; EMBL accession no. AJ316171; G+C content of the type strain 46·0 mol%), Vibrio brasiliensis (type strain LMG 20546T; EMBL accession no. AJ316172; G+C content of the type strain 45·9 mol%) and Vibrio xuii (type strain LMG 21346T; EMBL accession no. AJ316181; G+C content of the type strain 46·6 mol%). These species can be differentiated on the basis of phenotypic features, including fatty acid composition (particularly 14 : 0 iso, 14 : 0 iso 3-OH, 16 : 0 iso, 16 : 0, 17 : 0 and 17 : 1ω8c), enzyme activities and utilization and fermentation of various carbon sources.
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Spore-forming Serratia marcescens subsp. sakuensis subsp. nov., isolated from a domestic wastewater treatment tank
More LessA strain (KREDT) that formed endospores and produced the pigment prodigiosin was isolated from activated sludge. The presence of spores in cells of strain KREDT was evident upon electron microscopy examination, heat treatment and the detection of dipicolinic acid in the cells. Biochemical characteristics, and 16S rDNA sequence and DNA–DNA homology data identified strain KREDT as Serratia marcescens. The major respiratory quinone of strain KREDT was found to be ubiquinone Q-8. The formation of endospores by Gram-negative bacteria has not been observed previously, and has never been reported in any species of Serratia. Here, it is shown that strain KREDT (JCM 11315T=CIP 107489T) represents a novel subspecies of S. marcescens, for which the name Serratia marcescens subsp. sakuensis is proposed.
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Genetic relationships among avian isolates classified as Pasteurella haemolytica, ‘Actinobacillus salpingitidis’ or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov.
More LessBacteria of the avian [Pasteurella haemolytica]–‘Actinobacillus salpingitidis’ complex have been associated with different pathological conditions in birds, among which salpingitis and peritonitis in chickens of layer type seem to dominate. The aim of this study was to classify these bacteria by comparison of 37 strains tentatively classified as biovars of the avian [P. haemolytica]–‘A. salpingitidis’ complex or as Pasteurella anatis. PFGE, AFLP and plasmid profiling showed that strains representing different biovars were genotypically different. Phylogenetic analysis of 22 strains characterized by 16S rRNA gene sequence comparison showed that strains classified as biovars 5, 8 and 9 were closely related to the suggested type strain of ‘A. salpingitidis’ (98·4–99·9 % similarity), whereas the remaining strains classified in 12 biovars or as P. anatis were closely related to the type strain of P. anatis (98·1–100 % similarity). The two groups were related at 95·7–97·1 % similarity. The closest similarity outside this group was 94·6 %, between biovar 15 and Bisgaard taxon 3. DNA–DNA hybridization was performed with 34 strains and showed binding above 85 % for strains of biovars 5 and 8, including the suggested type strain of ‘A. salpingitidis’. Two strains of P. anatis (F 149T and F 279) were closely related at 79 % DNA binding to 27 strains of biovars 1, 3, 4, 11, 12, 17–20, 22 and 24. A new genus, Gallibacterium gen. nov., is proposed to include the avian [P. haemolytica]–‘A. salpingitidis’–P. anatis complex, since these taxa form a monophyletic unit with similarities above 95 % on the basis of 16S rRNA sequence comparison and they are unrelated to other genera of the family Pasteurellaceae Pohl 1981. The new genus consists of Gram-negative, non-motile, rod-shaped or pleomorphic bacteria. The bacteria are catalase-, oxidase- and phosphatase-positive. Nitrate is reduced and acid is produced without gas formation from glycerol, (−)d-ribose, (+)d-xylose, (−)d-mannitol, (−)d-fructose, (+)d-galactose, (+)d-glucose, (+)d-mannose, sucrose and raffinose. The genus Gallibacterium can be separated from other genera of Pasteurellaceae by differences in catalase, symbiotic growth, haemolysis, urease, indole, acid production from (+)d-xylose, (−)d-mannitol, (−)d-sorbitol, (+)d-mannose, maltose, raffinose and dextrin and ONPG and PNPG tests. Pasteurella anatis Mutters et al. 1985 is transferred to the new genus as Gallibacterium anatis gen. nov., comb. nov. Genomospecies 1 of Gallibacterium is proposed to include the former biovars 5 and 8 of the avian [P. haemolytica]–‘A. salpingitidis’ complex. The type strain of Gallibacterium anatis is F 149T (=ATCC 43329T=NCTC 11413T) and the reference strain of Gallibacterium genomospecies 1 is CCM 5974.
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Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the coral Pocillopora damicornis
More LessVibrio sp. YB1T (=ATCC BAA-450T =LMG 20984T), the aetiological agent of tissue lysis of the coral Pocillopora damicornis, was characterized as a novel Vibrio species on the basis of 16S rDNA sequence, DNA–DNA hybridization data (G+C content is 45·6 mol%), AFLP and GTG5-PCR genomic fingerprinting patterns and phenotypic properties, including the cellular fatty acid profile. The predominant fatty acids were 16 : 0 and 18 : 1ω7c. The name Vibrio coralliilyticus sp. nov. is proposed for the novel coral-pathogenic species. In addition to strain YB1T, which was isolated from the Indian Ocean, five additional strains of V. coralliilyticus have been isolated, three from diseased P. damicornis in the Red Sea, one from diseased oyster larvae (Kent, UK) and one from bivalve larvae (Brazil). The six V. coralliilyticus strains showed high genotypic and phenotypic similarities and all were pathogenic to P. damicornis. The closest phylogenetic neighbours to V. coralliilyticus are Vibrio tubiashii, Vibrio nereis and Vibrio shilonii.
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Description of Alcanivorax venustensis sp. nov. and reclassification of Fundibacter jadensis DSM 12178T (Bruns and Berthe-Corti 1999) as Alcanivorax jadensis comb. nov., members of the emended genus Alcanivorax
Two strains of a novel bacterium were isolated independently of each other, from different depths in the Mediterranean Sea, within a time period of 7 months, using two different isolation approaches that were focused on different objectives. Both strains, designated ISO1 and ISO4T, were halophilic, Gram-negative, strictly aerobic, straight rods that were oxidase- and catalase-positive. Both strains produced mucoid colonies in some defined minimal media and were able to grow with organic acids and some alkanes; they were also able to accumulate intracellular poly-β-hydroxybutyrate granules. The G+C content of the DNA of strain ISO4T was 66 mol%. Comparative analysis of 16S rRNA gene sequences showed that the closest described species to the novel strains were Alcanivorax borkumensis and Fundibacter jadensis, both of the γ-Proteobacteria. Both of these recognized species were originally isolated from North Sea waters and are able to degrade aliphatic compounds, a property shared with strains ISO1 and ISO4T. However, strains ISO1 and ISO4T were different from A. borkumensis and F. jadensis, not only in their 16S rDNA sequences but also in the motility of their cells (by polar flagella) and by the presence of C19 : 0cyclo in their cellular fatty acids, among other differential features. On the basis of biochemical and molecular data, it is suggested that strains ISO1 and ISO4T be recognized as a novel species of the genus Alcanivorax, for which the name Alcanivorax venustensis (ISO4T =DSM 13974T =CECT 5388T) is proposed. On the basis of its high phenotypic similarity and close phylogenetic relatedness to A. borkumensis, it is also proposed that F. jadensis (DSM 12178T) be reclassified as Alcanivorax jadensis in the genus Alcanivorax, and that the description of the genus Alcanivorax be emended.
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- Gram-Positive Bacteria
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Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.
More LessGenotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of dl-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G+C content was 37·5±0·2 mol%. The peptidoglycan was of the lysine–d-iso-asparagine (l-Lys–d-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA–DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).
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Nocardia cerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil
An isolate from Cerrado soil, provisionally assigned to the genus Nocardia, was shown to have chemical and morphological properties typical of nocardiae. The strain formed a distinct monophyletic clade in the 16S rDNA tree together with Nocardia africana, Nocardia vaccinii and Nocardia veterana, and showed a unique combination of phenotypic properties that distinguished it from representatives of all recognized species of Nocardia. DNA–DNA relatedness studies indicated that the isolate belongs to a genomic species that is readily distinguished from its nearest neighbours, the type strains of N. africana and N. veterana. The organism is considered to merit species status, and it is proposed that it be designated Nocardia cerradoensis sp. nov., with strain Y9T (=CCT 5601T =DSM 44546T) as the type strain.
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Corynebacterium spheniscorum sp. nov., isolated from the cloacae of wild penguins
Twenty unidentified Gram-positive, rod-shaped organisms were recovered from the cloacae of apparently healthy wild penguins (Spheniscus magellanicus) and subjected to a polyphasic taxonomic analysis. On the basis of cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Corynebacterium, although the organisms did not appear to correspond to any recognized species. Lipid studies confirmed this generic placement, and comparative 16S rRNA gene sequencing showed that the unidentified organisms represent a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium diphtheriae and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from penguins be classified in the genus Corynebacterium, as Corynebacterium spheniscorum sp. nov. The type strain is strain PG 39T (=CCUG 45512T =CECT 5986T).
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Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra)
A bacterial strain, designated XIL07T, isolated from a decayed tree, Ulmus nigra, in Salamanca (Spain) produced abundant cellulases and xylanases. The micro-organism was Gram-positive, aerobic, coccoid and non-motile. Growth was observed on many carbohydrates, including cellulose and xylan as the sole carbon sources. No growth was observed with acetate, citrate, gluconate, inositol, malate or mannitol as carbon sources. The strain showed very weak catalase activity. HPLC analysis of menaquinones revealed two peaks: the main peak corresponded with MK-9(H4) and the smaller one with MK-8(H4). The major fatty acid found was anteiso-C15 : 0 (12-methyl tetradecanoic acid). Mycolic acids were absent. The polar lipids detected were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. Peptidoglycan type was A4α, l-Lys–d-Asp. The cell-wall sugars detected were galactose and rhamnose. The complete 16S rDNA sequence of strain XIL07T was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the high-G+C-content Gram-positive bacteria and that the closest related genera are Promicromonospora and Cellulosimicrobium. The DNA G+C content was 73 mol%. According to the data obtained in this work, this bacterium belongs to a new genus in the family Promicromonosporaceae and the name Xylanimonas cellulosilytica gen. nov., sp. nov. is proposed; the type strain is strain XIL07T (=LMG 20990T =CECT 5975T).
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Lactobacillus ingluviei sp. nov., isolated from the intestinal tract of pigeons
More LessLactic acid bacteria were isolated from the crop and intestines of pigeons. One group of strains, showing similar genomic patterns after screening with tRNA intergenic spacer PCR, could not be identified to the species level. Sequencing of the 16S rRNA gene of one representative strain revealed about 96 % similarity to sequences from Lactobacillus fermentum and Lactobacillus mucosae. Determination of the DNA base composition, DNA–DNA hybridization experiments, SDS-PAGE of whole-cell proteins and biochemical testing confirmed that the seven strains studied constitute a single novel Lactobacillus species, for which the name Lactobacillus ingluviei sp. nov. is proposed. The type strain is strain KR3T (=LMG 20380T =CCUG 45722T).
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Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., from a sewage ditch and soil in southern China
Two soil isolates, strains 80-60T and 3.24T, were shown to have chemical and morphological properties consistent with their classification in the genus Actinomadura. The almost complete 16S rDNA sequences generated for the two organisms were aligned with available sequences of representatives of the genus Actinomadura and related taxa. It was apparent from the resultant phylogenetic trees that each of the strains formed a distinct phyletic line within the evolutionary radiation occupied by the genus Actinomadura. The two organisms could also be distinguished from one another and from representatives of all the validly described species of Actinomadura using a set of phenotypic properties. It is proposed that strains 3.24T (=AS 4.1522T =IFO 16341T) and 80-60T (=AS 4.1202T =IFO 14668T =JCM 16161T) be classified in the genus Actinomadura as Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., respectively.
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Emended description of Streptococcus ferus isolated from pigs and rats
Streptococcus ferus is a mutans-like streptococcus originally isolated from wild rats fed with sugar cane. Taxonomically, this species has not been studied extensively. Ten Gram-positive coccal strains, isolated from the tonsils and nasal conchae of piglets, were identified as S. ferus by 16S rDNA sequencing, tRNA-intergenic spacer length polymorphism analysis (tDNA-PCR), whole-cell protein profiling using SDS-PAGE, G+C content determination and extensive biochemical testing. In all these tests, the type strain of S. ferus (LMG 16520T), from a rat, was included. The results of the tests are described and an emended species description is presented.
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Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are γ-radiation resistant
More LessOne of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA–DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, γ-radiation, H2O2 and desiccation. The 16S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA–DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAA-519T =DSM 15077T).
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Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample
Strain CMS 76orT, an orange-pigmented bacterium, was isolated from a cyanobacterial mat sample from a pond located in McMurdo Dry Valley, Antarctica. On the basis of chemotaxonomic and phylogenetic properties, strain CMS 76orT was identified as a member of the genus Kocuria. It exhibited a 16S rDNA similarity of 99·8 % and DNA–DNA similarity of 71 % with Kocuria rosea (ATCC 186T). Phenotypic traits confirmed that strain CMS 76orT and K. rosea were well differentiated. Furthermore, strain CMS 76orT could be differentiated from the other reported species of Kocuria, namely Kocuria kristinae (ATCC 27570T), Kocuria varians (ATCC 15306T), Kocuria rhizophila (DSM 11926T) and Kocuria palustris (DSM 11025T), on the basis of a number of phenotypic features. Therefore, it is proposed that strain CMS 76orT (=MTCC 3702T =DSM 14382T) be assigned to a novel species of the genus Kocuria, as Kocuria polaris.
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‘Candidatus Pasteuria usgae’ sp. nov., an obligate endoparasite of the phytoparasitic nematode Belonolaimus longicaudatus
Taxonomically relevant characteristics of a fastidiously Gram-positive, obligately endoparasitic prokaryote (strain S-1) that uses the phytoparasitic sting nematode Belonolaimus longicaudatus as its host are reviewed. 16S rDNA sequence similarity (⩾93 %) confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans and corroborates morphological, morphometric and host range evidence suggesting a novel taxon. The 16S rDNA sequence of strain S-1 has greatest similarity (96 %) to the 16S rDNA sequences of both Pasteuria penetrans from root-knot nematodes (Meloidogyne species) and the recently reported strain of Pasteuria isolated from the soybean cyst nematode Heterodera glycines. Because the obligately endoparasitic nature of prokaryotes in the genus Pasteuria prevents isolation of definitive type strains, strain S-1 is proposed as ‘Candidatus Pasteuria usgae’ sp. nov.
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Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen
More LessTwo novel Gram-negative, anaerobic, non-spore-forming, butyrate-producing bacterial species, strains Mz 5T and JK 615T, were isolated from the rumen fluid of cow and sheep. Both strains were curved rods that were motile by means of single polar or subpolar flagellum and common in the rumen microbial ecosystem. Strain Mz 5T produced high xylanase, proteinase, pectin hydrolase and DNase activities; 1,4-β-endoglucanase was also detected in the culture medium. The bacterium utilized a wide range of carbohydrates. Glucose was fermented to formate, butyrate, lactate, succinate and ethanol. The DNA G+C content was 42·1 mol%. The complete 16S rDNA sequence was obtained and phylogenetic relationships were determined. Strain Mz 5T and related isolates were located in clostridial cluster XIVa and were closely related to Pseudobutyrivibrio ruminis, Butyrivibrio crossotus, Roseburia cecicola and Eubacterium rectale. The name proposed for this novel bacterium is Pseudobutyrivibrio xylanivorans; the type strain is Mz 5T (=DSM 14809T =ATCC BAA-455T). Strain JK 615T produced no fibrolytic activity, but utilized a wide range of carbohydrates. Glucose was fermented to formate, acetate, butyrate and ethanol. The DNA G+C content was 44·8 mol%. The complete 16S rDNA sequence was obtained and phylogenetic relationships were determined. Strain JK 615T was located in clostridial cluster XIVa and was closely related to Clostridium proteoclasticum, Butyrivibrio fibrisolvens and Eubacterium halii. The name proposed for this novel bacterium is Butyrivibrio hungatei; the type strain is JK 615T (=DSM 14810T =ATCC BAA-456T).
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Streptomyces yunnanensis sp. nov., a mesophile from soils in Yunnan, China
More LessA strain was isolated from red soil from the suburb of Kunming in Yunnan, China, during the screening of agricultural antibiotics which prevented and cured wheat-stem rust. This isolate, designated YIM 41004T (=CGMCC 4.1004T =DSM 41793T), was identified by a polyphasic approach. The test results suggested that this strain was clearly assigned to the genus Streptomyces and found to be marginally close to Williams cluster 32 based on the morphological and physiological data. The almost-complete 16S rRNA gene sequence of the strain was determined and compared with those of representative streptomycetes. The phylogenetic tree confirmed its membership in the genus Streptomyces and demonstrated that this strain represented a separate phyletic line in a clade encompassed by streptomycetes within cluster 32. Based on the polyphasic evidence, it is therefore proposed that strain YIM 41004T should be classified as Streptomyces yunnanensis sp. nov.
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