- Volume 59, Issue 7, 2009

Two 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.

An 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).

A 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).

The 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).

A 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).

A 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.

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.

A 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).

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.

During 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.

Two 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.

A 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).

A 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).

A 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.

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).

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).