- Volume 66, Issue 10, 2016
Volume 66, Issue 10, 2016
- Notification List
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- New taxa
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- Actinobacteria
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Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant actinobacterium isolated from the Sahara desert
A black-pigmented, aerobic actinobacterium, tolerant to ionizing radiation, designated BMG 825T, was isolated from desert limestone dust in Tunisia. The strain grew within the temperature range 10–40 °C, at pH 5.5–11.0 and in the presence of 2 % NaCl. The DNA G+C content was 75.7 mol%, and its cell-wall peptidoglycan contained meso-diaminopimelic acid. Sugars of whole-cell hydrolysates were galactose, glucose, and trace amounts of ribose and mannose. The predominant menaquinone was MK-9(H4), and the major fatty acids were iso-C16 : 0 and C16 : 1 ω7c. The polar lipid profile comprised phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine and an unspecified glycolipid. 16S rRNA gene sequence analysis revealed that the strain fell into the genus Geodermatophilus , showing the highest similarity with Geodermatophilus poikilotrophus DSM 44209T (99.1 %). DNA–DNA hybridization results, phylogenetic distinctiveness and phenotypic properties supported the classification of this strain as a representative of a novel species of the genus Geodermatophilus , for which the name Geodermatophilus pulveris sp. nov. is proposed. The type strain is BMG 825T (=CECT 9003T=DSM 46839T).
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Nocardiopsis sediminis sp. nov., isolated from mangrove sediment
A filamentous actinomycete, designated strain 1SS5-02T, was isolated from mangrove sediment collected from Ranong province, Thailand. The strain formed aerial and substrate mycelia composed of long, branched hyphae. Aerial mycelia differentiated into non-motile, rod-shaped spores. The organism contained meso-diaminopimelic acid and no diagnostic sugars in whole-cell hydrolysates. The predominant menaquinones were MK-11(H4), MK-11(H6) and MK-11(H8). Polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. The major fatty acids were iso-C16 : 0, C18 : 1 ω9c, 10-methyl C18 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 73.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1SS5-02T belonged to the genus Nocardiopsis . The strain showed the highest degree of 16S rRNA gene sequence similarity with ‘ Nocardiopsis mangrovei ’ HA11166 (97.9 %) and Nocardiopsis trehalosi VKM Ac-942T (97.8 %). However, strain 1SS5-02T could be distinguished from its nearest phylogenetic relatives in the genus Nocardiopsis on the basis of DNA–DNA relatedness values and the combination of phenotypic properties. On the basis of polyphasic taxonomy, strain 1SS5-02T is considered to represent a novel species of the genus Nocardiopsis , for which the name Nocardiopsis sediminis sp. nov. is proposed. The type strain is 1SS5-02T (=BCC 75410T=NBRC 110934T).
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Nocardioides intraradicalis sp. nov., isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu
A Gram-stain-positive, non-spore-forming and non-motile strain, designated YIM DR1091T, was isolated from the roots of Psammosilene tunicoides W. C. Wu et C. Y. Wu collected from Gejiu, Yunnan, China. The taxonomic position of strain YIM DR1091T was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM DR1091T is a member of the genus Nocardioides . Strain YIM DR1091T was closely related to Nocardioides pyridinolyticus OS4T, Nocardioides caricicola YC6903T, Nocardioides hankookensis DS-30T and Nocardioides aquiterrae GW-9T, with which it shared pairwise 16S rRNA gene sequence similarities of 97.6, 97.5, 97.2 and 97.2 %, respectively. Mean DNA–DNA relatedness values between strain YIM DR1091T and related type strains N. pyridinolyticus JCM 10369T, N. caricicola JCM 17686T, N. hankookensis JCM 15302T and N. aquiterrae JCM 11813T were 44.9±1.7, 50.2±1.3, 46.8±0.9 and 43.0±0.2 %, respectively. The respiratory menaquinone for strain YIM DR1091T was MK-8(H4) while the major fatty acids (>5 %) were iso-C16 : 0, C17 : 1 ω8c, C17 : 0, iso-C15 : 0 and iso-C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. Whole-cell hydrolysates contained mannose, ribose, glucose and galactose, along with ll-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The DNA G+C content was 74.6 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YIM DR1091T represents a novel species of the genus Nocardioides , for which the name Nocardioides intraradicalis sp. nov. is proposed. The type strain is YIM DR1091T (=JCM 30632T=CGMCC4.7251T).
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Streptomyces camponoticapitis sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicus Mayr)
More LessA novel single-spore-producing actinomycete, designated strain 2H-TWYE14T, was isolated from the head of an ant (Camponotus japonicus Mayr) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 2H-TWYE14T belongs to the genus Streptomyces , with highest sequence similarity to Streptomyces niveus NRRL 2466T (98.84 %). Analysis based on the gyrB gene also indicated that strain 2H-TWYE14T should be assigned to the genus Streptomyces . The chemotaxonomic properties of strain 2H-TWYE14T were consistent with those of members of the genus Streptomyces . The cell wall contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. DNA–DNA hybridization experiments and phenotypic tests were carried out between strain 2H-TWYE14T and its phylogenetically closely related strain S. niveus JCM 4251T, which further clarified their relatedness and demonstrated that 2H-TWYE14T could be distinguished from S. niveus. Therefore, it is concluded that strain 2H-TWYE14T can be classified as representing a novel species of the genus Streptomyces , for which the name Streptomyces camponoticapitis sp. nov. is proposed. The type strain is 2H-TWYE14T (=DSM 100523T=CGMCC 4.7275T).
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Amycolatopsis albispora sp. nov., isolated from deep-sea sediment
More LessA novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated strain WP1T, was isolated from a deep-sea sediment sample collected from the Indian Ocean, and examined in a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain WP1T formed a distinct phyletic lineage in the genus Amycolatopsis and was closely related to A. magusensis KT2025T (97.8 % 16S rRNA gene sequence similarity), A. palatopharyngis 1BDZT (97.3 %) and A. marina Ms392AT (97.2 %). The isolate grew at 4–45 °C, pH 5–11 and in the presence of 0–8 % (w/v) NaCl. The cell wall of the novel strain contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars. Major fatty acids identified were iso-C16 : 0, C17 : 1ω8c and C17 : 1ω6c. The predominant menaquinones were MK-9(H4) and MK-7. The polar lipids detected were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylmethylethanolamine, four unknown phospholipids and one unknown glycolipid. The genomic DNA G+C content was 72.2 mol%. Strain WP1T displayed low DNA–DNA reassociation with A. magusensis DSM 45510T (mean value 36.2 %), A. palatopharyngis JCM 12460T (31.5 %) and A. marina JCM 16121T (29.7 %). Based on the data reported here, strain WP1T represents a novel species within the genus Amycolatopsis , for which the name Amycolatopsis albisporasp. nov. is proposed. The type strain is WP1T (=KCTC 39642T=MCCC 1A10745T).
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Streptomyces phyllanthi sp. nov., isolated from the stem of Phyllanthus amarus
The novel endophytic actinomycete strain PA1-07T was isolated from the stem of Phyllanthus amarus. The strain displayed the consistent characteristics of members of the genus Streptomyces . The strain produced short spiral spore chains on aerial mycelia. It grew at pH 5–9, at 40 °C and with a maximum of 5 % (w/v) NaCl. It contained ll-diaminopimelic acid, glucose and ribose in the whole-cell hydrolysate. The major cellular menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8), while the major cellular fatty acids were C16 : 0, iso-C14 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and four unknown lipids. The DNA G+C content of the strain was 71 mol%. The strain showed the highest 16S rRNA gene sequence similarity with Streptomyces curacoi JCM 4219T (98.77 %). The DNA–DNA relatedness values between strain PA1-07T and S. curacoi JCM 4219T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of these phenotypic and genotypic characteristics, the strain could be distinguished from closely related species of the genus Streptomyces and thus represents a novel species of the genus Streptomyces, for which the name Streptomyces phyllanthi sp. nov. is proposed. The type strain is PA1-07T (=JCM 30865T=KCTC 39785T=TISTR 2346T).
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Gordonia hongkongensis sp. nov., isolated from blood culture and peritoneal dialysis effluent of patients in Hong Kong
Two bacterial strains, HKU50T and HKU46, were isolated in Hong Kong from the blood culture and the peritoneal dialysis effluent of two patients. The strains are Gram-stain-positive, acid-fast, non-motile, non-sporulating bacilli. They grow on Columbia agar with 5 % defibrinated sheep blood and brain–heart infusion agar under aerobic conditions with 5 % CO2 at 37 °C as pink-to-orange, non-haemolytic colonies. The strains are catalase-positive and oxidase-negative, and have a unique biochemical profile distinguishable from other closely related species. DNA sequencing revealed that both isolates possessed multiple intra-genomic 16S rRNA gene copies (99.8–100 % sequence identities to Gordonia lacunae NRRL B-24551T and Gordonia terrae NRRL B-16283T). Phylogenetic analysis of the 16S rRNA gene, secA1 and gyrB showed that the two isolates formed a distinct branch within the genus Gordonia and were most closely related to G. lacunae and G. terrae . DNA–DNA hybridization demonstrated ≤53.7 % and ≤49.4 % DNA relatedness between the two isolates and G. lacunae , and between the two isolates and G. terrae , respectively. Hierarchical cluster analysis of MALDI–TOF MS main spectrum profiles showed that strains HKU50T and HKU46 were closely related to each other, but were distinct from G. lacunae , G. terrae , or any other species of the genus Gordonia in the Bruker database. The chemotaxonomic traits of the two strains were highly similar, and the major fatty acids were summed feature 4 (iso-C15 : 0 2-OH/C16 : 1 trans-9), C16 : 0, C18 : 1 cis-9, and tuberculostearic acid. A novel species named Gordonia hongkongensis sp. nov. is proposed to accommodate strains HKU50T and HKU46, with strain HKU50T (=CCOS 955T=CIP 111027T=NBRC 111234T=NCCP 16210T) as the type strain.
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Jatrophihabitans huperziae sp. nov., an endophytic actinobacterium isolated from surface-sterilized tissue of the medicinal plant Huperzia serrata (Thunb.)
More LessA novel endophytic actinobacterium, designated strain CPCC 204076T, was isolated from surface-sterilized tissue of the medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The taxonomic position of the isolate was investigated by a polyphasic approach. The strainwas aerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped. Growth was observed at 10–37 °C, at pH 5.0–10.0 and with 0–3.0 % (w/v) NaCl. The polar lipid fraction consisted of diphosphatidylglycerol, a phospholipid, an aminolipid, a glycolipid, an aminophospholipid and phosphatidylinositol. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the peptidoglycan was of type A4γ. The menaquinone system consisted of MK-9(H4) and MK-8(H4). The major cellular fatty acids (>10 %) were iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content of strain CPCC 204076T was found to be 71.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that CPCC 204076T belongs to the genus Jatrophihabitans with highest sequence similarity to Jatrophihabitans endophyticus DSM 45627T (96.5 %), Jatrophihabitans soli DSM 45908T (96.5 %) and Jatrophihabitans fulvus JCM 30448T (96.1 %), and much lower similarities (<95.0 %) to other available 16S rRNA gene sequences from validly described pure cultures. However, DNA–DNA hybridyzation values between strain CPCC 204076T and the three recognized Jatrophihabitans species were 31±3.1 % ( J. endophyticus DSM 45627T), 33±2.9 % ( J. soli DSM 45908T) and 37±1.7 % ( J. fulvus JCM 30448T), which were all far below the recommended cut-off value of 70 %. The phenotypic and genomic characteristics distinctly indicated that strain CPCC 204076T represents a novel species of the genus Jatrophihabitans , for which the name Jatrophihabitans huperziae sp. nov. is proposed. The type strain is CPCC 204076T (I13A-01604) (=DSM 46866T=NBRC 110718T).
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Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil
More LessActinomycete strain CMU-AB204T was isolated from oil palm rhizosphere soil collected in Chiang Mai University (Chiang Mai, Thailand). Based on morphological and chemotaxonomic characteristics, the organism was considered to belong to the genus Streptomyces . Whole cell-wall hydrolysates consisted of ll-diaminopimelic acid, glucose, ribose and galactose. The predominant menaquinones were MK-9(H4), MK-9(H6), MK-9(H2) and MK-8(H4). The fatty acid profile contained iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as major components. The principal phospholipids detected were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content of strain CMU-AB204T was 70.9 mol%. Based on 16S rRNA gene sequence similarity, strain CMU-AB204T was closely related to Streptomyces orinoci JCM 4546T (98.7 %), Streptomyces lilacinus NBRC 12884T (98.5 %), Streptomyces abikoensis CGMCC 4.1662T (98.5 %), Streptomyces griseocarneus JCM 4905T (98.4 %) and Streptomyces xinghaiensis JCM 16958T (98.3 %). Phylogenetic trees revealed that the new strain had a distinct taxonomic position from closely related type strains of the genus Streptomyces . Spiny to hairy spores clearly differentiated strain CMU-AB204T from the five most closely related Streptomyces species, which produced smooth spores. On the basis of evidence from this polyphasic study, it is proposed that strain CMU-AB204T represents a novel species of the genus Streptomyces , namely Streptomyces palmae sp. nov. The type strain is CMU-AB204T (=JCM 31289T=TBRC 1999T).
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Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper
Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies. One of these subspecies is C. michiganensis subsp. michiganensis , which causes bacterial canker disease in tomato. Bacterial strains showing very similar canker disease symptoms to those of a strain originally classified as C. michiganensis have been isolated from pepper. In this paper, we reclassified strains isolated from pepper. On the basis of phylogenetic analysis with 16S rRNA gene sequences, the strains isolated from pepper were grouped in a separate clade from other subspecies of C. michiganensis . Biochemical, physiological and genetic characteristics of strain PF008T, which is the representative strain of the isolates from pepper, were examined in this study. Based on multi-locus sequence typing and other biochemical and physiological features including colony color, utilization of carbon sources and enzyme activities, strain PF008T was categorically differentiated from eight subspecies of C. michiganensis . Moreover, genome analysis showed that the DNA G+C content of strain PF008T is 73.2 %. These results indicate that PF008T is distinct from other known subspecies of C. michiganensis . Therefore, we propose a novel subspecies, C. michiganensis subsp. capsici , causing bacterial canker disease in pepper, with a type strain of PF008T (=KACC 18448T=LMG 29047T).
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Lipingzhangella halophila gen. nov., sp. nov., a new member of the family Nocardiopsaceae
An alkaliphilic and halophilic actinomycete strain, designated EGI 80537T, was isolated from a saline-alkali soil sample of Xinjiang, north-west China and subjected to a taxonomic characterization using a polyphasic approach. Strain EGI 80537T formed reticulate long aerial hyphae. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the cell-wall diamino acid and mannose as the diagnostic sugar. The major fatty acids identified were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0 (TBSA). The predominant menaquinones detected were MK-10(H8) and MK-10(H6). The G+C content of the genomic DNA of strain EGI 80537T was 67.6 mol%. Strain EGI 80537T showed the highest 16S rRNA gene sequence similarity to Allosalinactinospora lopnorensis CA15-2T (96.7 %). Phylogenetic analysis showed that strain EGI 80537T clustered with the members of the family Nocardiopsaceae . Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain EGI 80537T represents a novel species of a new genus in the family Nocardiopsaceae, for which the name Lipingzhangella halophila gen. nov., sp. nov. is proposed. The type strain of the type species is EGI 80537T(=CGMCC 4.7224T= DSM 102030T).
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Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard)
The taxonomic position of an actinobacterium, designated CPCC 204279T, which was isolated from a rhizosphere soil sample of the herb Limonium sinense collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain CPCC 204279T contained galactose and arabinose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The muramic acid residues in the peptidoglycan were N-acetylated. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16 : 0, iso-C16 : 0 2-OH, C16 : 1ω9c, iso-C16 : 1 and C16 : 0. The genomic DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CPCC 204279T should be placed in the family Pseudonocardiaceae , in which the strain formed a distinct lineage next to the genus Actinophytocola . Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained the Pseudonocardiaceae family-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis and phenotypic characteristics supported the conclusion that strain CPCC 204279T represents a novel species of a new genus in the family Pseudonocardiaceae , for which the name Herbihabitans rhizosphaerae gen. nov., sp. nov. is proposed. Strain CPCC 204279T (=NBRC 111774T=DSM 101727T) is the type strain of the type species.
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Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis
More LessAn endophytic actinobacterial strain, designated py1292T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, China, and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the family Dermacoccaceae and clustered with Yimella lutea (showing the highest similarity of 99.1 %). DNA–DNA relatedness between strain py1292T and Y. lutea YIM 45900T was 45.6±3.2 % (reciprocal 47.8±3.6 %). The novel isolate was found to be a Gram-staining-positive rod, catalase- and oxidase-positive. It grew at pH 6.0–8.0, with 0–9 % NaCl and at 20–45 ºC, optimally at pH 7.0, with 0–3 % NaCl and at 28 ºC. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phospholipids and two unknown polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole-cell hydrolysates contained mannose, ribose, rhamnose, glucose and galactose. The peptidoglycan contained alanine, glycine, serine, aspartic acid, glutamic acid and lysine. The genomic DNA G+C content was determined to be 65.6 mol%. Phylogenetic, phenotypic and chemotaxonomic data (especially the same peptidoglycan type) showed that strain py1292T should be classified as a representative of a novel species of the genus Yimella , for which the name Yimella radicis sp. nov. is proposed. The type strain is py1292T (=KCTC 39612T=LMG 29070T).
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Demequina litorisediminis sp. nov., isolated from a tidal flat, and emended description of the genus Demequina
More LessA Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, GHD-1T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. It grew optimally at 30 °C, at pH 6.5–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain GHD-1T fell within the cluster comprising the type strains of species of the genus Demequina . Strain GHD-1T exhibited 16S rRNA gene sequence similarity values of 97.0–98.8 % to the type strains of Demequina globuliformis , D. salsinemoris , D. flava , D. sediminicola and D. activiva , and of 95.5–96.9 % to the type strains of the other species of the genus Demequina . The peptidoglycan type of strain GHD-1T is A4β based on l-Orn−l-Ser−l-Asp. It contained DMK-9(H4) and DMK-8(H4) as the major menaquinones and anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified glycolipid. The DNA G+C content of strain GHD-1T was 68.7 mol%, and its DNA–DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 13–29 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GHD-1T is separated from other recognized species of the genus Demequina . On the basis of the data presented, strain GHD-1T is considered to represent a novel species of the genus Demequina , for which the name Demequina litorisediminis sp. nov. is proposed. The type strain is GHD-1T (=KCTC 52260T=NBRC 112299T).
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Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves
A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6–11 and 0–8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces , including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces . The determination of G+C ratio (69.5 mol%) and DNA–DNA hybridization values (13.4–31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA–DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).
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Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake
A novel actinobacterial strain, B2-12T, was isolated from soil of a crater lake, Baekrokdam, Hallasan, Jeju, Republic of Korea. Cells of strain B2-12T were Gram-stain-positive, non-motile, non-spore-forming and coccoid to short-rod-shaped. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that strain B2-12T belonged to the genus Nocardioides and shared highest sequence similarity with ‘Nocardioidespaucivorans’ KIS31-44 (98.4 %). The predominant isoprenoid quinone was MK-8(H4). The major fatty acids of strain B2-12T were C16 : 1 (ω7c and/or ω6c), summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), C17 : 0 10-methyl, iso-C16 : 0, C16 : 0 and C17 : 1 ω6c. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. It contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The DNA G+C content was 67.0 mol%. Based on phylogenetic, chemotaxonomic and phenotypic data, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, strain B2-12T represents a novel species in the genus Nocardioides , for which the name Nocardioidesbaekrokdamisolisp. nov. is proposed. The type strain is B2-12T (=KCTC 39748T=NRRL B-65313T=DSM 100725T).
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- Archaea
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Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern
More LessA novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange–red pigmented colonies. Strain 2a_47_2T grew at 20–48 °C (optimum 38–41 °C), pH 6.0–8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB′ amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae , and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).
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- Bacteroidetes
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Porphyromonas loveana sp. nov., isolated from the oral cavity of Australian marsupials
An obligatory anaerobic, Gram-stain-negative coccobacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic and molecular criteria showed that this bacterium was a distinct species within the genus Porphyromonas , and was closely related to Porphyromonas gingivalis and Porphyromonas gulae . This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterization by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight MS showed that this putative novel species could be differentiated phenotypically from P. gingivalis and P. gulae . Definitive identification by 16S rRNA gene sequencing showed that this bacterium belonged to a unique monophyletic lineage, phylogenetically distinct from P. gingivalis (94.9 % similarity) and P. gulae (95.5 %). This also was supported by 16S–23S rRNA intergenic spacer region and glutamate dehydrogenase gene sequencing. A new species epithet, Porphyromonas loveana sp. nov., is proposed for this bacterium, with DSM 28520T (=NCTC 13658T=UQD444T=MRK101T), isolated from a musky rat kangaroo, as the type strain.
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Hymenobacter glacieicola sp. nov., isolated from glacier ice
A Gram-stain-negative, rod-shaped, non-motile and red–pink-pigmented bacterial strain, designated B1909T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. A phylogenetic tree based on 16S rRNA gene sequences showed that strain B1909T formed a lineage within the genus Hymenobacter and was closely related to Hymenobacter xinjiangensis X2-1gT (96.16 % similarity) and Hymenobacter psychrotolerans Tibet-IIU11T (95.99 %). The predominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 4 (iso-C17 : 1 ω6c I/anteiso B), C16 : 1 ω5c, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major menaquinone was MK-7. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59 mol%. On the basis of the phenotypic, phylogenetic and chemotaxonomic data presented, strain B1909T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter glacieicola sp. nov. is proposed; the type strain is B1909T (=JCM 30596T=CGMCC 1.12990T).
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Lewinella aquimaris sp. nov., isolated from seawater
More LessA Gram-staining-negative, oval- or rod-shaped, non-motile bacterial strain, designated HDW-36T, was isolated from seawater off the Korean peninsula. Strain HDW-36T was found to grow optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain HDW-36T falls within the clade comprising thespecies of the genus Lewinella , clustering with the type strains of Lewinella xylanilytica and Lewinella marina , with which it exhibited 95.9 % and 95.2 % sequence similarity values, respectively. The 16S rRNA gene sequence similarity values between strain HDW-36T and type strains of other species of the genus Lewinella were 88.4–92.8 %. Strain HDW-36T was found to contain MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and C16 : 0 as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HDW-36T was determined to be 60.9 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrate that strain HDW-36T is distinguishable from other species of the genus Lewinella . On the basis of the data presented, strain HDW-36T is considered to represent a novel species, for which the name Lewinella aquimaris sp. nov. is proposed. The type strain of Lewinella aquimaris is HDW-36T (=KCTC 42719T=CECT 8901T).
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Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root
A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain, designated 65T, was isolated from surface-sterilized root tissue of maize, collected from Fangshan District of Beijing, People’s Republic of China, and was subjected to a taxonomic study by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 65T belonged to the genus Dyadobacter and had highest 16S rRNA gene sequence similarity to Dyadobacter jiangsuensis CGMCC 1.12969T (99.1 %), Dyadobacter beijingensis CGMCC 1.6375T (98.8 %), Dyadobacter fermentans DSM 18053T (98.6 %) and Dyadobacter soli KCTC 22481T (98.6 %). However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. jiangsuensis CGMCC 1.12969T (18.2±1.3 %), D. beijingensis CGMCC 1.6375T (14.2±2.0 %), D. fermentans DSM 18053T (14.1±2.0 %) and D. soli KCTC 22481T (13.8±0.6 %). The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1 ω5c, iso-C15 : 0 3-OH, C16 : 0 3-OH and C16 : 0. The polar lipid profile of strain 65T revealed the presence of phosphatidylethanolamine, four aminolipids and two unidentified phospholipids. The DNA G+C content was 46.6 mol%. The results of physiological and biochemical tests and the differences in the fatty acid profiles allowed the clear phenotypic differentiation of strain 65T from closely related species of the genus Dyadobacter . Strain 65T thus represents a novel species within the genus Dyadobacter , for which the name Dyadobacter endophyticus sp. nov. is proposed. The type strain is 65T (=CGMCC 1.15288T=DSM 100786T).
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Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas
A Gram-stain-negative bacterium was isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1458T had a sequence similarity to Filimonas lacunae YT21T, Sediminibacterium goheungense HME7863T, Parasegetibacter terrae SGM2-10T, Sediminibacterium ginsengisoli DCY13T, Terrimonas ferruginea DSM 30193T, Lacibacter cauensis NJ-8T, Flavihumibacter solisilvae 3-3T, Parasegetibacter luojieneis RHYL-37T, Vibrionimonas magnilacihabitans MU-2T and Parafilimonas terrae 5GHs7-2T with values of 93.4, 92.3, 91.9, 91.9, 91.8, 91.6, 91.6, 91.6, 91.5 and 90.4 %, respectively. The primary cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1G and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c). The primary polar lipids were phosphatidylethanolamine and an unidentified polar lipid only detectable after total polar lipid staining. The quinone system was menaquinone MK-7, and in the polyamine pattern, sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 15 to 40 °C and pH 5.0 to 8.0, a salt tolerance range of 0 to 2.0 % (w/v), production of orange cell-bound pigment flexirubin, and gliding motility. After phenotypic, chemotaxonomic and molecular analyses, strain 1458T was identified as a novel species of the genus Filimonas, for which the name Filimonas aurantiibacter sp. nov. is proposed. The type strain is 1458T (=NRRL B-65305T=LMG 29039T). An emended description of the genus Filimonas is also provided.
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Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field
More LessStrain TBZ30T was isolated from soil of a heavy-metal-contaminated paddy field. Cells of strain TBZ30T were Gram-staining-negative, rod-shaped, non-motile and non-spore-forming. The isolate was strictly aerobic, pink-pigmented, catalase- and oxidase-positive and produced exopolysaccharides. On the basis of 16S rRNA gene phylogeny, strain TBZ30T belonged to the genus Mucilaginibacter and appeared most closely related to Mucilaginibacter gynuensis YC7003T (95.8 %), Mucilaginibacter litoreus BR-18T (95.4 %) and Mucilaginibacter mallensis MP1X4T (95.4 %). Strain TBZ30T contained menaquinone-7 as the only ubiquinone. The main cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and C16 : 1 ω5c. The polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, four unidentified aminolipids, three unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 49.0 mol%. On the basis of polyphasic taxonomy analyses, strain TBZ30T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter pedocola sp. nov. is proposed. The type strain is TBZ30T (=KCTC 42833T=CCTCC AB 2015301T).
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Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field
More LessA ginsenoside-transforming bacterium, designated Gsoil 1550T, was isolated from soil of a ginseng field and subjected to a polyphasic taxonomic analysis. Colonies of strain Gsoil 1550T were yellow, of low convexity and with regular margin. Cells were long rods, 0.5–1.2 µm wide and 1.6–3 µm long. The isolate grew at 10–37 °C and at pH 5–9 on R2A agar medium; maximum growth occurred at 30 °C and pH 6–7. Phylogenetic study based on the 16S rRNA gene sequence positioned Gsoil 1550T in a distinct lineage in the family Chitinophagaceae , sharing 92.5–92.8 % sequence similarity with members of the closely related genera Terrimonas , Parafilimonas , Sediminibacterium and Parasegetibacter . Strain Gsoil 1550T contained menaquinone MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and iso-C15 : 1 G as major fatty acids. The DNA G+C content was 44.6 mol%. Strain Gsoil 1550T could be distinguished from other members of the family Chitinophagaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipid of strain Gsoil 1550T was phosphatidylethanolamine. Based on this polyphasic taxonomic analysis, strain Gsoil 1150T represents a novel species within a new genus, for which the name Panacibacter ginsenosidivorans gen. nov., sp. nov. is proposed. The type strain of Panacibacter ginsenosidivorans is Gsoil 1550T (=KCTC 12658T=JCM 31452T).
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Chryseobacterium montanum sp. nov. isolated from mountain soil
More LessA Gram-staining-negative, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated WG4T, was isolated from soil of the Tianmen Mountain located in Hunan province, PR China. 16S rRNA gene sequence analysis showed that the strain belongs to the genus Chryseobacterium in the family Flavobacteriaceae , with 97.4 % and 97.1 % sequence identities to Chryseobacterium anthropi NF 1366T and Chryseobacterium haifense H38T, respectively. In comparison with the other strains representing the genus Chryseobacterium , the 16S rRNA gene sequence identities were less than 97.0 %. The DNA–DNA relatedness values were 63.3 % (±1) between C. anthropi NF 1366T and strain WG4T and 62.7 % (±2) between C. haifense DSM 19056T and strain WG4T. The DNA G+C content of strain WG4T was 37.7 mol%. The predominant fatty acids of strain WG4T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified lipids and two unidentified aminolipids. The major menaquinone of strain WG4T was menaquinone 6. Strain WG4T showed some unique physiological and biochemical characteristics, such as being negative for gelatin hydrolysis, and valine arylamidase and α-glucosidase activity, and positive for acid production from cellobiose. Based on the differentiating phylogenetic inference and biochemical data, strain WG4T represents a novel species, for which the name Chryseobacterium montanum sp. nov. is proposed, with the type strain WG4T (=KCTC 52204T=CCTCC AB 2016058T).
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Proposal of Mucilaginibacter phyllosphaerae sp. nov. isolated from the phyllosphere of Galium album
A pink-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterial strain, PP-F2F-G21T, was isolated from the phyllosphere of Galium album. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence of strain PP-F2F-G21T showed the closest relationship to type strains of the species Mucilaginibacter lutimaris (97.7 %), Mucilaginibacter soli (97.3 %) and Mucilaginibacter rigui (97.1 %). Sequence similarities to all other type strains were below 97 %. The predominant cellular fatty acids of strain PP-F2F-G21T are C16 : 1 ω7c/iso-C15 : 0 2-OH (measured as summed feature 3 fatty acids) and iso-C15 : 0 followed by iso-C17 : 0 3-OH, C16 : 1 ω5c and C16 : 0. The major compound in the polyamine pattern was sym-homospermidine and the diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was exclusively composed of menaquinone MK-7. The polar lipid profile contained the major lipid phosphatidylethanolamine and in addition 18 unidentified lipids. Based on phylogenetic, chemotaxonomic and phenotypic analyses, we propose a novel species of the genus Mucilaginibacter named Mucilaginibacter phyllosphaerae sp. nov. The type strain is PP-F2F-G21T (=CCM 8625T=CIP 110921T=LMG 29118T).
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Pseudoflavitalea rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere of tomato, and proposal to reclassify Flavitalea soli as Pseudoflavitalea soli comb. nov.
A bacterial strain, designated T16R-265T, was isolated from rhizosphere of tomato in Buyeo-gun, Chungcheongnam-do, South Korea. The strain was Gram-stain-negative, aerobic, non-flagellated and rod- or long-rod-shaped. It grew at the range of 10–40 °C (optimum 28–30 °C), pH 6.0–9.0 (optimum pH 7.0) and with 0–3 % (w/v) NaCl (optimum 0 %). 16S rRNA gene sequence analysis showed that strain T16R-265T had the highest sequence similarity (98.0 %) with Flavitalea soli KIS20-3T and low sequence similarities of below 95 % with all other taxa. The phylogenetic tree revealed that the strain formed a robust monophyletic line with Flavitalea soli KIS20-3T separable from other clades. The predominant quinone of strain T16R-265T was MK-7, the polar lipids consisted of large amounts of phosphatidylethanolamine and an unknown lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. DNA–DNA hybridization values with Flavitalea soli KACC 17319T were below 70 %. The DNA G+C content of strain T16R-265T is 46.2 mol%. Based on phylogenetic evidence and the results of phenotypic, genotypic and chemotaxonomic analyses, strain T16R-265T represents a novel species of a new genus, for which the name Pseudoflavitalea rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of the type species is T16R-265T (=KACC 18655T=NBRC 111880T). We also propose the reclassification of Flavitalea soli as Pseudoflavitalea soli comb. nov. (type strain KIS20-3T=KACC 17319T=JCM 19937T).
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Pontibacter litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-flagellated, motile by gliding and ovoid or rod-shaped bacterial strain, designated YKTF-7T, was isolated from a tidal flat sediment on the Yellow Sea, South Korea. Strain YKTF-7T grew optimally at pH 7.0–8.0, at 30–37 °C and in the presence of 0.5–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YKTF-7T fell within the clade comprising the type strains of species of the genus Pontibacter , clustering with the type strains of Pontibacter odishensis and Pontibacter korlensis with which it exhibited 98.0–98.7 % sequence similarity. Strain YKTF-7T exhibited 16S rRNA gene sequence similarities of 94.7–96.8 % to the type strains of the other species of the genus Pontibacter and of less than 91.7 % to those of other recognized species. Strain YKTF-7T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C15 : 0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain YKTF-7T was 54.0 mol%, and its mean DNA–DNA relatedness values with the type strains of P . odishensis and P . korlensis were 25 and 14 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain YKTF-7T is separated from recognized species of the genus Pontibacter . On the basis of the data presented, strain YKTF-7T is considered to represent a novel species of the genus Pontibacter , for which the name Pontibacter litorisediminis sp. nov. is proposed. The type strain is YKTF-7T(=KCTC 52252T=NBRC 112298T).
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Maribacter litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, HPTF-2T, was isolated from a tidal flat in the Yellow Sea in South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain HPTF-2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain HPTF-2T fell within the clade comprising the type strains of species of the genus Maribacter . Strain HPTF-2T exhibited 16S rRNA gene sequence similarity values of 97.1–98.0 % to the type strains of Maribacter stanieri , M. orientalis, M. arcticus, M. dokdonensis , M. confluentis, M. aquivivus, M. sedimenticola and M. caenipelagi , and of 95.1–96.7 % to the type strains of the other species of the genus Maribacter . Strain HPTF-2T contained MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 G as the major fatty acids. The major polar lipids of strain HPTF-2T were phosphatidylethanolamine and two unidentified lipids. Mean DNA–DNA relatedness values of strain HPTF-2T with the type strains of the nine phylogenetically related species of the genus Maribacter were 10–26 %. The DNA G+C content of strain HPTF-2T was 38.4 mol%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain HPTF-2T is separated from other species of the genus Maribacter . On the basis of the data presented, strain HPTF-2T represents a novel species of the genus Maribacter , for which the name Maribacter litorisediminis sp. nov. is proposed. The type strain is HPTF-2T (=KCTC 52251T=NBRC 112297T).
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Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales
More LessA Gram-stain-negative, facultatively anaerobic, moderately halophilic, filamentous, non-motile bacterium, designated FA102T, was isolated from marine sediment from the coast of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FA102T formed a distinct evolutionary lineage within the family Marinifilaceae and its closest relative was Marinifilum fragile JCM 15579T (93.2 % sequence similarity). The DNA G+C content of the novel strain was 36.5 mol%. The predominant cellular fatty acids and respiratory quinone were iso-C15 : 0 and iso-C15 : 0 3-OH, and MK-7, respectively. On the basis of the phylogenetic, phenotypic and physiological data, strain FA102T represents a novel genus and species, for which the name Ancylomarina subtilis gen. nov., sp. nov. is proposed. The type strain of Ancylomarina subtilis is FA102T (=KCTC 42257T=DSM 28825T=CICC 10902T). Furthermore, a new order named Marinilabiliales is proposed to accommodate three families previously classified in the order Bacteroidales . Marinilabiliales ord. nov. encompasses the families Marinilabiliaceae , Prolixibacteraceae and Marinifilaceae.
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Flavobacterium terriphilum sp. nov., isolated from soil
A novel aerobic, yellow-pigmented, Gram-stain-negative, rod-shaped bacterial strain, CUG00004T, was isolated from a soil sample. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CUG00004T was a member of the genus Flavobacterium and showed high sequence similarity with Flavobacterium soli DSM 19725T (96.9 %) and Flavobacterium glaciei CGMCC 0499T (95.6 %). The level of DNA–DNA relatedness between strain CUG00004T and F . soli DSM 19725T and F . glaciei CGMCC 1.5380T was 42.5 and 43.4 %, respectively. Strain CUG00004T was moderately alkaliphilic and grew optimally at pH 8.0, at 28 °C and in the presence of 0–1 % (w/v) NaCl. This organism contained menaquinone-6 (MK-6) as the only isoprenoid quinone and iso-C15 : 0, iso-C17 : 0 3-OH, anteiso-C15 : 0 and summed feature 9 (comprising iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) as the major fatty acids. The DNA G+C content of strain CUG00004T was 36.3 mol%. On the basis of phylogenetic, physiological and chemotaxonomic analyses, strain CUG00004T represents a novel species, for which the name Flavobacterium terriphilum sp. nov. is proposed. The type strain is CUG00004T (=CCTCC AB 2014151T=KCTC 42876T).
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- Firmicutes and related organisms
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Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver
Two Gram-stain-positive strains, VE80T and VE116, which were resistant to vancomycin, were isolated from retail chicken meat and liver in Ho Chi Minh, Vietnam, respectively. These strains were characterized by sequence analyses of 16S rRNA, RNA polymerase α-subunit (rpoA), ATP synthase α-subunit (atpA), and phenylalanyl-tRNA synthase α-subunit (pheS) genes, determination of DNA G+C content, cellular fatty acid methyl ester analysis, DNA–DNA hybridization, and conventional morphological and biochemical tests. Strains VE80T and VE116 had 99.6 % 16S rRNA gene sequence similarity with Enterococcus canintestini LMG 13590T, and 99.1 % 16S rRNA gene sequence similarity with Enterococcus dispar ATCC 51266T. However, the two isolates could be clearly differentiated from these reference strains by the low sequence similarities (86.1–86.8 %) of the atpA gene, low DNA–DNA relatedness (<22.8 %), and differences in the production of acid from melezitose and methyl α-d-glucoside. Based on the results obtained in the present study, these two isolates are considered to represent a novel species of the genus Enterococcus , for which the name Enterococcus saigonensis sp. nov., is proposed. The type strain is VE80T (=JCM 31193T=CCUG 68827T).
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Lactococcus garvieae subsp. bovis subsp. nov., lactic acid bacteria isolated from wild gaur (Bos gaurus) dung, and description of Lactococcus garvieae subsp. garvieae subsp. nov.
More LessA taxonomic investigation was performed on a Gram-stain-positive coccus, designated strain BSN307T, isolated from gaur (Indian bison, Bos gaurus) dung based on phenotypic and molecular approaches. Based on the biochemical tests, cellular morphology and 16S rRNA gene sequence similarity, this strain was found to be a member of the genus Lactococcus and closely related to Lactococcus garvieae ATCC 49156T (99.6 % 16S rRNA gene sequence similarity) and L.actococcus formosensis 516T (99.0 %). However, DNA–DNA hybridization studies showed that the level of relatedness between strain BSN307T and L. garvieae ATCC 49156T was 75.8 %, suggesting that it represented a novel subspecies of L. garvieae . The inability to grow in brain heart infusion (BHI) medium at pH 9.6, in tryptic soy agar (TSA) with 4 % (w/v) NaCl and at 42 °C (MRS agar) clearly differentiated BSN307T from L. garvieae ATCC 49156T. Rep-PCR fingerprint patterns, substantial differences in summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C19 : 0 cyclo ω8c and C16 : 0 also differentiated strain BSN307T from the reference strain of L. garvieae. Moreover, analysis of the housekeeping genes pheS and rpoA revealed sequence similarities that were at the limit for species differentiation (92.2 and 97.8 %, respectively). Combined genotypic and phenotypic data indicate that strain BSN307T represents a subspecies of L. garvieae for which the name Lactococcus garvieae subsp. bovis subsp. nov. is proposed. The type strain is BSN307T (=DSM 100577 T=MCC 2824T=KCTC 21083T).
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Salinicoccus amylolyticus sp. nov., isolated from a saltern
More LessA Gram-stain-positive coccus, strain JC304T, was isolated from a saltern of Nari along the Bhavnagar Coast, Gujarat, India. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC304T represented a member of the genus Salinicoccus and was most closely related to Salinicoccus roseus 9T (99.6 %), Salinicoccus luteus YIM 70202T (97.0 %), Salinicoccus hispanicus J-82T (97.0 %) and the remaining species of the genus Salinicoccus (<97 %). Genome relatedness based on DNA–DNA hybridization of JC304T with the type strains of the most closely related species was less than 46 % and the ΔTm was >5 °C indicating that the strain represents a novel species of the genus Salinicoccus . Independent and concatenated phylogenetic analysis of recA/fusA gene translated product showed a clear distinction of JC304T from its phylogenetic neighbors. Diphosphotidylglycerol, phosphatidylglycerol, an unidentified glycolipid and three unidentified lipids (L1, L2 and L3) were the polar lipids of JC304T. Iso-C15 : 0 and anteiso-C15 : 0 were the major (>10 %) fatty acids in strain JC304T. The cell-wall amino acids were l-lysine and d-glycine. Hopanoids were not detected. The major isoprenoid quinone was menaquinone (MK-6). The DNA G+C content of JC304T was 48 mol%. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC304T is considered to represent a novel species of the genus Salinicoccus , for which the name Salinicoccus amylolyticus sp. nov. is proposed. The type strain is JC304T (=KCTC 33661T=LMG 28757T).
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Anaerosporomusa subterranea gen. nov., sp. nov., a spore-forming anaerobe belonging to the class Negativicutes isolated from saprolite
More LessA Gram-stain-negative, spore-forming, anaerobic bacterium designated strain RU4T was isolated from a saprolite core collected from Oak Ridge, Tennessee, USA. Cells were slightly curved rods and exhibited an outer membrane exterior to a thin cell wall. Strain RU4T formed heat-resistant endospores in late-log phase and stationary phase cultures. Under anaerobic conditions, strain RU4T grew by fermenting fumarate and maleate, but did not grow on glucose, glycerol, pyruvate, lactate, succinate, citrate, formate, acetate, propionate, butyrate or valerate. Strain RU4T did not reduce sulfate or ferric iron. The main cellular fatty acids were C17 : 0 cyclo, C16 : 0 and C15 : 0. The DNA G+C content was 52 mol%. Analysis of the 16S rRNA, rpoB, recA, infB, gyrB and atpD gene sequences indicated that the isolate is related to members of the family Sporomusaceae . Based on 92 % sequence similarity of the 16S rRNA gene to its closest relatives in the family Sporomusaceae and divergent physiological traits, the newly-cultivated isolate was assigned to a novel species of a new genus, Anaerosporomusa subterranea gen. nov., sp. nov. The type strain of Anaerosporomusa subterranea is RU4T (=DSM 29728T=ATCC BAA-2723T).
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Paenibacillus silagei sp. nov. isolated from corn silage
More LessA Gram-stain-negative, rod-shaped, endospore-forming bacterium, strain LOOC204T, was isolated from corn silage that had been prepared and stored in Hokkaido, Japan. The isolate grew well at 4–37 °C and at pH 6.0–8.5. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C16 : 0. The major menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, one unidentified phospholipid, two unidentified aminolipids and three unidentified lipids were detected as the cellular polar lipids. The genomic DNA G+C content of LOOC204T was 52.2±0.7 mol%. A comparative 16S rRNA gene sequence analysis showed that LOOC204T represented a member of the genus Paenibacillus , and high levels of sequence similarity of LOOC204T with Paenibacillus borealis KK19T (97.5 %) and Paenibacillus jilunlii Be17T (97.4 %) were found. Based on sequence analysis of the RNA polymerase β subunit (rpoB) gene, LOOC204T was clearly separated from its phylogenetic neighbors in the genus Paenibacillus . DNA–DNA hybridisation experiments showed that LOOC204T displayed less than 40 % reassociation values toward its nearest phylogenetic neighbours of the genus Paenibacillus , indicating the unique taxonomic status of LOOC204T. Based on these data, we conclude that strain LOOC204T represents a novel species of the genus Paenibacillus , named Paenibacillus silagei sp. nov. The type strain is LOOC204T (=JCM 30974T=DSM 101953T).
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Streptococcus dentiloxodontae sp. nov., isolated from the oral cavity of elephants
More LessA Gram-stain-positive, catalase-negative, coccus-shaped organism was isolated from oral cavity samples collected from healthy elephants. The isolated strain, NUM 2404T, was tentatively identified as a streptococcal species based on the results of biochemical tests. Although a comparative 16S rRNA gene sequence analysis suggested the classification of this organism into the genus Streptococcus , it did not correspond to any recognized species of the genus. Strain NUM 2404T was related most closely to Streptococcus saliviloxodontae NUM 6306T with 95.8 % 16S rRNA gene sequence similarity, but the phylogenetic tree reconstructed based on the 16S rRNA gene sequence showed that NUM 2404T clustered with Streptococcus mutans NCTC 10449T and Streptococcus troglodytae TKU 31T. Comparative sequence analysis based on two housekeeping genes, groEL, which encodes the 60 kDa heat-shock protein, and rpoB, encoding the β subunit of RNA polymerase, of NUM 2404T indicated that it was most closely related to those of Streptococcus orisratti A63T and Streptococcus sobrinus ATCC 33478T with 82.7 and 85.1 % sequence similarities, respectively. On the basis of genotypic and phenotypic differences, it is proposed that the novel isolate be classified in the genus Streptococcus as representative of a novel species, Streptococcus dentiloxodontae sp. nov. The type strain is NUM 2404T (=JCM 19284T=DSM 27381T).
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Pontibacillus salipaludis sp. nov., a slightly halophilic bacterium isolated from a salt pan
Two novel Gram-stain-positive, facultatively anerobic, rod-shaped, motile, endospore-forming bacterial strains, 9DMT and 6DM, were isolated from Tuticorn, India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA–DNA relatedness (88±2 %) indicated that strains 9DMT and 6DM were members of a single species. Based on 16S rRNA gene sequence analysis these strains were identified as belonging to the genus Pontibacillus and were related most closely to the type strains of Pontibacillus chungwhensis (99.7 % sequence similarity) and Pontibacillus marinus (97.9 %). The DNA G+C content of strains 9DMT and 6DM was 41.6 and 41.4 mol%, respectively. However, the level of DNA–DNA relatedness of these strains with P. chungwhensis KCTC 3890T and P. marinus KCTC 3917T was only 40.9 + 0.8 and 39.8 + 0.9 %, respectively. Strains 9DMT and 6DM were facultative anaerobes with optimal growth at 37 °C, at pH 7.0–8.0 and with 2–3 % (w/v) NaCl. The cell-wall peptidoglycan of strain 9DMT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The isoprenoid quinone was MK-7. Major fatty acids of strain 9DMT were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strains 9DMT and 6DM, which are considered to represent a novel member of the genus Pontibacillus , for which the name Pontibacillus salipaludis sp. nov. is proposed. The type strain is 9DMT (= KCTC 33742T=LMG 29102T= CGMCC 1.15353T).
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Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses
Species of the genus Trichococcus share high similarity of their 16S rRNA gene sequences (>99 %). Digital DNA–DNA hybridization values (dDDH) among type strains of all described species of the genus Trichococcus ( T. flocculiformis DSM 2094T , T. pasteurii DSM 2381T , T. collinsii DSM 14526T , T. palustris DSM 9172T, and T. patagoniensis DSM 18806T) indicated that Trichococcus sp. strain R210T represents a novel species of the genus Trichococcus . The dDDH values showed a low DNA relatedness between strain R210T and all other species of the genus Trichococcus (23–32%). Cells of strain R210T were motile, slightly curved rods, 0.63–1.40×0.48–0.90 µm and stained Gram-positive. Growth was optimal at pH 7.8 and at temperature of 30 °C. Strain R210T could utilize several carbohydrates, and the main products from glucose fermentation were lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain R210T was 47.9 mol%. Based on morphological, physiological and biochemical characteristics along with measured dDDH values for all species of the genus Trichococcus , it is suggested that strain R210T represents a novel species within the genus Trichococcus , for which the name Trichococcus ilyis sp. nov. is proposed. The type strain is R210T (=DSM 22150T=JCM 31247T).
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Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater
A Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9T were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9T grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI) when H2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S0). The G+C content of the DNA from strain Z9T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus , T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9T represents a novel species within the genus Tepidibacillus , for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9T (=ATCC BAA-2644T=DSM 103037T).
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Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum
More LessMore than 100 isolates of a Gram-stain-negative, curved rod-shaped, so far uncultured bacterium were isolated from chicken caecal content. The strains were obligate anaerobes which formed endospores. They were catalase-positive, cytochrome-oxidase-negative and did not hydrolyse aesculin. The detected predominant metabolic end product in reinforced clostridial bedium broth was acetate. The DNA G+C content was 62.2 mol%. The cell fatty acid composition was dominated by C15 : 0 iso, C15 : 0 anteiso, C16 : 0, C13 : 0 iso, C14 : 0 iso and C16 : 0 DMA. Analysis of the 16S rRNA gene sequences of the novel isolates showed 99 % similarity to each other. Phylogenetically they are placed in Clostridium cluster IV. They exhibited 99 % 16S rRNA gene sequence similarity to uncultured bacterial clone SJTU_C_03_83 (GenBank accession no. EF404038.1) and to three other so far uncultured strains. The closest related type strains, Hydrogenoanaerobacterium saccharovorans SW51T and Anaerotruncus colihominis WAL 14565T, exhibited a 16S rRNA gene sequence divergence of at least 8 % to the newly described isolates. In addition, morphological and biochemical characteristics allowed differentiation of the novel isolates from these and other related and validly published species, including Clostridium methylpentosum and Acetanaerobacterium elongatum . Therefore, a new genus, Harryflintia gen. nov., is proposed for the isolated hitherto unknown strains with V20-281aT (=DSM 100433T =CECT 8892T) as the type strain of its type species, Harryflintia acetispora gen. nov., sp. nov.
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Reclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces
More LessA Gram-positive-staining, coccoid-shaped, non-motile, asporogenous, obligately anaerobic and butyrate-producing bacterium was recovered from a healthy human’s faeces. The organism was isolated by the enrichment culture technique using yeast extract-casein hydrolysate-fatty acids broth supplemented with 0.5 % mucin. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that the novel strain should be classified as a member of the Eubacterium desmolans -related cluster in the family Ruminococcaceae . Furthermore, this analysis demonstrated that the type strains of Butyricicoccus pullicaecorum (95.6 %) and Eubacterium desmolans (94.7 %) were the closest phylogenetic neighbours to strain YIT 12789T. However, DNA‒DNA reassociation values with these closest strains were less than 20 %. On the basis of the phenotypic, genotypic and chemotaxonomic features, the novel coccoid-shaped bacterium should be designated as a representative of a novel species of the genus Butyricicoccus , for which the name Butyricicoccus faecihominis sp. nov. is proposed. The type strain is YIT 12789T (=JCM 31056T=DSM 100989T). It is also proposed that Eubacterium desmolans be reclassified in the genus Butyricicoccus as Butyricicoccus desmolans comb. nov.
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Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor
More LessPhylogenetic studies were performed on a group of novel Gram-stain-positive, anaerobic, non-sporulating rod-shaped bacteria isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene sequence comparison indicated that the isolates SD1DT, SD1G, SD1I and RK1P share 100 % sequence identity, and are most closely related to Herbinix hemicellulosilytica T3/55T with which they share a 16S rRNA gene sequence similarity of 96.4 %. As a representative of the whole group of isolates, strain SD1DT was further characterized. Strain SD1DT was catalase-negative, indole-negative, and produced acetate, ethanol, butyric acid and hydrogen as major end-products during fermentative cellobiose utilization. Cells are rod-shaped, growing optimally at 40–65 °C and pH 6.5–8.5. The major cellular fatty acids (>10 %) were C19 : 0 cyc 9,10 dimethyl acetal, C16 : 0 and C14 : 0. The DNA G+C content was 35.1 mol%. Due to the genetic and phenotypic differences to the most closely affiliated species, the isolates represent a novel species of the genus Herbinix within the family Lachnospiraceae , for which the name Herbinix luporum sp. nov. is proposed. The type strain is SD1DT(=DSM 100831T=CECT 8959T).
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Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China
Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus . They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis . In silico DNA–DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA–DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus ), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus , Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.
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Oceanobacillus longus sp. nov., a moderately halophilic bacterium isolated from a salt lake
A Gram-stain-positive, endospore-forming, long rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain T9BT, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain T9BT were motile and produced colonies with a brown pigment. Growth occurred between 1.0 and 20 % (w/v) NaCl and the isolate grew optimally at 5.0 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, while it was able to grow over pH and temperature ranges of pH 6.0–9.0 and 25–45 °C. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain T9BT is a member of the genus Oceanobacillus . The closest relative to this strain was Oceanobacillus rekensis PT-11T with a similarity of 97.4 %, followed by Oceanobacillus profundus CL-MP28T and Oceanobacillus polygoni SA9T with 97.3 and 97.1 % similarity, respectively. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The polar lipids of strain T9BT consisted of phosphatidylglycerol, diphosphatidylglycerol, three phospholipids and one aminoglycolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 42.9 mol%. Phylogenetic analysis, DNA–DNA hybridization data and phenotypic characteristics allowed strain T9BT to be differentiated from other members of the genus Oceanobacillus . A novel species, Oceanobacillus longus sp. nov., is therefore proposed to accommodate this strain. The type strain is T9BT (=IBRC-M 10703T=LMG 29250T).
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- Other bacteria
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Thermodesulfatator autotrophicus sp. nov., a thermophilic sulfate-reducing bacterium from the Indian Ocean
More LessA novel sulfate-reducing bacterium, strain S606T, was isolated from a sulfide sample collected at a depth of 2764 m from a deep-sea vent chimney wall in the Indian Ocean. Phylogenetic 16S rRNA gene sequence analyses placed strain S606T within the genus Thermodesulfatator , with highest sequence similarity of 98.2 % to Thermodesulfatator indicus DSM 15286T, followed by Thermodesulfatator atlanticus AT1325T (97.4 %). The average nucleotide identity (ANI) values between S606T and the two other type strains (T. indicus DSM 15286T and T. atlanticus AT1325T) were 79.2 % and 71.5 %, respectively. The digital DNA–DNA hybridization estimate values between S606T and these two type strains were 22.7±2.4 % and 18.1±2.3 %, respectively. Cells were Gram-stain-negative, anaerobic, motile rods (1–1.8×0.5–0.7 µm). The novel isolate grew at NaCl concentrations ranging from 1.5 to 4.5 % (optimum 2.5–3 %), from pH 5.5 to 8 (optimum 6.5–7.0) and at temperatures between 50 and 80 °C (optimum 65–70 °C). S606T grew chemolithoautotrophically in an H2/CO2 atmosphere (80 : 20, v/v; 200 kPa), used sulfate as a terminal electron acceptor, but not sulfur, sulfite nor thiosulfate. The predominant fatty acids were C16 : 0 (24.2 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c, 26.3 %), C18 : 0 (22.2 %) and C18 : 1ω9c (9.2 %). The DNA G+C content of the chromosomal DNA was 43.1 mol%. The combined genotypic, chemotaxonomic and phenotypic traits show that S606T should be described as representing a novel species of the genus Thermodesulfatator , for which the name Thermodesulfatator autotrophicus sp. nov. is proposed. The type strain is S606T (=DSM 101864T=MCCC 1A01871T).
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- Proteobacteria
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Sulfitobacter faviae sp. nov., isolated from the coral Favia veroni
More LessThree closely related, non-sporulating, aerobic, Gram-stain-negative, motile, rod-shaped isolates (S5-53T, S6-62 and S6-64) were obtained from mucus of corals Favia veroni from the Andaman Sea, India. Colonies grown on marine agar were small, circular and cream-coloured. Heterotrophic growth was observed at 10–40 °C and pH 6–10; optimum growth occurred at 25–30 °C and pH 7–8. 16S rRNA gene sequence analysis confirmed the isolates belonged to the genus Sulfitobacter and the three isolates shared more than 99 % pairwise sequence similarity. Strain S5-53T shared highest 16S rRNA gene sequence similarity of 98.43 % with Sulfitobacter dubius KMM 3554T. DNA–DNA relatedness among the three isolates was above 70 % whereas strain S5-53T showed less than 70 % relatedness with the type strains of closely related species. The DNA G+C content of strain S5-53T was 61 mol%. It contained phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Predominant fatty acids included C18 : 1 ω7c, C18 : 1 ω7c 11-methyl, C16 : 0 and C10 : 0 3-OH. Q10 was the major respiratory quinone. Based on this polyphasic analysis, the new isolates (S5-53T, S6-62 and S6-64) are considered to represent a novel species of the genus Sulfitobacter , for which the name Sulfitobacter faviae sp. nov. is proposed. The type strain is S5-53T(=JCM 31093T=LMG 29156T).
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Roseomonas rubra sp. nov., isolated from lagoon sediments
More LessA novel Gram-stain-negative, coccus to oval-shaped, non-motile bacterium, designated strain S5T, was isolated from lagoon sediments collected from North Carolina, USA. Strain S5T was able to grow at 12–45 °C (optima, 30–37 °C) and at pH 6.3–9.0 (optima, 6.5–7.5). No added NaCl was required for growth of strain S5T. Strain S5T was positive for catalase and oxidase activity. C18 : 1 ω6c/C18 : 1 ω7c, C16 : 1 ω6c/C16 : 1 ω7c and C16 : 0 were predominant fatty acids with minor amounts of C8 : 0 3-OH, C14 : 0, C16 : 0 3-OH, C18 : 1 2-OH, C14 : 1 ω5c, C16 : 1 ω5c and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were major polar lipids. Minor amounts of an unidentified amino lipid and three unidentified lipids were also detected. The G+C content of the genomic DNA was 73.5 mol%. 16S rRNA gene sequence comparisons indicated that strain S5T represents a member of the genus Roseomonas within the family Acetobacteraceae of the class Alphaproteobacteria . Strain S5T had a sequence similarity of 97.80 % with Roseomonas rhizosphaerae YW11T, 97.69 % with Roseomonas aestuarii JC17T and <97 % with other members of the genus Roseomonas . However, strain S5T showed only 45.2±2 and 17±2 % relatedness (based on DNA–DNA hybridization) with R . rhizosphaerae KACC 17225T (=YW11T) and R . aestuarii KCTC 22692T (=JC17T), respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain S5T as a representative of a novel species in the genus Roseomonas , for which the name Roseomonas rubra sp. nov. is proposed. The type strain is S5T (=KEMB 563-468T=JCM 31177T).
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Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment
More LessA Gram-stain-negative, moderately halophilic bacterium, designated strain CPS11T, was isolated from the sediment of a solar pond located in Shinan, Korea. Strain CPS11T was a strictly aerobic, motile, straight rod-shaped bacterium that grew at pH 5.0–9.0 (optimum, pH 7.0–8.0), at 10–37 °C (optimum, 28 °C) and at salinities of 1–20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CPS11T belonged to the genus Halomonas , with sequence similarity of 98.5–94.3 % to existing type strains, showing highest sequence similarity to Halomonas fontilapidosi 5CRT (98.5 %), Halomonas ventosae Al12T (98.5 %), Halomonas campaniensis 5AGT (98.2 %), Halomonas huangheensis BJGMM-B45T (98.0 %), Halomonas alimentaria YKJ-16T (98.0 %), Halomonas mongoliensis Z-7009T (97.8 %), Halomonas shengliensis SL014B-85T (97.5 %) and Halomonas cupida DSM 4740T (97.5 %). The predominant ubiquinone was Q-9. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C17 : 0 cyclo, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, an unknown phospholipid and unknown lipids. The DNA G+C content of this novel isolate was 64.3 mol%. Levels of DNA–DNA relatedness between strain CPS11T and the type strains of ten other species of the genus ranged from 50 to 21 %. On the basis of the polyphasic analysis conducted in this study, strain CPS11T represents a novel species of the genus Halomonas , for which the name Halomonas sediminicola sp. nov. is proposed. The type strain is CPS11T(=KACC 18262T=NBRC 110636T).
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Volumes and issues
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Volume 74 (2024)
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