- Volume 59, Issue 7, 2009
Volume 59, Issue 7, 2009
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 4, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- List Of Changes In Taxonomic Opinion
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Notification of changes in taxonomic opinion previously published outside the IJSEM
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429-1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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- New Taxa
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- Actinobacteria
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Promicromonospora flava sp. nov., isolated from sediment of the Baltic Sea
More LessA Gram-positive, non-spore-forming actinomycete, designated strain CC 0387T, was isolated from a sediment sample from the Baltic Sea, Germany. Classification using a polyphasic approach and comparative 16S rRNA gene sequencing showed that strain CC 0387T belonged to the genus Promicromonospora and displayed more than 3 % 16S rRNA gene sequence divergence from all Promicromonospora species with validly published names. Strain CC 0387T did not produce aerial mycelium. Substrate mycelia were yellowish white to pale orange-yellow and fragmented into bacillary or coccoid elements. The cell wall contained lysine and alanine. Whole-cell hydrolysates contained galactose, glucose, rhamnose and ribose. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The predominant menaquinone was MK-9(H4) (86 %). The G+C content of the DNA was 71.87 mol%. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain CC 0387T (=CCTCC AA208024T=DSM 21481T) represents a novel species, for which the name Promicromonospora flava sp. nov. is proposed.
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Sphaerisporangium flaviroseum sp. nov. and Sphaerisporangium album sp. nov., isolated from forest soil in China
More LessTwo Gram-positive, aerobic actinomycete strains, designated YIM 48771T and YIM 48782T, were isolated from virgin forest soil samples collected in Hunan Province, China. 16S rRNA gene sequence similarities of the two novel isolates ranged from 96.3 to 97.6 % with species of the genus Sphaerisporangium with validly published names but, in the tree based on 16S rRNA gene sequences, the isolates formed distinct phyletic lines. The level of 16S rRNA gene sequence similarity between the two novel isolates was 97.1 %. DNA–DNA hybridization of strains YIM 48771T and YIM 48782T with recognized species of the genus Sphaerisporangium revealed that the level of DNA–DNA relatedness was below 70 %. The DNA G+C contents of strains YIM 48771T and YIM 48782T were 67.1 and 71 mol%, respectively. Chemotaxonomic data [major menaquinone, MK-9(H4); major polar lipids, diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylethanolamine and phosphoglycolipids; major fatty acids, iso-C16 : 0 and 10-methyl C17 : 0] supported the affiliation of the two isolates with the genus Sphaerisporangium. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the two isolates from recognized Sphaerisporangium species. Based on morphological, chemotaxonomical and phylogenetic data, strains YIM 48771T and YIM 48782T are considered to represent two novel species of the genus Sphaerisporangium, for which the names Sphaerisporangium flaviroseum sp. nov. (type strain, YIM 48771T=DSM 45170T=KCTC 19393T) and Sphaerisporangium album sp. nov. (type strain, YIM 48782T=DSM 45172T=CCTCC AA 208026T) are proposed.
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Streptosporangium canum sp. nov., isolated from soil
More LessAn actinomycete strain, designated HBUM 170018T, was isolated from soil from Hebei Province, China, and subjected to a polyphasic taxonomic analysis. This study included morphological and physiological investigations and analyses concerning cell chemistry, genomic DNA G+C content, DNA–DNA hybridization and phylogeny. The data obtained were consistent with the assignment of strain HBUM 170018T to the genus Streptosporangium and were confirmed by the results of 16S rRNA gene sequence analysis. Strain HBUM 170018T can be differentiated from all Streptosporangium species with validly published names with reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results. On the basis of 16S rRNA gene sequencing, DNA–DNA hybridization and phenotypic data, strain HBUM 170018T represents a novel species of the genus Streptosporangium, for which the name Streptosporangium canum sp. nov. is proposed. The type strain is HBUM 170018T (=7177T =DSM 45034T =CGMCC 4.2126T).
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Microbacterium insulae sp. nov., isolated from soil
More LessA Gram-positive, non-motile, rod- or coccoid-shaped Microbacterium-like bacterium, designated strain DS-66T, was isolated from soil of Dokdo, Korea, and its exact taxonomic position was investigated by using a polyphasic approach. Strain DS-66T grew optimally at 30 °C and pH 6.5–7.0 in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-66T belonged to the genus Microbacterium. Strain DS-66T had a peptidoglycan type based on B2β with partial substitution of glutamic acid by 3-hydroxy glutamic acid (Glu/Hyg–Gly–d-Orn), and galactose, rhamnose and ribose as whole-cell sugars. The acyl type was glycolyl. Strain DS-66T contained MK-13, MK-12 and MK-14 as predominant menaquinones and anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0 and iso-C16 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 69.9 mol%. Phylogenetic distinctiveness, DNA–DNA relatedness data and differential phenotypic properties demonstrated that strain DS-66T is distinguishable from recognized Microbacterium species. On the basis of the data presented, strain DS-66T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium insulae sp. nov. is proposed. The type strain is DS-66T (=KCTC 19247T=CCUG 54523T).
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Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov.
More LessThe diversity of bacteria associated with inflamed mucosa was investigated by culturing ileal samples from TNFdeltaARE mice on a selective medium containing mucin. Among eight isolates, two strains (Mt1B3 and Mt1B8T) belonged to bacterial groups not yet cultured from the mouse intestine. Whereas strain Mt1B3 was identified as a member of the family Planococcaceae and is closely related to Sporosarcina species and Filibacter limicola DSM 13886T, strain Mt1B8T was a novel bacterium. Based on phylogenetic analysis, strain Mt1B8T is a member of the family Coriobacteriaceae. The closest relatives with validly published names were Asaccharobacter celatus, Adlercreutzia equolifaciens (<96 % similarity) and Eggerthella species (<92 %). With respect to Asaccharobacter celatus and Eggerthella, the phylogenetic position of strain Mt1B8T was confirmed at the chemotaxonomic level by Fourier-transform infrared spectroscopic analysis. The major fatty acid of strain Mt1B8T is C16 : 0 (23.9 %). Menaquinones were monomethylated. DNA–DNA relatedness between strain Mt1B8T and Asaccharobacter celatus DSM 18785T was 28 %. Strain Mt1B8T is a Gram-positive-staining rod that does not form spores and has a high DNA G+C content (64.2 mol%). Cells are aerotolerant but grow only under strictly anoxic conditions. They are sensitive to cefotaxime, clarithromycin, erythromycin, metronidazole, tetracycline, tobramycin and vancomycin. API and VITEK analysis showed the ability of strain Mt1B8T to convert a variety of amino acid derivatives. According to these findings, it is proposed to create a novel genus and species, Enterorhabdus mucosicola gen. nov., sp. nov., to accommodate strain Mt1B8T. The type strain of Enterorhabdus mucosicola is Mt1B8T (=DSM 19490T =CCUG 54980T).
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- Archaea
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Desulfurococcus kamchatkensis sp. nov., a novel hyperthermophilic protein-degrading archaeon isolated from a Kamchatka hot spring
More LessA novel obligately anaerobic, hyperthermophilic, organotrophic archaeon, designated strain 1221nT, was isolated from a hot spring of Uzon Caldera (Kamchatka Peninsula, Russia). Cells of strain 1221nT were non-motile regular cocci, 0.6–1 μm in diameter. The temperature range for growth at pH 6.5 was 65–87 °C, with an optimum at 85 °C. The pH range for growth at 85 °C was 5.5–7.5, with an optimum at pH 6.5. Growth was not observed at or below 6 °C or at or above 90 °C, as well as at or below pH 5.0 and at or above pH 8.0. The isolate fermented a wide range of substrates including proteins: α-keratin, albumin and gelatin. Elemental sulfur was not essential for growth, but stimulated growth. Strain 1221nT synthesized 40 and 120 kDa proteinases localized on the cell envelope. The G+C content of the DNA was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that strain 1221nT was affiliated with the genus Desulfurococcus. The level of 16S rRNA gene sequence similarity with other Desulfurococcus species was 96.7–98.1 %, and Desulfurococcus amylolyticus was found to be the most closely related organism. Based on the data from the phylogenetic analysis and the physiological properties of the novel isolate, strain 1221nT should be classified as representing a novel species, for which the name Desulfurococcus kamchatkensis sp. nov. is proposed. The type strain is 1221nT (=DSM 18924T=VKM B-2413T).
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- Bacteroidetes
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Adhaeribacter terreus sp. nov., isolated from forest soil
More LessA bacterial strain, designated DNG6T, was isolated from forest soil of the Changbai mountains, Heilongjiang province, China. Cells of strain DNG6T were Gram-negative, 0.3–0.5 μm in diameter and 1.0–2.0 μm in length, strictly aerobic and produced large amounts of extracellular fibrillar material. Growth occurred at 16–33 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0–1 % NaCl (optimum, 0 %). Strain DNG6T contained MK-7 as the major respiratory quinone and iso-C15 : 0 (40.6 %) and summed feature 4 comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B (26.5 %) as the major cellular fatty acids. The DNA G+C content was 48.1 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest relative of strain DNG6T was Adhaeribacter aquaticus MBRG1.5T with 93.9 % sequence similarity. Based on these results, it is concluded that strain DNG6T represents a novel species of the genus Adhaeribacter, for which the name Adhaeribacter terreus is proposed, with strain DNG6T (=CGMCC 1.6961T=NBRC 104235T) as the type strain.
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Tenacibaculum crassostreae sp. nov., isolated from the Pacific oyster, Crassostrea gigas
A rod-shaped, yellow-pigmented, aerobic, Gram-negative bacterium, designated strain JO-1T, was isolated from an apparently healthy Pacific oyster, Crassostrea gigas, collected at Wan Island, Korea. It grew at 15–37 °C (optimum 30 °C) only in the presence of sea salts. Strain JO-1T hydrolysed casein, Tween 80 and starch. The major fatty acids were iso-C15 : 0 (23.8 %), summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 14.5 %) and iso-C15 : 1 G (14.1 %). Analysis of the 16S rRNA gene sequence indicated that strain JO-1T was a member of the genus Tenacibaculum in the family Flavobacteriaceae, with sequence similarity of 94.6–97.8 % to the type strains of recognized members of the genus. The G+C content of the genomic DNA was 31.4 mol%. DNA–DNA relatedness levels between strain JO-1T and the five closest relatives, Tenacibaculum litoreum KCCM 42115T, T. lutimaris KCTC 12302T, T. aestuarii KCTC 12569T, T. mesophilum DSM 13764T and T. adriaticum JCM 14633T, were less than 28 %. Phylogenetic analyses and differences in physiological and biochemical characteristics suggested that strain JO-1T (=KCTC 22329T =JCM 15428T) should be classified as the type strain of a novel species within the genus Tenacibaculum, for which the name Tenacibaculum crassostreae sp. nov. is proposed.
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Planobacterium taklimakanense gen. nov., sp. nov., a member of the family Flavobacteriaceae that exhibits swimming motility, isolated from desert soil
More LessA Gram-negative and rod-shaped bacterial strain, X-65T, isolated from desert soil of Xinjiang, China, was subjected to phenotypic and phylogenetic studies. On the basis of 16S rRNA gene sequence analyses, the isolate showed closest relationship to members of the genera Chryseobacterium (92.4–95.4 % similarity), Cloacibacterium (94.0 %), Sejongia (93.9 %) and Elizabethkingia (93.8 %) and to Riemerella columbina LMG 11607T (93.3 %). The strain differed from its phylogenetic neighbours by its swimming motility in liquid cultures and the presence of long appendages and large amounts of the straight-chain fatty acids 16 : 0 and 18 : 0. Growth was observed at 18–37 °C (optimum 30 °C), at pH 6–12 (optimum pH 7–8) and in the presence of 0–3 % NaCl (optimum 0 %). Flexirubin pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content of X-65T was 41.5 mol%. The data presented in this study indicate that the isolate should be classified in a novel genus and species within the family Flavobacteriaceae, for which the name Planobacterium taklimakanense gen. nov., sp. nov. is proposed. The type strain of Planobacterium taklimakanense is X-65T (=CCTCC AB 208154T =NRRL B-51322T).
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Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil
Three Gram-negative, rod-shaped, non-spore-forming eubacterial strains were isolated in western Montana, USA, and subjected to taxonomic studies. Strains NWG-II14T and NWER-II11T were isolated from hyporheic sediments of a large alluvial flood plain, whereas strain G-1T was isolated from a conifer forest soil. On the basis of 16S rRNA gene sequence similarity, strains NWG-II14T, NWER-II11T and G-1T were shown to belong to the family Sphingobacteriaceae and are most closely related to various species of the genus Pedobacter. The results of molecular, physiological and biochemical tests allowed genotypic and phenotypic differentiation of these three strains from 23 Pedobacter species with validly published names. The three isolates therefore represent novel species, for which the names Pedobacter nyackensis sp. nov. (type strain NWG-II14T =DSM 19625T =LMG 24260T), Pedobacter alluvionis sp. nov. (type strain NWER-II11T =DSM 19624T =LMG 24258T) and Pedobacter borealis sp. nov. (type strain G-1T =DSM 19626T =LMG 24259T) are proposed.
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Porphyromonas bennonis sp. nov., isolated from human clinical specimens
More LessDuring our investigation of the bacteriology of human wound infections and abscesses, a novel anaerobic, non-spore-forming, Gram-negative bacillus was frequently isolated. On the basis of morphological and biochemical criteria, the strains were tentatively identified as belonging to the family Bacteroidaceae, but they did not appear to correspond to any recognized species of this family. Comparative 16S rRNA gene sequencing showed that the 14 novel strains were genotypically homogeneous and confirmed their placement in the genus Porphyromonas. Sequence divergence values >10 % with respect to reference Porphyromonas species demonstrated that the strains isolated represent a novel species. On the basis of biochemical criteria and phylogenetic considerations, it is proposed that these strains isolated from human sources should be assigned to a novel species of the genus Porphyromonas, named Porphyromonas bennonis sp. nov., with WAL 1926CT (=ATCC BAA-1629T =CCUG 55979T) as the type strain.
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Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family ‘Porphyromonadaceae’ isolated from rat faeces
More LessTwo bacterial strains, designated MT01T and MT12T, isolated from rat faeces were characterized by using a polyphasic taxonomic approach that included analysis of their phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogeny based on 16S rRNA gene sequences. The 16S rRNA gene sequence analysis showed that these strains were members of the family ‘Porphyromonadaceae’. The strains shared 94 % 16S rRNA gene sequence similarity with each other and were related to Odoribacter splanchnicus NCTC 10825T (86–87 % sequence similarity). The strains consisted of obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The two strains produced significant levels of butyric and isobutyric acids as end products from glucose. Although the major cellular fatty acid of these two strains and O. splanchnicus JCM 15291T was iso-C15 : 0, strains MT01T and MT12T showed a higher level of iso-C15 : 0 (66 and 74 %, respectively) than did O. splanchnicus JCM 15291T (48 %). In addition, the ratios of iso-C15 : 0 to anteiso-C15 : 0 in whole-cell methanolysates of the two isolates were very much higher than that of O. splanchnicus JCM 15291T. The major menaquinone of the isolates was MK-10. This menaquinone composition was different from those of other genera of the family ‘Porphyromonadaceae’, such as Barnesiella (predominant menaquinones: MK-11 and MK-12), Odoribacter (MK-9), Paludibacter (MK-8), Parabacteroides (MK-9 and MK-10), Porphyromonas (MK-9 and MK-10) and Tannerella (MK-10 and MK-11). Menaquinone composition is therefore an important chemotaxonomic characteristic of these micro-organisms. Strains MT01T and MT12T have DNA G+C contents of 46 mol%. On the basis of these data, strains MT01T and MT12T represent two novel species of a novel genus, for which the names Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., respectively, are proposed. The type strains of B. synergistica and B. virosa are MT01T (=JCM 15148T =CCUG 56610T) and MT12T (=JCM 15149T=CCUG 56611T), respectively.
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Flavobacterium chungangense sp. nov., isolated from a freshwater lake
More LessA yellow-pigmented, rod-shaped, Gram-staining-negative, aerobic bacterial strain, designated CJ7T, was isolated from a freshwater lake at Chung-Ang University in Anseong, South Korea. Results from 16S rRNA gene sequence analysis revealed that the isolate was phylogenetically affiliated with members of the genus Flavobacterium. Strain CJ7T showed sequence similarity values of 91.5–98.0 % to the type strains of recognized Flavobacterium species. The DNA–DNA relatedness between strain CJ7T and Flavobacterium hercynium DSM 18292T, which showed the highest 16S rRNA gene sequence similarity, was 25.4 %. The predominant cellular fatty acids were iso-C15 : 0 (18.3 %), summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c) (16.1 %), iso-C17 : 0 3-OH (8.9 %), iso-C15 : 0 3-OH (7.2 %), iso-C17 : 1 ω9c (6.1 %) and iso-C15 : 1 (5.9 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was menaquinone-6. The DNA G+C content was 34.5 mol%. The results obtained from this study, with a polyphasic taxonomic approach, suggested that strain CJ7T represents a novel species of the genus Flavobacterium for which the name Flavobacterium chungangense sp. nov. is proposed. The type strain is CJ7T (=KACC 13353T=JCM 15651T).
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Algoriphagus aquatilis sp. nov., isolated from a freshwater lake
More LessA Gram-negative, non-spore-forming, non-motile bacterium, strain A8-7T, was isolated from fresh water of a slightly alkaline lake, Longhu Lake, in Daqing, north-east China, and its taxonomic position was studied by using a polyphasic approach. Strain A8-7T was aerobic, heterotrophic and positive for catalase and oxidase. It grew at 20–37 °C (optimum 30 °C) and pH 5.5–10.5 (optimum pH 7.5) and in the presence of 0–3 % (w/v) NaCl. It formed pink-pigmented, smooth and circular colonies, 1–2 mm in diameter, on R3A-V agar plates after incubation at 30 °C for 3 days. Cells of strain A8-7T were rods, 0.2–0.4 μm wide and 1.6–4.0 μm long. The major fatty acids (>10 %) were iso-C15 : 0 (40.3 %) and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 12.1 %). The menaquinone was MK-7. The DNA G+C content was 43 mol% (T m). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A8-7T was phylogenetically related to members of the genus Algoriphagus, with sequence similarities of 92.6–95.2 %, the highest sequence similarity being to the sequence from Algoriphagus mannitolivorans IMSNU 14012T. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain A8-7T was considered to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus aquatilis sp. nov. is proposed. The type strain is A8-7T (=CGMCC 1.7030T =NBRC 104237T).
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- Firmicutes And Related Organisms
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Gracilibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a salt lake
More LessA novel Gram-positive-staining, aerobic, spore-forming, rod-shaped bacterium, designated strain YIM 91119T, was isolated from Ebinur Lake in Xinjiang Province, north-west China. Cells were motile, produced terminal endospores and grew at pH 6.0–8.0 (optimally at pH 7.0), 4–45 °C (optimally at 28–37 °C) and 1–22 % (w/v) NaCl, (optimally at 10–15 %, w/v). Comparative 16S rRNA gene sequence analysis showed that strain YIM 91119T belongs to the genus Gracilibacillus, exhibiting the highest sequence similarity with respect to the type strain of Gracilibacillus orientalis (97.8 %); the next most similar 16S rRNA gene sequences were those of the type strains of Gracilibacillus boraciitolerans (96.8 %), Gracilibacillus dipsosauri (96.5 %) and Gracilibacillus halotolerans (95.8 %). DNA–DNA hybridization with G. orientalis AS 1.4250T showed a relatedness of 55 %. The major fatty acids of strain YIM 91119T were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The peptidoglycan type was A1γ (directly cross-linked meso-diaminopimelic acid). The genomic DNA G+C content was 40.1 mol% and the predominant respiratory quinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the evidence from this polyphasic study, strain YIM 91119T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus saliphilus sp. nov. is proposed, with YIM 91119T (=DSM 19802T =CCTCC AA 208015T) as the type strain.
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Jeotgalicoccus marinus sp. nov., a marine bacterium isolated from a sea urchin
A novel non-sporulating, non-motile, catalase- and oxidase-positive, facultatively anaerobic, moderately halophilic, Gram-positive coccus, designated JSM 076033T, was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. Strain JSM 076033T was able to grow in the presence of 0.5–25.0 % (w/v) total salts and at pH 6.0–10.0 and 10–45 °C; optimum growth was observed with 5.0–10.0 % (w/v) total salts and at pH 7.0–8.0 and 25–30 °C. The major amino acid constituents of the cell wall were glycine, lysine and alanine. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The respiratory quinones were MK-7 (60.7 %) and MK-6 (39.3 %) and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 40.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 076033T should be assigned to the genus Jeotgalicoccus. The sequence similarities between the novel isolate and the type strains of recognized Jeotgalicoccus species were in the range 95.2–97.2 %. The results of the phylogenetic analysis, combined with DNA–DNA relatedness data, phenotypic characteristics and chemotaxonomic information, support the view that strain JSM 076033T represents a novel species of the genus Jeotgalicoccus, for which the name Jeotgalicoccus marinus sp. nov. is proposed. The type strain is JSM 076033T (=CCTCC AA 207028T =DSM 19772T =KCTC 13189T).
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Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchin
A Gram-positive-staining, moderately halophilic, strictly aerobic, catalase- and oxidase-positive, rod-shaped bacterium, designated strain JSM 076056T, was isolated from a sea urchin collected from the South China Sea. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Strain JSM 076056T was able to grow at salinities of 2–25 % (w/v) total salts and at pH 6.0–10.0 and 15–40 °C; optimum growth was observed with 5–10 % (w/v) total salts and at pH 7.0–8.0 and 25–30 °C. It was incapable of growing with NaCl as the sole salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, anteiso-C15 : 0 and C16 : 1 ω7c alcohol. The predominant respiratory quinone was MK-7 and the genomic DNA G+C content was 45.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 076056T belonged to the family Bacillaceae and was related most closely to the type strains of the two recognized species of the genus Pontibacillus, namely Pontibacillus chungwhensis BH030062T (96.4 % sequence similarity) and Pontibacillus marinus BH030004T (96.2 %); these three strains formed a robust cluster in the phylogenetic tree. In combination, the phylogenetic, phenotypic and chemotaxonomic data indicate that strain JSM 076056T represents a novel species of the genus Pontibacillus, for which the name Pontibacillus halophilus sp. nov. is proposed. The type strain is JSM 076056T (=CCTCC AA 207029T =DSM 19796T =KCTC 13190T).
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Sediminibacillus albus sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a hypersaline lake, and emended description of the genus Sediminibacillus Carrasco et al. 2008
More LessA moderately halophilic, Gram-positive-staining, endospore-forming, rod-shaped and strictly aerobic bacterium, designated strain NHBX5T, was isolated from Lake Nanhuobuxun in China. Strain NHBX5T was able to grow at NaCl concentrations of 0–22 % (w/v) (optimally at 7 %, w/v), at pH 6.0–9.0 (optimally at pH 7.5) and at temperatures of 10–45 °C (optimally at 37 °C). The cell-wall peptidoglycan of strain NHBX5T contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and a glycolipid. The genomic DNA G+C content of strain NHBX5T was 44.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain NHBX5T was most closely related to Sediminibacillus halophilus EN8dT (98.6 % gene sequence similarity). The level of DNA–DNA relatedness between strain NHBX5T and S. halophilus CGMCC 1.6199T was 34.6 %. Based on the data presented, strain NHBX5T represents a novel species of the genus Sediminibacillus, for which the name Sediminibacillus albus sp. nov. is proposed. The type strain is NHBX5T (=DSM 19340T =CGMCC 1.6502T). In addition, an emended description of the genus Sediminibacillus is presented.
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Clostridium sulfidigenes sp. nov., a mesophilic, proteolytic, thiosulfate- and sulfur-reducing bacterium isolated from pond sediment
More LessA novel strictly anaerobic, endospore-forming, rod-shaped, Gram-positive bacterium, designated strain SGB2T, was isolated from a mixed culture from a pond sediment during screening for sulfate-reducing bacteria capable of degrading cyanophycin (CGP). In this study, the taxonomic characterization of this mesophilic, proteolytic Clostridium isolate and the role which it, and its phylogenetic relatives, may play in peptide degradation and in the sulfur cycle are reported. Strain SGB2T was a commensal strain, utilizing CGP degradation products produced by other micro-organisms. Cells were motile until sporulation, forming oval, terminal spores that swell the cells. It showed optimum growth at 34 °C, pH 6.6 and in the absence of NaCl. Strain SGB2T utilized proteinaceous compounds such as peptone, Casamino acids, gelatin and trypticase soy, in addition to several amino acids and pyruvate. Utilization of many of these compounds was enhanced in the presence of thiosulfate. The isolate was unable to use any of the carbohydrates or alcohols investigated or CGP as carbon and energy sources. Thiosulfate and elemental sulfur were used as terminal electron acceptors. Phylogenetic analysis revealed that strain SGB2T belongs to the low-G+C-containing Clostridiales group. It exhibited 99 % 16S rRNA gene sequence similarity to its closest relatives Clostridium thiosulfatireducens Lup21T and Clostridium subterminale DSM 6970T. DNA–DNA hybridization values with these two strains were 39.4 and 42.1 %, respectively. Based on phenotypic, genotypic and phylogenetic characteristics, we conclude that the isolate represents a novel species of the genus Clostridium, Clostridium sulfidigenes sp. nov. The type strain is SGB2T (=DSM 18982T =ATCC BAA-1538T).
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Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra
More LessEight psychrotolerant, xylan-degrading strains of bacteria that were catalase-positive, oxidase-negative and able to reduce nitrate to nitrite were isolated from soil beneath moist non-acidic and acidic tundra in northern Alaska. The DNA G+C contents for the strains ranged from 46.4–50.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each strain belonged to the genus Paenibacillus. The highest level of 16S rRNA gene similarity was found between the eight strains and Paenibacillus amylolyticus NRRL NRS-290T (98.9–99.1 %). However, despite relatively high 16S rRNA gene similarity, DNA–DNA hybridization, repetitive elements genotyping and phenotypic analysis revealed that at least two of the strains differed from P. amylolyticus NRRL NRS-290T. DNA–DNA hybridization values between strain A10bT and P. amylolyticus NRRL NRS-290T (4.3 %), between strain B22aT and P. amylolyticus NRRL NRS-290T (48.8 %) and between strain A10bT and strain B22aT (11.0 %) were below those recommended by the ad hoc committee for those belonging to the same species. Significant phenotypic features that differentiate these novel strains from P. amylolyticus included their inability to utilize l-arabinose and ability to utilize glycogen as sole carbon sources. Unlike strains 1B4a and B22aT, strains A6a and A10bT produced ethanol as an end product of glucose fermentation, utilized acetic acid and 2,3-butanediol and did not utilize d-gluconic acid. MK-7 was the major isoprenoid quinone and anteiso-C15 : 0 was the most abundant fatty acid for strains A10bT and B22aT. On the basis of these results, strains A10bT and B22aT are each considered to represent a novel species of the genus Paenibacillus, for which the names Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov. are proposed, respectively. The type strain of Paenibacillus tundrae sp. nov. is A10bT (=NRRL B-51094T=DSM 21291T). The type strain of Paenibacillus xylanexedens sp. nov. is B22aT (=NRRL B-51090T=DSM 21292T).
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Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge
Two novel anaerobic, moderately thermophilic and cellulose-/cellobiose-digesting bacteria, EBR45T and EBR596T, were isolated from anaerobic sludge of a cellulose-degrading methanogenic bioreactor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belonged to cluster III within the low-G+C-content Gram-positive bacteria. The close relatives of EBR45T were Clostridium straminisolvens DSM 16021T (sequence identity, 94.6 %) and Clostridium thermocellum DSM 1237T (93.4 %). The closest relative of EBR596T was Clostridium stercorarium DSM 8532T (95.9 %). Both isolates were rod-shaped sporulators, growing optimally at 60 °C. EBR45T was Gram-staining-reaction-variable and non-motile, formed bright-yellow colonies on solid media, and grew on a relatively narrow range of carbohydrates including cellulose and cellobiose. EBR596T was Gram-staining-reaction-negative and motile, formed glossy white colonies and grew on cellobiose and various carbohydrates except cellulose. Major fatty acid compositions were 16 : 0 iso, 16 : 0 and 16 : 0 dimethylacetal (strain EBR45T) and 15 : 0 iso, 16 : 0 iso, 15 : 0 anteiso and 17 : 0 anteiso (strain EBR596T). The DNA G+C contents were 36.9 mol% (EBR45T) and 51.1 mol% (EBR596T). Based on the phenotypic and phylogenetic data and genomic distinctiveness, strains EBR45T and EBR596T represent two novel species, for which the names Clostridium clariflavum sp. nov. (type strain EBR45T =DSM 19732T =NBRC 101661T) and Clostridium caenicola sp. nov. (type strain EBR596T =DSM 19027T =NBRC 102590T) are proposed.
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Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China
More LessA Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26T, was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30–37 °C and pH 7–8. It grew with 0–8% NaCl (optimum, 0–2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26T was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077T (97.1 %), B. shackletonii LMG 18435T (97.0 %), B. siralis 171544T (97.0 %), B. circulans IAM 12462T (96.7 %) and B. pocheonensis Gsoil 420T (96.7 %). Strain ZLC-26T contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C15 : 0, C16 : 1 ω11c and anteiso-C15 : 0. The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26T to the genus Bacillus. However, low DNA–DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26T from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26T (=CCTCC AB 207172T=NRRL B-51302T).
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- Other Bacteria
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Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835
More LessA novel obligately anaerobic, mesophilic, alkaliphilic spirochaete, strain ASpC2T, was isolated from an anaerobic sediment of alkaline, hypersaline Owens Lake in California, USA. The Gram-negative cells are motile, helical in shape and 0.23×8.0–18.0 μm. Growth occurs within the following ranges: 13–41 °C, with optimal growth at 35 °C; 1–3 % (w/v) NaCl, with optimal growth at 2 % (w/v) NaCl; and pH 7.8–10.5, with optimal growth at pH 10.0. The novel isolate is strictly alkaliphilic and requires high concentrations of carbonate ions in the medium. It utilizes some sugars, some organic acids, some amino acids, Casamino acids, yeast extract and peptone. The main end products of glucose fermentation are CO2 and acetate. Strain ASpC2T is resistant to kanamycin and rifampicin, but sensitive to ampicillin, chloramphenicol, gentamicin and tetracycline. The DNA G+C content of the new isolate is 43.8 mol%, its genome size is 6×108 Da and the melting temperature of its genomic DNA is 71 °C. DNA–DNA hybridization experiments demonstrated 46 % similarity with the phylogenetically most closely related species, Spirochaeta asiatica Z-7591T. On the basis of physiological and molecular properties, the new isolate belongs taxonomically to a novel species within the genus Spirochaeta, for which the name Spirochaeta dissipatitropha sp. nov. is proposed (type strain, ASpC2T=ATCC BAA-1083T=JCM 12856T). S. dissipatitropha ASpC2T is the second strain in the genus (after Spirochaeta smaragdinae SEBR 4228T) that is able to use proteolysis products as the sole energy source, and additional tests have shown that other halo-alkaliphilic spirochaetes (Spirochaeta americana, Spirochaeta alkalica and Spirochaeta africana) are also able to grow on yeast extract alone; therefore, an emended description for the genus Spirochaeta is given.
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- Proteobacteria
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Sediminimonas qiaohouensis gen. nov., sp. nov., a member of the Roseobacter clade in the order Rhodobacterales
Two aerobic bacterial strains, YIM B024T and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15–37 °C, pH 6.5–9.0 and 0.25–20 % (w/v) NaCl; optimum growth was observed at 28–30 °C, pH 7.0–8.5 and 1.5–10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA–DNA hybridization experiments revealed high relatedness values (90±0.4 %) between strains YIM B024T and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C18 : 1 ω7c, C16 : 0, C18 : 1 ω9c, 11-methyl C18 : 1 ω7c and C19 : 0 cyclo ω8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0–64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024T (=KCTC 22349T=CCTCC AA 208033T).
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Marivita cryptomonadis gen. nov., sp. nov. and Marivita litorea sp. nov., of the family Rhodobacteraceae, isolated from marine habitats
More LessTwo strictly aerobic, Gram-negative, rod-shaped bacteria containing photosynthesis-related genes, designated strains CL-SK44T and CL-JM1T, were isolated from a culture of the marine phytoplankton Cryptomonas sp. and coastal seawater from Korea, respectively. Phylogenetic analysis of 16S rRNA gene sequences revealed that the two strains were related to members of the genera Thalassobius (95.3–96.7 % similarity), Pelagibaca (95.3–96.0 %) and Donghicola (95.6 %) in the family Rhodobacteraceae. However, the two novel strains did not form a robust clade with any species of the Roseobacter clade, forming a distinct clade. The major polar lipids of the strains were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid and an unidentified lipid, profiles that were distinguishable from those of the related genera examined. Although the level of 16S rRNA gene sequence similarity between strains CL-SK44T and CL-JM1T was very high (99.1 %), DNA–DNA relatedness between the strains was 13 %, suggesting that they represent genomically distinct species. In addition, the two strains could be differentiated based on the presence of a minor polar lipid, on the hydrolysis of gelatin and the utilization of carbon sources. Based on the data from the present study, strains CL-SK44T and CL-JM1T are considered to represent separate novel species of a new genus of the family Rhodobacteraceae, for which the names Marivita cryptomonadis gen. nov., sp. nov. (type species) and Marivita litorea sp. nov. are proposed. The type strains of Marivita cryptomonadis and Marivita litorea are CL-SK44T (=KCCM 90070T=JCM 15447T) and CL-JM1T (=KCCM 90071T=JCM 15446T), respectively.
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Thauera butanivorans sp. nov., a C2–C9 alkane-oxidizing bacterium previously referred to as ‘Pseudomonas butanovora’
More LessThe placement of ‘Pseudomonas butanovora’ in the genus Thauera was proposed previously, based on 16S rRNA gene sequence analysis, upon further studies of taxonomical characteristics. In this study, physiological characteristics and DNA–DNA reassociation data are presented and the transfer of ‘P. butanovora’ to the genus Thauera is proposed. The original description of the strain (strain Bu-B1211) indicated that it was capable of denitrification but not anaerobic growth. ‘P. butanovora’ is capable of anaerobic respiration and growth, utilizing nitrate as a terminal electron acceptor during the oxidation of organic acids and alcohols, but not aromatic hydrocarbons or open-chain terpenoids. The total fatty acid composition supported the assignment of strain Bu-B1211 to the Betaproteobacteria and resembled that of members of the genus Thauera. The combination of 16S rRNA gene phylogenetic evidence, physiological and taxonomical characteristics and DNA–DNA reassociation data supported the placement of ‘Pseudomonas butanovora’ Bu-B1211 in the genus Thauera as representing a novel species, for which the name Thauera butanivorans sp. nov. is proposed. The type strain is Bu-B1211T (=IAM 12574T=ATCC 43655T=DSM 2080T).
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Bowmanella pacifica sp. nov., isolated from a pyrene-degrading consortium
More LessA taxonomic study was carried out on a strain, designated W3-3AT, which was isolated from a pyrene-degrading consortium, enriched from sediment of the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W3-3AT belonged to the genus Bowmanella, with the highest sequence similarity (99.0 %) with Bowmanella denitrificans BD1T, whereas sequence similarities with other species were less than 93 %. The nucleotide sequence similarity of both gyrB and rpoD genes of strain W3-3AT and B. denitrificans BD1T was 81.1 %. However, the protein sequence similarities of the gyrB and rpoD genes of strain W3-3AT and B. denitrificans BD1T were 96.1 % and 91.0 %, respectively. Phylogenetic trees based on these housekeeping genes showed that strain W3-3AT and B. denitrificans BD1T formed a distinct lineage in the Gammaproteobacteria. The DNA–DNA hybridization value between strain W3-3AT and B. denitrificans BD1T was 43 %. Strain W3-3AT could also be differentiated from B. denitrificans BD1T based on the repetitive extragenic palindromic DNA-PCR fingerprint. The G+C content of the chromosomal DNA of strain W3-3AT was 49 mol%. The combined genotypic and phenotypic data showed that strain W3-3AT represents a novel species of the genus Bowmanella, for which the name Bowmanella pacifica sp. nov. is proposed, with the type strain W3-3AT (=CGMCC 1.7086T=LMG 24568T=MCCC 1A01018T).
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Comparative studies on [Pasteurella] testudinis and [P.] testudinis-like bacteria and proposal of Chelonobacter oris gen. nov., sp. nov. as a new member of the family Pasteurellaceae
A collection of 12 strains, isolated from diseased tortoises and tentatively identified as [Pasteurella] testudinis-like based on phenotypic characters, was compared with three reference strains of [P.] testudinis. All strains could be separated from the reference strains with respect to 16S rRNA gene sequences, partial sequences of the rpoB housekeeping gene and by phenotypic characters. Based upon differences in 16S rRNA and rpoB gene sequences, the new isolates are suggested to represent a novel species in a new genus of the family Pasteurellaceae Pohl 1981, for which the name Chelonobacter oris gen. nov., sp. nov. is proposed. The type strain is 1662T (=CCUG 55632T=DSM 21392T). β-Haemolysis and acid production from (+)-l-arabinose, dulcitol, (−)-d-mannitol, (+)-d-mannose, trehalose and salicin separated the new strains from members of existing genera of the family Pasteurellaceae, in addition to the β-galactosidase, urease and α-glucosidase reactions. Differences in indole production, phosphatase, β-glucosidase and production of acid from dulcitol and trehalose separated C. oris from [P.] testudinis. Several phenotypic characters separated C. oris from Bisgaard's taxa 14 and 32.
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Vibrio breoganii sp. nov., a non-motile, alginolytic, marine bacterium within the Vibrio halioticoli clade
More LessSeven non-motile, facultatively anaerobic, alginolytic marine bacteria were isolated from the cultured clams Ruditapes philippinarum and Ruditapes decussatus. Phylogenetic analysis based on 16S rRNA gene sequences showed that these marine bacteria were closely related to the recently described species Vibrio comitans, Vibrio rarus and Vibrio inusitatus (≥99.0 % sequence similarity). Phylogenetic analysis based on the housekeeping genes rpoA, recA and atpA grouped the isolates together and allocated them to the Vibrio halioticoli species group. Amplified fragment length polymorphism DNA fingerprinting also grouped them together and enabled them to be differentiated from recognized species of the V. halioticoli clade. DNA–DNA hybridizations showed that the isolates belonged to a novel species; phenotypic features such as the ability to grow at 4 °C and in the presence of 6 % NaCl also enabled them to be separated from other species. The DNA G+C content of RD 15.11T is 44.4 mol%. The genotypic and phenotypic data showed that the isolates represent a novel species in the V. halioticoli clade. The name Vibrio breoganii sp. nov. is proposed, with RD 15.11T (=CECT 7222T =LMG 23858T) as the type strain.
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Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae)
A novel red-pigmented, Gram-negative, motile, fluorescent, rod-shaped strain, DZ0503SBS1T, with a single lateral flagellum, was isolated from the intestine of the nematode Heterorhabditidoides chongmingensis. Comparative 16S rRNA gene sequence analysis indicated that the strain is a member of the genus Serratia, sharing highest sequence similarities with Serratia marcescens subsp. sakuensis JCM 11315T (99.8 %), S. marcescens subsp. marcescens DSM 30121T (99.5 %) and Serratia ureilytica LMG 22860T (98.3 %). Similarities between the rpoB gene sequence of strain DZ0503SBS1T and those of S. marcescens subsp. sakuensis JCM 11315T, S. marcescens subsp. marcescens DSM 30121T and S. ureilytica LMG 22860T were 98.0, 97.4 and 98.3 %, respectively. DNA–DNA hybridization values of strain DZ0503SBS1T with S. marcescens subsp. sakuensis JCM 11315T, S. marcescens subsp. marcescens DSM 30121T and S. ureilytica LMG 22860T were 68.2, 65.1 and 53.0 %, respectively. The major isoprenoid quinone of strain DZ0503SBS1T was Q-8 and the predominant fatty acids were C16 : 0 (34.76 %), cyclo-C17 : 0 (20.03 %) and cyclo-C19 : 0 ω8c (17.24 %). The cyclo-C19 : 0 ω8c content (17.24 %) was significantly different from those found in S. marcescens subsp. sakuensis JCM 11315T and S. marcescens subsp. marcescens DSM 30121T. Some characteristics of strain DZ0503SBS1T, i.e. fluorescence and its symbiotic association with nematodes, have not been reported previously in any species of the genus Serratia. Phenotypic and biochemical characteristics and molecular data show that strain DZ0503SBS1T represents a novel species, for which the name Serratia nematodiphila sp. nov. is proposed; the type strain is DZ0503SBS1T (=KCTC 22130T =CGMCC 1.6853T).
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Rhodovulum lacipunicei sp. nov., an obligate sulfide-demanding phototrophic alphaproteobacterium isolated from a purple pond in India
More LessAn ovoid-rod-shaped, phototrophic, purple non-sulfur bacterium, designated strain JA322T, was isolated in pure culture from a water sample collected from a saline pond with purple-coloured water, located near Satpada in Orissa, India. Strain JA322T was Gram-negative and non-motile and grew photoheterotrophically with a number of organic compounds serving as carbon sources or electron donors. Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as photosynthetic pigments. Biotin and thiamine were required for growth of strain JA322T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA322T was related most closely to the type strains of Rhodovulum euryhalinum (95.8 % similarity) and Rhodovulum strictum (94.8 %) and clustered with species of the genus Rhodovulum of the family Rhodobacteraceae. On the basis of phenotypic and molecular genetic evidence, it is suggested that strain JA322T represents a novel species of the genus Rhodovulum, for which the name Rhodovulum lacipunicei sp. nov. is proposed. The type strain is JA322T (=NBRC 104147T=KCTC 5700T).
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Roseomonas frigidaquae sp. nov., isolated from a water-cooling system
More LessA non-motile, coccobacilli-shaped, pale-pink-pigmented bacterium, designated strain CW67T, was isolated from a water-cooling system in Gwangyang, Republic of Korea. Cells were found to be Gram-negative, catalase-positive and oxidase-positive, the major fatty acids were C18 : 1 ω7c (43.6 %) and C16 : 0 (15.8 %), the predominant respiratory lipoquinone was Q-10 and the DNA G+C content was 69.5 mol%. A phylogenetic tree based on 16S rRNA gene sequence comparisons showed that strain CW67T forms an evolutionary lineage within the radiation of the genus Roseomonas and that its closest relative is Roseomonas gilardii subsp. rosea MDA5605T (94.7 % sequence similarity). Evidence from this polyphasic study showed that strain CW67T could not be assigned to any recognized species. It therefore represents a novel species, for which the name Roseomonas frigidaquae sp. nov. is proposed, with CW67T (=KCTC 22211T =JCM 15073T) as the type strain.
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Vibrio azureus sp. nov., a luminous marine bacterium isolated from seawater
Two luminous marine bacterial strains, LC2-005T and LC2-102, were isolated from seawater at Kuroshio Region and Sagami Bay in Japan, respectively. These bacteria were Gram-negative, oxidase-positive, catalase-positive, motile and rod-shaped. On the basis of 16S rRNA gene sequence analysis, strains LC2-005T and LC2-102 formed a cluster within the Vibrio harveyi species group. However, multilocus sequence analysis using five loci (pyrH, ftsZ, mreB, gyrB and gapA) and DNA–DNA hybridization experiments indicated that these strains were distinct from the currently known Vibrio species. Additionally, these strains differ from related Vibrio species in utilization of glucose, mannitol, inositol, sorbitol, rhamnose, sucrose, melibiose and arabinose, production of lysine decarboxylase, ornithine decarboxylase, tryptophan deaminase, esterase (C4), lipase (C4), chymotrypsin, acid phosphatase, α-glucosidase, β-glucosidase and N-acetyl-β-glucosaminidase and the ability to reduce nitrate to nitrite. The major fatty acids were C15 : 0 iso 2-OH and/or C16 : 1 ω7c, C16 : 0, C18 : 1 ω7c and C14 : 0. The DNA G+C contents of strains LC2-005T and LC2-102 were 45.2 and 45.5 mol%, respectively. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains LC2-005T and LC2-102 belong to the same genospecies and represent a novel species of the genus Vibrio, for which the name Vibrio azureus sp. nov. is proposed. The type strain is LC2-005T (=NBRC 104587T =KCTC 22352T).
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Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia
More LessTwelve facultatively anaerobic, endophytic diazotrophs were isolated from surface-sterilized roots of the wild rice species Oryza latifolia and characterized by phenotypic and molecular methods. Six isolates were grouped together as group A by phenotypic characters, and this grouping was confirmed by SDS-PAGE whole-cell protein patterns and insertion sequence-based PCR (IS-PCR) methods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that group A, represented by strain Ola 51T, is closely related to Enterobacter radicincitans D5/23T (98.9 % similarity, except that E. radicincitans D5/23T has a 70 bp insertion) and Enterobacter cloacae (98.0 % similarity to the type strain). rpoB gene sequence analysis also showed strain Ola 51T has the highest sequence similarity to E. radicincitans DSM 16656T (98.3 %), but supported the distinct position. Biological and biochemical tests, protein patterns, genomic DNA fingerprinting, antibiotic resistance and comparison of cellular fatty acids showed differences among group A, E. radicincitans DSM 16656T and E. cloacae ATCC 13047T. DNA–DNA hybridization distinguished strain Ola 51T from closely phylogenetically related Enterobacter species. Based on these data, the novel species Enterobacter oryzae sp. nov. is proposed, with strain Ola 51T (=LMG 24251T =CGMCC 1.7012T) as the type strain.
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Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples
Two bacterial isolates, designated strains 5420S-26T and 5516S-1T, were recovered from air samples collected in Suwon, Korea. Cells of both strains were aerobic, Gram-negative, motile rods. Phylogenetically, these strains were positioned within the radius of the genus Massilia. 16S rRNA gene sequence analysis showed that the strains shared 97.3 % sequence similarity and had sequence similarities of 94.9–98.1 % with respect to type strains of species belonging to the genus Massilia. In DNA–DNA hybridization tests, the two strains showed <39 % relatedness with respect to strains of closely related species of the genus Massilia and 27 % relatedness to each other. Both strains contained Q-8 as the predominant isoprenoid quinone and possessed summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acid. Strain 5516S-1T was found to contain the fatty acid C20 : 0 (in small amounts), a feature that served to distinguish it from both 5420S-26T and recognized members of the genus Massilia. The DNA G+C contents of 5420S-26T and 5516S-1T were 67.8 and 66.6 mol%, respectively. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that 5420S-26T and 5516S-1T represent novel species of the genus Massilia, for which the names Massilia niabensis sp. nov. (type strain 5420S-26T =KACC 12632T =DSM 21312T) and Massilia niastensis sp. nov. (type strain 5516S-1T =KACC 12599T =DSM 21313T) are proposed, respectively.
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Campylobacter cuniculorum sp. nov., from rabbits
More LessEight strains of an unknown thermotolerant Campylobacter species were isolated from the caecal contents of rabbits (Oryctolagus cuniculus). All strains were initially identified as belonging to the genus Campylobacter by means of genus-specific PCR, but none were identified using species-specific PCR for known thermophilic species. Cells were spiral shaped with bipolar unsheathed flagella, with no periplasmic fibres, and appeared coccoid after 10–12 days of incubation. Phylogenetic analyses based on 16S rRNA gene, rpoB and groEL sequences revealed that all strains formed a robust clade that was very distinct from recognized Campylobacter species. 16S rRNA gene sequence pairwise comparisons of strain 150BT with the type strains of other Campylobacter species revealed that the nearest phylogenetic neighbour was Campylobacter helveticus NCTC 12470T, with 96.6 % similarity. The uniqueness of these rabbit isolates was confirmed by whole-cell protein electrophoresis. Taken together, these data indicate that the strains belong to a novel Campylobacter species for which the name Campylobacter cuniculorum sp. nov. is proposed, with 150BT (=LMG 24588T =CCUG 56289T) as the type strain.
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Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil
More LessTwo novel strains isolated from soils, JS12-10T and JS14-6T, were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10T and JS14-6T to the genus Dyella. However, chemotaxonomic data and DNA–DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10T and JS14-6T showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046T (98.4 %) and Dyella japonica XD53T (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA–DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29–38 %. Therefore, strains JS12-10T and JS14-6T represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10T =KACC 12747T =JCM 15423T) and Dyella terrae sp. nov. (type strain JS14-6T =KACC 12748T =JCM 15424T) are proposed.
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Marinobacter lacisalsi sp. nov., a moderately halophilic bacterium isolated from the saline-wetland wildfowl reserve Fuente de Piedra in southern Spain
A Gram-negative, non-spore-forming, motile, moderately halophilic, aerobic, rod-shaped bacterium, designated strain FP2.5T, was isolated from the inland hypersaline lake Fuente de Piedra, a saline-wetland wildfowl reserve located in the province of Málaga in southern Spain. Strain FP2.5T was subjected to a polyphasic taxonomic study. It produced colonies with a light-yellow pigment. Strain FP2.5T grew at salinities of 3–15 % (w/v) and at temperatures of 20–40 °C. The pH range for growth was 5–9. Strain FP2.5T was able to utilize various organic acids as sole carbon and energy source. Its major fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 1 ω9c. The DNA G+C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FP2.5T appeared to be a member of the genus Marinobacter and clustered closely with the type strains of Marinobacter segnicrescens, Marinobacter bryozoorum and Marinobacter gudaonensis (levels of 16S rRNA gene sequence similarity of 98.1, 97.4 and 97.2 %, respectively). However, DNA–DNA relatedness between the new isolate and the type strains of its closest related Marinobacter species was low; levels of DNA–DNA relatedness between strain FP2.5T and M. segnicrescens LMG 23928T, M. bryozoorum DSM 15401T and M. gudaonensis DSM 18066T were 36.3, 32.1 and 24.9 %, respectively. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain FP2.5T is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter lacisalsi sp. nov. is proposed. The type strain is FP2.5T (=CECT 7297T=LMG 24237T).
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Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod–coccus cell cycle in association with the growth phase
Phylogenetic and taxonomic characterization was performed for 14 strains of bacteria that produce anticancer antibiotics (pelagiomicins) (represented by strain Ni-2088T) and one strain that produces UV-absorbing substances (strain F-104T), isolated from marine algae and seagrass collected from coastal areas of tropical Pacific islands and a subtropical island of Japan. All 15 isolates were Gram-negative, strictly aerobic, non-motile and non-spore-forming. Sequence analysis of the 16S rRNA gene showed that the isolates occupied positions in the phylogenetic radiation of the genus Microbulbifer, with similarities of 93.6–97.6 %. The cells possessed a clearly discernible rod–coccus cell cycle in association with the growth phase; cells were rods during the growth phase and all converted to coccoid–ovoid cells when proliferation ceased. The coccoid–ovoid cells were optically denser than the rod cells and were viable for extended periods. They were considered to constitute a resting form. The type strains of described species of Microbulbifer were also found to possess identical rod–coccus cell cycles. The G+C content of the DNA was 48.1–49.7 mol%. The major respiratory quinone system was ubiquinone-8. The major fatty acids were C18 : 1 ω7c and C16 : 0, and the hydroxy acids comprised C10 : 0 3-OH, C12 : 0 3-OH and iso-C11 : 0 3-OH. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The group of 14 pelagiomicin-producing strains and strain F-104T each constituted a single genomic species. Based on phylogenetic affiliation, phenotypic characteristics and genomic distinctness, the isolates represent two novel species in the genus Microbulbifer, for which the names Microbulbifer variabilis sp. nov. (type strain Ni-2088T =MBIC01082T =ATCC 700307T) and Microbulbifer epialgicus sp. nov. (type strain F-104T =MBIC03330T =DSM 18651T) are proposed.
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Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean
More LessA taxonomic study was carried out on strain P24T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium, enriched from a deep-seawater sample collected from the Indian Ocean. The isolate was Gram-negative, rod-shaped, motile by means of a polar flagellum, moderately halophilic and capable of reducing nitrate to nitrite. Growth was observed at salinities of 0–9 % and at temperatures of 10–42 °C. The strain was unable to degrade Tween 80 or gelatin. The dominant fatty acids were C16 : 0 (15.2 % of the total), C18 : 0 (10.3 %), C18 : 1 ω7c (52.0 %), C18 : 1 2-OH (4.7 %) and C19 : 0 ω8c cyclo (4.7 %). The G+C content of the chromosomal DNA was 64.8 mol%. 16S rRNA gene sequence comparisons showed that strain P24T was related most closely to Thalassobaculum litoreum CL-GR58T (92.7 % similarity); levels of similarity between strain P24T and type strains of recognized species in the family Rhodospirillaceae were all less than 90.8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P24T formed a distinct evolutionary lineage within the family Rhodospirillaceae. Strain P24T could be distinguished from phylogenetically related genera based on differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data presented, strain P24T is considered to represent a novel species of a new genus, for which the name Oceanibaculum indicum gen. nov., sp. nov. is proposed. The type strain is P24T (=CCTCC AB 208226T=LMG 24626T=MCCC 1A02083T).
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Parasutterella excrementihominis gen. nov., sp. nov., a member of the family Alcaligenaceae isolated from human faeces
More LessA novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859T) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859T in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859T was related most closely to the type strains of Sutterella species, with 90.8–88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859T was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859T represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C18 : 1 ω9c (75 % of the total). The main respiratory quinones were menaquinone (MK–6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859T represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859T (=DSM 21040T =JCM 15078T).
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- Eukaryotic Micro-Organisms
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Pseudozyma pruni sp. nov., a novel ustilaginomycetous anamorphic fungus from flowers in Taiwan
More LessTwo ustilaginomycetous anamorphic strains were isolated from flowers in Taiwan. Phylogenetic analysis based on the combined rRNA gene sequence of internal transcribed spacer 1 (ITS1)–5.8S–ITS2 and large-subunit D1/D2 domains indicated that the closest recognized species was Pseudozyma fusiformata. The results of DNA–DNA hybridization and physiological characteristics showed that the two strains represent a novel species within the genus Pseudozyma. The name Pseudozyma pruni sp. nov. is proposed, with FIRDI 005T (=BCRC 34227T =CBS 10937T) as the type strain.
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Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan
More LessA novel yeast species, Lachancea dasiensis sp. nov., is proposed in this paper based on two strains isolated from leaves and one strain from soil in Taiwan. The strains produce one or two spherical ascospores in each ascus, preceded by conjugation of individual cells. Genus assignment and distinction of the species from other recognized species of Lachancea are based on morphological and physiological characteristics and on phylogenetic analysis of nucleotide sequences of the D1/D2 domains of the large subunit (LSU) rRNA gene. Sequence analysis of the D1/D2 domains of the LSU rRNA gene reveals that the phylogenetically closest relatives of L. dasiensis sp. nov. are Lachancea thermotolerans and Lachancea waltii. The novel species could be differentiated from the latter two species based on electrophoretic karyotypes. The type strain of Lachancea dasiensis sp. nov. is SC5L02T (=CBS 10888T =BCRC 23139T), which was isolated from a leaf of Angiopteris lygodiifolia Rosenst. in Dasi, Taoyuan, Taiwan.
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- Methods
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Differentiation of species of the family Acetobacteraceae by AFLP DNA fingerprinting: Gluconacetobacter kombuchae is a later heterotypic synonym of Gluconacetobacter hansenii
More LessAmplified fragment length polymorphism (AFLP) DNA fingerprinting was investigated as a tool for fast and accurate identification of acetic acid bacteria (AAB) to the species level. One hundred and thirty five reference strains and 15 additional strains, representing 50 recognized species of the family Acetobacteraceae, were subjected to AFLP analysis using the restriction enzyme combination ApaI/TaqI and the primer combination A03/T03. The reference strains had been previously subjected to either DNA–DNA hybridization or 16S–23S rRNA spacer region gene sequence analysis and were regarded as being accurately classified at the species level. The present study revealed that six of these strains should be reclassified, namely Gluconacetobacter europaeus LMG 1518 and Gluconacetobacter xylinus LMG 1510 as Gluconacetobacter xylinus and Gluconacetobacter europaeus, respectively; Gluconacetobacter kombuchae LMG 23726T as Gluconacetobacter hansenii; and Acetobacter orleanensis strains LMG 1545, LMG 1592 and LMG 1608 as Acetobacter cerevisiae. Cluster analysis of the AFLP DNA fingerprints of the reference strains revealed one cluster for each species, showing a linkage level below 50 % with other clusters, except for Acetobacter pasteurianus, Acetobacter indonesiensis and Acetobacter cerevisiae. These three species were separated into two, two, and three clusters, respectively. At present, confusion exists regarding the taxonomic status of Gluconacetobacter oboediens and Gluconacetobacter intermedius; the AFLP data from this study supported their classification as separate taxa. The 15 additional strains could all be identified at the species level. AFLP analysis further revealed that some species harboured genetically diverse strains, whereas other species consisted of strains showing similar banding patterns, indicating a more limited genetic diversity. It can be concluded that AFLP DNA fingerprinting is suitable for accurate identification and classification of a broad range of AAB, as well as for the determination of intraspecific genetic diversity.
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- International Committee On Systematics Of Prokaryotes
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Proposed minimal standards for describing new genera and species of the suborder Micrococcineae
The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names.
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- Errata
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