- Volume 72, Issue 5, 2022
Volume 72, Issue 5, 2022
- Validation List
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- Notification List
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- New Taxa
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Genome analysis of Pseudomonas species reveals that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980)
More LessWe described the comparative genomic analysis of Pseudomonas panacis DSM 18529T and Pseudomonas marginalis DSM 13124T of the genus Pseudomonas to define the taxonomic assignment. When conducting this analysis, genomic information for 203 type strains was available in the NCBI genome database. The ANI, AAI and isDDH data were higher than the threshold values between Pseudomonas panacis DSM 18529T and Pseudomonas marginalis DSM 13124T. Whole-genome comparisons show 97 % average nucleotide identity, 98 % average amino acid identity and 75 % in silico DNA–DNA hybridization values. Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980) have priority over the name Pseudomonas panacis Park et al. 2005, therefore nomenclatural authorities propose that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980). The type strain is ATCC 10844T (=DSM 13124T=NCPPB 667T).
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- Actinobacteria
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Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea
More LessA Gram-stain-positive, aerobic, non-pigmented and non-motile actinobacterium, designated strain SCSIO 67246T, was isolated from a stony coral sample collected from the Sanya sea area, Hainan province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SCSIO 67246T shared the highest similarities with Nocardioides rotundus MCCC 1A10561T (96.5 %) and Nocardioides sonneratiae KCTC 39565T (96.1%). The novel strain grew at 15–37 °C, at pH 5.0–10.0 and in the presence of 0–10 % (w/v) NaCl. The genome length of strain SCSIO 67246T was 3.52 Mbp with a DNA G+C content of 72.0 mol% and 3397 protein-coding genes. The novel strain showed an average nucleotide identity value of 76.5 % and a digital DNA–DNA hybridization value of 20.1 % with N. rotundus MCCC 1A10561T. Strain SCSIO 67246T contained MK-8(H4) as the major menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and five phospholipids. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω8c and summed feature 9 (iso-C17 : 1 ω9c/10-methyl C16 : 0). ll-2,6-Diaminopimelic acid was the diagnostic diamino acid. The whole-cell sugars were galactose, glucose and ribose. Based on this polyphasic taxonomic study, strain SCSIO 67246T represents a novel species of the genus Nocardioides , for which the name Nocardioides coralli sp. nov. is proposed. The type strain is SCSIO 67246T (=MCCC 1K06251T=KCTC 49719T).
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Kitasatospora humi sp. nov., isolated from a tropical peat swamp forest soil, and proposal for the reclassification of Kitasatospora psammotica as a later heterotypic synonym of Kitasatospora aureofaciens
More LessA polyphasic approach was used to describe strain RB6PN24T, a novel actinobacterium isolated from peat swamp forest soil collected from Rayong province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Kitasatospora and showed the highest sequence similarities to Kitasatospora kifunensis IFO 15206T (98.7 %) and Kitasatospora acidiphila MMS16-CNU292T (98.5 %). Strain RB6PN24T contained major amounts of meso-diaminopimelic acid, galactose, mannose and ribose in the whole-cell hydrolysates. MK-9(H6) and MK-9(H8) were the predominant menaquinones of the micro-organism. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, four unidentified aminolipids and six unidentified phospholipids. Mycolic acids were not present. The major fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0, iso-C17:0, anteiso-C17 : 0 and C16 : 0. The draft genome size of strain RB6PN24T was 8.09 Mbp, with 72.1 mol% G+C content and predicted to contain at least 44 biosynthetic gene clusters encoding diverse secondary metabolites. Furthermore, the strain exhibited low average nucleotide identity and digital DNA–DNA hybridization values with K. acidiphila MMS16-CNU292T (89.1 %, 42.4 %) and K. kifunensis DSM 41654T (79.5 %, 25.5 %). The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses revealed that strain RB6PN24T represents a novel species of the genus Kitasatospora , for which the name Kitasatospora humi sp. nov. is proposed. The type strain is RB6PN24T (=TBRC 14818T=NBRC 115116T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that Kitasatospora aureofaciens and Kitasatospora psammotica belong to the same species. Therefore, it is proposed that K. psammotica is reclassified as a later heterotypic synonym of K. aureofaciens .
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Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment
More LessAn actinobacterium, designated strain EGI L10124T, was isolated from saline lake sediment collected in Xinjiang province, PR China. The taxonomic position of the isolate was determined based on polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L10124T formed a distinct clade with Rhabdothermincola sediminis SYSU G02662T, with a shared sequence identity of 95.2 %. The novel isolate could be distinguished from species in the genus Rhabdothermincola by its distinct phenotypic, physiological and genotypic characteristics. The cells of strain EGI L10124T were aerobic, Gram-stain-positive and short rod-shaped. Optimal growth conditions of strain EGI L10124T on marine agar 2216 were registered at pH 8.0 at 37 °C. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major respiratory quinone was MK-9 (H8), while the major fatty acids were iso-C16 : 0, C17 : 0 and C16 : 0. The polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. Based on the genome sequence of strain EGI L10124T, it appears that the G+C content of the novel isolate was 71.8 mol%. According to our data, strain EGI L10124T represents a new species of the genus Rhabdothermincola , for which the name Rhabdothermincola salaria sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L10124T (=CGMCC 1.19113T=KCTC 49679T).
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Streptomyces barringtoniae sp. nov., isolated from rhizosphere of plant with antioxidative potential
A novel actinomycete strain, JA03T, belonging to the genus Streptomyces , was isolated from the rhizosphere of Barringtonia racemosa (L.) Spreng. It was characterized taxonomically using a polyphasic approach. It grew at 25–37 °C, at pH 5–10 and with 6 % (w/v) NaCl. It contained ll-diaminopimelic acid in the cell-wall peptidoglycan. Ribose and glucose were detected in its whole-cell hydrolysate. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C15 : 0. Detected polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, unidentified phospholipids and unidentified amino lipids. Based on the results of 16S rRNA gene sequence analyses, strain JA03T showed highest similarity to Streptomyces filipinensis NBRC 12860T (98.76 %), Streptomyces fodineus TW1S1T (98.69 %) and Streptomyces shenzhennensis 172115T (98.68 %). Strain JA03T has a genome size of 9 092 851 bp with DNA G+C content of 71.28 mol%. The average nucleotide identity (ANI)-blast and ANI-MUMmer values of strain JA03T and related type strains were 79.6–89.2 and 86.7–92.5 %, respectively, and the digital DNA–DNA hybridization values were 27.3–46.4 %. Ethyl acetate extract of JA03T exhibited total phenolic content (33.4±0.6 µg mg−1 gallic acid equivalent), ferric reducing power value (70.8±1.8 µg mg−1 ascorbic acid equivalent) and 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity (IC50=67.0±21.1 µg ml−1). Intracellular reactive oxygen species and NO production in RAW264.7 macrophage cells induced by H2O2 and lipopolysaccharide were inhibited with IC50 of 67.40 and 16.95 µg ml−1, respectively. Based on the taxonomic results, it has been concluded that strain JA03T represents a novel species of the genus Streptomyces for which the name Streptomyces barringtoniae sp. nov., is proposed. The type strain is JA03T (=LMG 32415T=TISTR 2999T).
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Mycobacterium senriense sp. nov., a slowly growing, non-scotochromogenic species, isolated from sputum of an elderly man
A slowly growing mycobacteria, identified as strain TY59T, was isolated from sputum of an elderly man with pneumonia. Sequencing of the 16S rRNA gene indicated that this strain was similar to members of the Mycobacterium avium complex and closely related species. Strain TY59T has highest 16S rRNA gene sequence similarities to the type strains of Mycobacterium colombiense (99.80 % sequence similarity), Mycobacterium vulneris (99.74 %), Mycobacterium timonense (99.54 %), Mycobacterium avium subsp. avium (99.54 %) and Mycobacterium avium subsp. silvaticum (99.54 %). Analysis of the internal transcribed spacer (ITS) and DNA-directed RNA polymerase subunit beta (rpoB) sequences gave similar results to the 16S rRNA gene analysis. The closest species to strain TY59T were M. colombiense and M. vulneris with 97.90–98.25 % identity in ITS and 96.4–96.6 % in rpoB. The strain's 65 kDa heat shock protein (hsp65) gene was different from those of M. vulneris , M. colombiense and M. avium subsp. silvaticum with 72.4–74.2 % identity. Average nucleotide identity results showed a 93.4 % match to M. vulneris as the maximum value. Phenotypically, the non-chromogenicity, rough colonies, growth at 42 °C, negative results for nitrate reduction, β-glucosidase and Tween 80 hydrolysis, and positive results for catalase activity set this strain apart from closely related species. We propose that Mycobacterium senriense sp. nov. is a novel species of slowly growing mycobacteria. The type strain is TY59T (RIMD 1371001T=CIP 111917T).
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Arsenicicoccus cauae sp. nov., isolated from the blood of a pediatric gastroenteritis patient
A Gram-stain-positive coccus was isolated from the blood of a paediatric patient suffering from gastroenteritis. The taxonomic position of this catalase-positive, non-motile, non-spore-forming facultative anaerobe designated as strain MKL-02T was investigated using a polyphasic approach. Colonies grown on tryptic soy agar with 10 % sheep blood were circular, creamy yellow, and convex. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that this strain was most closely related to Arsenicicoccus bolidensis CCUG 47306T within the cluster of the genus Arsenicicoccus . Average nucleotide identity and digital DNA–DNA hybridization values between strain MKL-02T and A. bolidensis DSM 15745T, A. dermatophillus DSM 25571T and A. piscis DSM 22760T were 89.5 and 37.0 %, 79.6 and 22.4 %, and 75.9 and 21.0 %, respectively. The genomic size of strain MKL-02T was 3 423 857 bp with a 72.7 mol% G+C content. Growth was observed at 10–45 °C (optimum, 37–40 °C) and pH 6.0–10.0 (optimum, pH 7.0), in the presence of 0–10 % (w/v) NaCl (optimum, 0.5 %). Cells of strain MKL-02T were non-motile cocci and 0.50–0.60 µm long, as determined by transmission electron microscopy. The strain was catalase-positive and oxidase-negative. The major fatty acid type (>10 % of total) was C15 : 0. The polar lipid profile consisted of two unidentified phospholipids, three unidentified lipids and an unidentified aminophospholipid. The strain contained MK-8 (H4) as the predominant menaquinone. Based on phylogenetic and phenotypic considerations, it is proposed that strain MKL-02T be classified as a new species, named Arsenicicoccus cauae sp. nov. The type strain is MKL-02T (=NCCP 16967T=JCM 34624T).
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Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera)
More LessA novel bifidobacteria (designated S053-2T) was isolated from the gut of honeybee (Apis mellifera). Strain S053-2T was characterized using a polyphasic taxonomic approach. The result of 16S rRNA gene sequence analysis indicated that strain S053-2T was phylogenetically related to the type strains of Bifidobacterium asteroides , Bifidobacterium indicum , Bifidobacterium actinocoloniiforme , Bifidobacterium xylocopae , Bifidobacterium coryneforme , Bifidobacterium apousia , Bifidobacterium choladohabitans and Bifidobacterium polysaccharolyticum , and had 95.5–99.7 % 16S rRNA gene sequence similarities. Based on the 16S rRNA gene sequence analysis, strain S053-2T was most closely related to the type strain of B. asteroides , having 99.7 % 16S rRNA gene sequence similarity. Strain S053-2T had relatively low (91.6–95.7 %) pheS, atpA, clpC, dnaG, fusA, glnA, glyS, hsp60, argS, pyrG and recA sequence similarities to the type strain of B. asteroides . Strain S053-2T had 94.5–95.3% atpA, clpC, dnaG, dnaK and pyrG sequence similarities to the type strain of B. apousia . The phylogenomic tree indicated that strain S053-2T belonged to the B. asteroides group, and was most closely related to the type strains of B. asteroides , B. apousia , B. choladohabitans and B. polysaccharolyticum , and distantly related to type strains of other phylogenetically related species in the B. asteroides group. Strain S053-2T shared the highest average nucleotide identity (ANI, 93.8 %), digital DNA–DNA hybridization (dDDH, 52.4 %) and average amino acid identity (AAI, 95.6%) values with B. apousia W8102T. Strain S053-2T shared 91.1 % ANI, 41.9 % dDDH and 92.5 % AAI values with B. asteroides DSM 20089T. Acid production from l-arabinose, d-xylose, d-mannose, amygdalin, cellobiose, maltose, melibiose, sucrose, raffinose, gentiobiose and l-fucose, and activity of esterase lipase (C8) and α-fucosidase could differentiate strain S053-2T from B. asteroides DSM 20089T. Acid production from d-mannose, maltose, sucrose, melezitose and gentiobiose, and activity of α-fucosidase could differentiate strain S053-2T from B. apousia W8102T. Based upon the data obtained in the present study, a novel species, Bifidobacterium mizhiense sp. nov., is proposed, and the type strain is S053-2T (=JCM 34710T=CCTCC AB 2021129T).
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- Archaea
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Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea
More LessA novel methylotrophic methanogen Methanococcoides orientis sp. nov. was isolated from East China Sea sediment. Type strain LMO-1T of Methanococcoides orientis sp. nov. was irregular 1–2 µm cocci without flagella. Strain LMO-1T could utilize a variety of methylated compounds including methanol, methylamine, dimethylamine and trimethylamine for growth and methanogenesis, while H2/CO2 or acetate could not be used for growth or methanogenesis. Optimum growth temperature was 30–35 °C, optimum pH range for growth was 7.0–7.5, while the optimum salinity spectrum for growth was 1.0%–5.0% NaCl. Based on 16S rRNA gene similarity, strain LMO-1T belongs to Methanococcoides , with the highest sequence similarity to Methanococcoides methylutens DSM 2657T (99.8 %), Methanococcoides vulcani SLH33T(99.4 %), followed by Methanococcoides alaskense AK-5T(98.1 %), Methanococcoides burtonii DSM 6242T (98.0 %). Digital DNA–DNA hybridization also showed highest similarity with Methanococcoides methylutens DSM 2657T, with the value of 58.4 %. The average nucleotide identity between strain LMO-1T and Methanococcoides methylutens DSM 2657T was 94.06 %. In summary, LMO-1T represents a novel species of the genus Methaococcoides, for which the name Methanococcoides orientis sp. nov. is proposed. The type strain is LMO-1T (=MCCC 4K00106T=JCM 39195T).
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Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov., Natrinema amylolyticum sp. nov. and Haloterrigena alkaliphila sp. nov., four extremely halophilic archaea isolated from salt mine, saline soil and salt lake
More LessFour halophilic archaeal strains, YPL8T, SLN56T, LT61T and KZCA68T, were isolated from a salt mine, saline soil and a salt lake located in different regions of China. Sequence similarities of 16S rRNA and rpoB′ genes among strains YPL8T, SLN56T, LT61T and the current members of Natrinema were 94.1–98.2 % and 89.3–95.1 %, respectively, while these values among strain KZCA68T and the current members of Haloterrigena were 97.2–97.4 % and 91.7–91.9 %, respectively. The average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among these four strains and their closely related species were all lower than the threshold values for species boundary. All four strains were unable to hydrolyse casein, gelatin, or Tween 80. Strain YPL8T contained phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), disulfated mannosyl glucosyl diether (S2-DGD) and sulfated mannosyl glucosyl diether-phosphatidic acid (S-DGD-PA). Strain SLN56T contained PA, PG, phosphatidylglycerol sulphate (PGS), PGP-Me, S-DGD-1, S2-DGD and S-DGD-PA. Strain LT61T contained PA, PG, PGS, PGP-Me, S-DGD-1 and S2-DGD. The phospholipids of strain KZCA68T were PA, PG and PGP-Me. These results showed that strains YPL8T (=CGMCC 1.13883T=JCM 31181T), SLN56T (=CGMCC 1.14945T=JCM 30832T) and LT61T (=CGMCC 1.14942T=JCM 30668T) represent novel species of the genus Natrinema , for which the names, Natrinema halophilum sp. nov., Natrinema salinisoli sp. nov. and Natrinema amylolyticum sp. nov. are proposed. Strain KZCA68T (=CGMCC 1.17211T=JCM 34158T) represents a novel species of Haloterrigena , for which the name Haloterrigena alkaliphila sp. nov. is proposed.
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- Bacteroidetes
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Chryseobacterium subflavum sp. nov., isolated from soil
More LessA Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated LAMRS1T, was isolated from a soil sample collected in Hebei Province, PR China. Strain LAMRS1T was able to grow optimally in the presence of 0.5 % (w/v) NaCl, at pH 7.5 and at 30 °C. On the basis of 16S rRNA gene sequence analysis, strain LAMRS1T was closely related to members of the genus Chryseobacterium , with highest levels of sequence similarity to Chryseobacterium soli DSM 19298T (97.9 %), Chryseobacterium soldanellicola DSM 17072T (97.6%) and Chryseobacterium piperi CTMT (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between LAMRS1T and the closely related species of C. soli DSM 19298T, C. soldanellicola DSM 17072T and C. piperi CTMT were 78.1, 78.2 and 80.7 %, and 21.7, 22.0 and 23.7 %, respectively. The draft genome sequence of LAMRS1T was 4.61 Mb, with DNA G+C content of 36.2 mol%. The major isoprenoid quinone was menaquinone-6 and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) constituted the major cellular fatty acids. The main polar lipids were phosphatidylethanolamine, four aminolipids, three glycolipids and seven unidentified lipids. On the basis of evidence presented in this study, strain LAMRS1T represents a novel species of the genus Chryseobacterium , for which the name Chryseobacterium subflavum sp. nov. is proposed. The type strain is LAMRS1T (=JCM 33868T=KCTC 72823T).
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Hyunsoonleella ulvae sp. nov., isolated from algae in China
Han Wang, Yumei Liang, Haibin Li, Jin Li and Zhong HuA novel Gram-stain-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterial strain, designated HU1-3T, was isolated from Ulva in China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HU1-3T represented a member of the genus Hyunsoonleella within the family Flavobacteriaceae , phylum Bacteroidota , and showed the highest 16S rRNA gene sequence similarity to Hyunsoonleella flava T58T (97.6 %). Strain HU1-3T grew at 15–35 °C (optimum, 25–30 °C), pH 6.0–8.0 (optimum, pH 7.0) and in the presence of 2–6 % (w/v) NaCl (optimum, 2–4 %). The draft genome of strain HU1-3T comprised 4.1 Mbp with a G+C content of 33.9mol%. Compared with the reference strain Hyunsoonleella jejuensis CNU004T, the average nucleotide identity value of strain HU1-3T was 77.9 %. The major fatty acids (>10 % of the total) were iso-C15 : 0, iso G-C15 : 1 and iso-C17 : 0 3-OH. MK-6 was the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and three unknown polar lipids. Many genes that encode glycoside hydrolases (e.g. glucosidase, xylosidase, mannosidase, galactosidase, etc.) were annotated in the genome of strain HU1-3T, which indicated that it might have the ability to degrade various kinds of polysaccharides. Given the phylogenetic, chemotaxonomic, biochemical and genomic data, strain HU1-3T is considered to represent a novel species of the genus Hyunsoonleella , for which the name Hyunsoonleella ulvae sp. nov. is proposed. The type strain is HU1-3T (=KCTC 82511T=MCCC 1K05798T).
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Marinifilum caeruleilacunae sp. nov., isolated from Yongle Blue Hole in the South China Sea
A Gram-stain-negative, non-motile, facultatively anaerobic and non-flagellated marine bacterium, designated JC070T was isolated from the Yongle Blue Hole in the South China Sea. The temperature, pH and NaCl ranges for growth of strain JC070T were 4–37 °C (optimum, 16 °C), pH 6.0–9.0 (optimum, pH 7.0) and 1.0 –6.0% (w/v; optimum, 3.0%). The predominant isoprenoid quinone of strain JC070T was identified as menaquinone-7. The dominant fatty acids (>10%) were iso-C15:0 (59.6%) and iso-C17:0 3-OH (17.2%). The major polar lipids were aminophospholipid, aminolipid, two unknown phospholipids and two unidentified lipids. The genomic DNA G+C content was determined to be 37.0 mol%. Based on the results of polyphasic analysis, a new species, named Marinifilum caeruleilacunae sp. nov., within the genus Marinifilum was proposed. The type strain is JC070T (= JCM 39045T=MCCC 1K03774T).
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Algoriphagus algorifonticola sp. nov., a marine bacterium isolated from cold spring area of South China Sea
A Gram-stain-negative, aerobic, non-motile, short-rod-shaped bacterium, designated strain hg1T, was isolated from marine sediment within the cold spring area of South China Sea and subjected to a polyphasic taxonomic investigation. Colonies were circular and 1.0–2.0 mm in diameter, coral in colour, convex and smooth after growth on marine agar at 28 °C for 3 days. Strain hg1T was found to grow at 4–40 °C (optimum, 35–37 °C), at pH 6.5–9.0 (optimum, pH 7.5) and with 0–8 % (w/v) NaCl (optimum, 1.5–2 %). Chemotaxonomic analysis showed the sole respiratory quinone was MK-7, and the principal fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and iso-C16 : 0. The major polar lipids are phosphatidylethanolamine, an unidentified phospholipid and five unidentified glycolipids. The DNA G+C content of strain hg1T was 39.6 mol% based on the genome sequence. The comparison of 16S rRNA gene sequence similarities showed that hg1T was closely related to Algoriphagus ornithinivorans DSM 15282T (98.6 % sequence similarity), Algoriphagus zhangzhouensis MCCC 1F01099T (97.9 %) and Algoriphagus vanfongensis DSM 17529T (97.2 %); it exhibited 97.0 % or less sequence similarity to the type strains of other species of the genus Algoriphagus with validly published names. Phylogenetic trees reconstructed with the neighbour-joining, maximum-parsimony and maximum-likelihood methods based on 16S rRNA gene sequences showed that strain hg1T constituted a separate branch with A . ornithinivorans , A. zhangzhouensis , A. vanfongensis in a clade of the genus Algoriphagus . OrthoANI values between strain hg1T and A . ornithinivorans , A. zhangzhouensis and A. vanfongensis were 94.3, 74.1, 73.2 %, respectively, and in silico DNA–DNA hybridization values were 56.2, 18.5 and 18.3 %, respectively. Differential phenotypic properties, together with phylogenetic distinctiveness, demonstrated that strain hg1T is clearly distinct from recognized species of genus Algoriphagus . On the basis of these features, we propose that strain hg1T (=MCCC 1K03570T=KCTC 72111T) represents a novel species of the genus Algoriphagus with the name Algoriphagus algorifonticola sp. nov.
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Fibrella aquatilis sp. nov., Fibrella rubiginis sp. nov. and Fibrella forsythiae sp. nov., isolated from freshwater, rusty iron and forsythia flower
More LessThree novel strains, designated as HMF5036T, HMF5335T and HMF5405T, were isolated from freshwater, rusty iron and forsythia flower, in Yong-in, Republic of Korea, respectively. They were Gram-stain-negative, facultatively anaerobic, non-motile, reddish-pigmented and rod-shaped bacteria. The predominant fatty acids of three strains were C16 : 1 ω5c and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). They were found to contain MK-7 as the predominant menaquinone. The major polar lipids are phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. Strains HMF5036T, HMF5335T and HMF5405T exhibited the highest 16S rRNA gene sequence similarities of 91.8, 92.6 and 93.6 % to Fibrella aestuarina BUZ 2T and less than 88.7 % to other members of the family Spirosomaceae . Similarity values among the three isolates ranged from 94.9 to 96.6 %. Phylogenetic analysis based on the 16S rRNA gene sequences of the three isolates revealed that they formed a distinct clade within the family Spirosomaceae . The genome sizes of strains HMF5036T, HMF5335T and HMF5405T were 6.8, 6.4 and 7.8 Mbp, and their DNA G+C contents were 54.9, 54.0 and 52.1 mol%, respectively. The average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values between three isolates and F. aestuarina BUZ 2T were 73.8–82.2, 19.6–25.4 and 75.0–87.5 %, respectively. These values were lower than the recommended threshold values for species delimitation. Based on the results of the phenotypic, genotypic, chemotaxonomic and phylogenetic investigations, three novel species, Fibrella aquatilis sp. nov., Fibrella rubiginis sp. nov. and Fibrella forsythiae sp. nov. are proposed. The type strains are HMF5036T (=KCTC 82476T=NBRC 115092T), HMF5335T (=KCTC 82477T=NBRC 115093T) and HMF5405T (=KCTC 82478T=NBRC 115094T), respectively.
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Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum
Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus Chryseobacterium , being closely related to strain Chryseobacterium indologenes DSM 16777T (98.4%), followed by Chryseobacterium gleum NCTC11432T (98.3%) and Chryseobacterium lactis KC1864T (98.2%). Average nucleotide identity value between DH-B6T and C. indologenes DSM 16777T was 81.1% and digital DNA–DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus Chryseobacterium , for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus Chryseobacterium and eight species of this genus based on polar lipid characterisation are also proposed.
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Arachidicoccus terrestris sp. nov., isolated from greenhouse soil
More LessA Gram-stain-negative, aerobic, non-motile, rod-shaped or occasionally filamentous-shaped bacterial strain, designated 5GH13-10T, was isolated from greenhouse soil sampled in Yeoju-si, Republic of Korea. Colonies were milky-coloured, round and convex, and catalase- and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5GH13-10T was related to the genus Arachidicoccus and had highest 16S rRNA gene sequence identity with Arachidicoccus rhizosphaerae Vu-144T (98.4 %). The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant quinone was menaquinone MK-7, and the polar lipids were composed of phosphatidylethanolamine, one unidentified aminolipid, three unidentified aminophospholipids, one unidentified phospholipid and five unidentified lipids. The genomic DNA G+C content of strain 5GH13-10T was 43.8 mol%. The average nucleotide identity values between strain 5GH13-10T and the closely related species Arachidicoccus ginsenosidivorans Gsoil 809T, Arachidicoccus rhizosphaerae Vu-144T and Archidicoccus soli KIS59-12T were 74.86, 74.74 and 69.52 %, and the digital DNA-DNA hybridization values were 20.0, 19.8 and 18.6 %, respectively. Combined phenotypic, phylogenetic and genomic data demonstrated that strain 5GH13-10T is representative of a novel species of the genus Arachidicoccus , for which we propose the name Arachidicoccus terrestris sp. nov. (type strain 5GH13-10T=KACC 18014T=NBRC 113162T).
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Bacteroides propionicigenes sp. nov., isolated from human faeces
An anaerobic bacterial strain, designated as NSJ-90T, was isolated from the faeces of a healthy adult in China. Cells of strain NSJ-90T were Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Based on 16S rRNA gene sequence analysis, strain NSJ-90T belonged to the genus Bacteroides and was phylogenetically closely related to Bacteroides clarus YIT 12056T (16S rRNA gene identity was 97.04 %). The DNA G+C content of strain NSJ-90T was 44.85 mol% (calculated from the genome). The average nucleotide identity between strain NSJ-90T and B. clarus YIT 12056T was 87.60 %. The major cellular fatty acids (>10 %) of strain NSJ-90T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. Menaquinone-10 was detected as the respiratory quinone. The major products of glucose fermentation were acetic, propionic and isovaleric acids. Based on its phylogenetic, phenotypic and chemotaxonomic characteristics, we propose that strain NSJ-90T represents a novel species of the genus Bacteroides , for which the name Bacteroides propionicigenes sp. nov. is proposed. The type strain is NSJ-90T (=CGMCC 1.17886T=KCTC 25305T).
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Chryseobacterium faecale sp. nov., isolated from camel feces
More LessStrain F4T (=KACC 22401T=JCM 34836T), a novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, was isolated from camel (Camelus bactrianus) faeces. The newly identified bacterial strain F4T was grown in Reasoner's 2A medium [0–2 % (w/v) NaCl (optimum, 0 %), pH 7.0–8.0 (optimum, pH 7.0), and 18–40 °C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain F4T belonged to the genus Chryseobacterium , with its closest neighbours being Chryseobacterium haifense DSM 19056T (98.0 %), Chryseobacterium anthropi CCUG 52764T (97.3 %), Chryseobacterium montana WG4T (95.7 %) and Chryseobacterium koreensis Chj70T (94.7 %). Complete genome sequence of strain F4T was obtained using a hybrid assembly pipeline integrating sequences obtained using both the Oxford Nanopore and Illumina platforms. Genomic comparisons of strain F4T with type species in the genus Chryseobacterium were conducted using digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity, resulting in values of ≤20.5, ≤77.9 and ≤80.8 %, respectively. The genomic DNA G+C content of type strain F4T was 39.7 mol%. The major fatty acids of the strain F4T were anteiso-C15 : 0 and iso-C18 : 3, and MK-6 was its major respiratory quinone. Moreover, the major polar lipid of strain F4T was phosphatidylethanolamine. The genome of strain F4T harbours only one antibiotic resistance gene (blaCME-1) encoding a β-lactamase, which attributes β-lactam antibiotic resistance. Based on the results of our chemotaxonomic, genotypic and phenotype analyses, strain F4T is identified as a novel species of the genus Chryseobacterium , for which the name Chryseobacterium faecale sp. nov. is proposed.
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- Firmicutes and Related Organisms
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Description and characterization of three endophytic Bacillaceae from the halophyte Suaeda salsa: Paenalkalicoccus suaedae gen. nov., sp. nov., Cytobacillus suaedae sp. nov., and Bacillus suaedae sp. nov
More LessThree strains of members of the family Bacillaceae , which can inhibit the growth of some Gram-stain-positive strains, designated M4U3P1T, HD4P25T and RD4P76T, were isolated from Suaeda salsa halophytes in Baotou, Inner Mongolia, PR China. A phylogenetic analysis based on the 16S rRNA gene and the whole genome sequences revealed that HD4P25T clustered with Cytobacillus luteolus YIM 93174T with a similarity of 98.4 %, and RD4P76T shared the highest similarity of 16S rRNA gene with Bacillus mesophilus SA4T (97.5 %). M4U3P1T clustered with strains of genera Salipaludibacillus and Alkalicoccus based on whole-genome sequence analyses, but its 16S rRNA gene had the highest similarity to ' Evansella tamaricis ' EGI 80668 (96.1 %). The average nucleotide’s identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values of the three isolated strains to their close relatives were well below the threshold value for identifying a novel species.On the basis of the phylogenetic, physiological and phenotypic results, Paenalkalicoccus suaedae gen. nov., sp. nov. [type strain M4U3P1T (=CGMCC 1.17076T=JCM 33851T)], Cytobacillus suaedae sp. nov. [type strain HD4P25T (=CGMCC 1.18651T =JCM 34524T)], and Bacillus suaedae sp. nov. [type strain RD4P76T (=CGMCC 1.18659T=JCM 34525T)] were proposed, respectively. All three species are ubiquitous in the bulk saline–alkaline soils, but only the species represented by strain RD4P76T was widely distributed in the rhizosphere soil, the above-ground part and the roots of S. salsa. The species represented by M4U3P1T can be detected in the roots of S. salsa, and rarely detected in the above-ground parts of S. salsa. The species represented by HD4P25T was rarely detected in the interior of S. salsa. The three strains could inhibit some of the Gram-stain-positive bacteria (i.e. members of the genera Planococcus , Zhihengliuella and Sanguibacter ) in the saline–alkali soil. A genomic analysis of these three strains revealed that they can synthesize different antagonistic compounds, such as aminobenzoate and bacitracin or subtilisin.
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Lentilactobacillus laojiaonis sp. nov., isolated from the mud in a fermentation cellar for the production of Chinese liquor
A novel Gram-stain-positive, rod-shaped, non-motile bacterial strain, designated IM3328T, was isolated from a mud cellar which has been continuously used over hundreds of years for the fermentative production of Chinese strong-flavour baijiu. It is asporogenous, facultative anaerobic and does not exhibit catalase activity. Strain IM3328T can grow at pH 4.5–8.5 (optimum, pH 7.0), 15–45 °C (optimum, 37 °C), with 0–75% (w/v) ethanol with and 0–6% (w/v) NaCl. The API 50CH assay revealed that strain IM3328T can metabolize l-arabinose, d-ribose, d-xylose, d-glucose, d-fructose, d-mannose, N-acetylglucosamine, gluconate, methyl β-d-pyranoside, methyl α-d-glucopyranoside, methyl α-d-glucopyranoside and raffinose among the 49 studied carbon sources. Lactic acid, acetic acid, ethanol, isopentanol and butyl acetate are he predominant metabolites in the fermentation broth of strain IM3328T when cultured in liquid de Man, Rogosa and Sharpe medium under micro-aerobic or anaerobic conditions. The polar lipids of strain IM3328T consist of diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, two unidentified glycolipids and two unidentified lipids. The major cellular fatty acids (≥10%) consist of C16 : 0, C18:1 ω9c and summed feature 7. The cell wall contains ribose, glucose, galactose, lysine, alanine, glutamic acid and aspartic acid. The complete genome of strain IM3328T contains a circular chromosome of 1242019 bp with 1242 genes and 33 mol% G+C content. On the basis of the 16S rRNA gene phylogenetic tree, Lentilactobacillus senioris DSM 24302T (95.9% similarity), Lentilactobacillus rapi DSM 19907T (95.7% similarity) and Lentilactobacillus parabuchneri DSM 5707T (95.1% similarity) were chosen to compare with strain IM3328T to reveal the physiological differences. The low average nucleotide identity values (69.7–71.2%) between strain IM3328T and phylogenetically related reference strains demonstrated that this strain represents a novel species of the genus Lentilactobacillus , and the name Lentilactobacillus laojiaonis sp. nov. (type strain IM3328T=CGMCC 1.18832T=JCM 34630T) is proposed.
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Alteribacter keqinensis sp. nov., a moderately halophilic bacterium isolated from a soda lake
A Gram-stain-positive, aerobic, endospore-forming and rod-shaped bacterium (KQ-3T), which grew at 10–45 °C (optimum 35 °C), pH 8.0–10.5 (optimum pH 9.0) and in the presence of 0–16 % (w/v) NaCl (optimum 3.0 %), was isolated from a soda lake and identified as representing a novel species using a polyphasic taxonomic approach. Strain KQ-3T was catalase-positive, oxidase-negative and non-motile. Phylogenetic analysis based on 16S rRNA gene sequence affiliated KQ-3T to the genus Alteribacter and showed the highest similarities to Alteribacter natronophilus M30T (97.90 %), Alteribacter aurantiacus K1-5T (97.84 %) and Alteribacter populi FJAT-45347T (97.22 %). Digital DNA–DNA hybridization and average nucleotide identity analyses revealed that KQ-3T displayed 21.4 and 72.81% genomic DNA relatedness with the most closely related strain, A. natronophilus M30T, respectively. KQ-3T contained all of the conserved signature indels that are specific for members of the genus Alteribacter . The DNA G+C content was 45.03 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. The predominant menaquinone was MK-7 (100%) and the major fatty acids (>10 %) comprised anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. Based on the data from the current polyphasic studies, KQ-3T represents a novel species of the genus Alteribacter , for which the name Alteribacter keqinensis sp. nov. is proposed. The type strain is KQ-3T (=ACCC 61799T=KCTC 33933T).
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Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product
More LessTwo lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to Lentilactobacillus rapi . However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from L. rapi DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584T and L. rapi DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from L. rapi DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1 ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2 ω6c and/or C18 : 2 ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species L. rapi with the proposed name Lentilactobacillus rapi subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).
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Bacillus suaedae sp. nov., isolated from the stem of Suaeda aralocaspica in north-west China
A bacterial strain, designated YZJH907-2T, was isolated from the stem of Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, Xinjiang, PR China. Cells of strain YZJH907-2T were Gram-stain-positive, aerobic and rod-shaped. They formed white or colourless circular colonies with smooth convex surfaces. Strain YZJH907-2T grew at 4–50 °C (optimum, 28–30 °C), pH 7.0–10.0 (optimum, pH 8.0–9.0) and with 0–10 % (w/v) NaCl (optimum, 3–7 %). The genomic DNA G+C content of strain YZJH907-2T was 38.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the strain was most closely related to Bacillus alcalophilus DSM 485T (97.37 %), Bacillus kiskunsagensis B16-24T (96.87 %) and Bacillus bogoriensis LBB3T (96.71 %). Average nucleotide identity values between YZJH907-2T and B. alcalophilus DSM 485Tand B. bogoriensis LBB3T were 69.2 and 69.0 %, respectively. Digital DNA–DNA hybridization values of YZJH907-2T with B. alcalophilus DSM 485T and B. bogoriensis LBB3T were 19.6 and 20.4 %, respectively. The cell wall of strain YZJH907-2T contained meso-diaminopimelic acid, and the major and secondary isoprenoid quinones were MK-7 and MK-5, respectively. Results of fatty acids showed that anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 were the predominant cellular fatty acids. Two-dimensional thin-layer chromatography analysis indicated that the polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. Based on the genomic, phylogenetic and phenotypic analyses, strain YZJH907-2T represented a novel species of the genus Bacillus , and thus the name Bacillus suaedae sp. nov. is proposed. The type strain is YZJH907-2T (=CGMCC 1.18763T=KCTC 43335T).
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Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere
A facultative anaerobic, Gram-stain-positive, endospore-forming bacterium, isolated from the rhizosphere of maize roots (Zea mays), was taxonomically studied. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-79T clustered only loosely with Neobacillus species and showed the highest similarity to Neobacillus soli (97.9%). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were 97.5 % and below. Chemotaxonomic features supported the grouping of the strain to the Neobacillus group, e.g. the major fatty acids were C15 : 0 anteiso, C15 : 0 iso and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7, and major compound in the polyamine pattern was spermidine. However, the JJ-79T genome assembly did not share most of the 11 conserved signature indels that are indicative of the genus Neobacillus . The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-79T genome assembly and those of the closest relative Bacillaceae type strains were <71, <71 and <25 %, respectively. Physiological and biochemical test results were also different from those of the most closely related Bacillaceae species. As a consequence, JJ-79T represents a novel genus for which we propose the name Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., with JJ-79T (=CIP 111885T=CCM 9045T) as the type strain.
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Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces
A strictly anaerobic, motile bacterium, designated as strain NSJ-9T, was isolated from human faeces. Cells were Gram-negative, non-spore-forming, non-pigmented, and spiral-shaped or slightly curved rods with flagella. Optimal growth in M2GSC medium was observed at 37 °C (growth range 30–45 °C) and pH 6.5–7.0 (growth range 6.5–7.5) under anaerobic conditions. Phylogenetic analysis of the 16S rRNA gene revealed that strain NSJ-9T formed a distinct phylogenetic lineage that reflects a new genus in the family Lachnospiraceae , with high levels of similarity to Roseburia hominis A2-183T (95.2 %), Roseburia cecicola ATCC 33874T (95.2 %), Pseudobutyrivibrio ruminis DSM 9787T (95.2 %), Pseudobutyrivibrio xylanivorans MZ 5T (94.8%) and Roseburia faecis M72/1T (94.4 %). Genomic similarity (average nucleotide identity and digital DNA–DNA hybridization) values between strain NSJ-9T and its phylogenetic neighbours were below 71 and 31 %, respectively, indicating that strain NSJ-9T represented a novel species. The average amino acid identity and the percentage of conserved proteins between strain NSJ-9T and other related members of the family Lachnospiraceae were below 63 and 50 %, respectively, supporting that strain NSJ-9T was a member of a new genus. The predominant cellular fatty acids of strain NSJ-9T were C16 : 0 and C17 : 0 2-OH, and major polar lipids were glycolipids. The end products of glucose fermentation were acetate, propionate, iso-butyrate, butyrate and valerate. Phylogenetic and phylogenomic lineage, pairwise determined genome identity analysis suggested that strain NSJ-9T represents a novel genus in the family Lachnospiraceae . The genome size of strain NSJ-9T is 2.56 Mbp with 44.9 mol% G+C content. Collectively, the genotypic and phenotypic differences between phylogenetic relatives suggested strain NSJ-9T represented a novel species of a new genus, for which the name Pararoseburia lenta gen. nov., sp. nov. is proposed. The type strain of Pararoseburia lenta is NSJ-9T (=CGMCC 1.32469T=KCTC 15957T).
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Copranaerobaculum intestinale gen. nov., sp. nov., a novel anaerobic bacterium isolated from human faeces
A novel obligate anaerobic organism, designated DONG20-135T, was isolated from human faeces collected in Beijing, PR China. Cells were Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 25‒45 °C (optimum, 30‒35 °C), a pH range of 6–9 (optimum, pH 8) and in the presence of 0‒3.5 % (w/v) NaCl (optimum, 0.5‒1.5 %). The major fatty acids were C16 : 0, C18 : 1 ω9c and C10 : 0, the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, four glycolipids, six aminolipids, three aminophospholipids and four unidentified lipids. No respiratory quinones were detected. The cell-wall peptidoglycan of the strain was A1γ type, containing meso-diaminopimelic acid. The 16S rRNA gene sequences shared a lower identity (<92.7 % similarity) with the described species. The phylogenetic tree based on 16S rRNA gene sequences and the protein-concatamer tree showed that strain DONG20-135T formed a distinct lineage within the family Erysipelotrichaceae . The genomic DNA G + C content was 42.2 mol%. Based on the results of phenotypic, chemotaxonomic and genomic analyses, strain DONG20-135T represents a novel genus of the family Erysipelotrichaceae , for which the name Copranaerobaculum intestinale gen. nov., sp. nov. is proposed (=KCTC 15868T=CGMCC 1.17357T).
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Tannockella kyphosi gen. nov., sp. nov., a member of the family Erysipelotrichaceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus
A Gram-stain-positive, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP52GT, was isolated from the hindgut of a Silver Drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belonged to the family Erysipelotrichaceae in the phylum Firmicutes and was most closely related to Clostridium saccharogumia with 93.3 % sequence identity. Isolate BP52GT grew on agar medium containing mannitol as the sole carbon source. White, opaque and shiny colonies of the isolate measuring approximately 1 mm diameter grew within a week at 20–28 °C (optimum, 24 °C) and pH 6.9–8.5 (optimum, pH 7.8). BP52GT tolerated the addition of up to 1 % NaCl to the medium. Formate and acetate were the major fermentation products. The major cellular fatty acids were C16 : 0, C16:1n-7t and C18:1n-7t. The genome sequence of the isolate was determined. Its G+C content was 30.7 mol%, and the 72.65 % average nucleotide identity of the BP52GT genome to its closest neighbour with a completely sequenced genome ( Erysipelatoclostridium ramosum JCM 1298T) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species Tannockella kyphosi gen. nov., sp. nov. is proposed for isolate BP52GT (=NZRM 4757T=JCM 34692T).
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Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea
More LessA starch-degrading novel strain, designated as strain ITR2T, was isolated from a soil sample collected from a garden near Dongguk University located in Goyang, Republic of Korea. The strain was identified as Gram-stain-positive, rod-shaped, and motile by means of peritrichous flagella. Moreover, 16S rRNA gene analysis revealed the novel strain to form a separate clade with Tumebacillus permanentifrigoris Eur1 9.5T (98.3 %) while also clustering with Tumebacillus flagellatus GST4T (97.9 %). Strain ITR2T grew optimally at temperatures of 20–30 °C, at pH 6.0–7.0 and at NaCl concentrations of 0–1 %. The sole quinone was menaquinone-7 and the cell-wall peptidoglycan comprised alanine, aspartic acid, glutamic acid, lysine and meso-diaminopimelic acid (type-A1γ peptidoglycan). The major fatty acids (>10%) of the novel strain were C16 : 0, iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Other polar lipids of the novel strain included, two unidentified glycolipids, three unidentified phospholipids and one unidentified lipid. The in silico DNA–DNA hybridization values between strain ITR2T and its reference strains ( T. permanentifrigoris DSM 18773T and T. flagellatus GST4T) were 21.3 and 23.9 %, respectively, while the average nucleotide identity values were 78.5 and 81.2 %, respectively. The genomic DNA G+C content was 54.9 mol%. Based on the phylogenetic, chemotaxonomic and genomic data obtained in the present study, we propose Tumebacillus amylolyticus sp. nov. to be a novel species within the genus Tumebacillus . The type strain is ITR2T (=KCTC 43280T=NBRC 114753T).
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Description of two novel anaerobic members in the family Clostridiaceae, Anaeromonas gelatinilytica gen.nov., sp. nov., and Anaeromonas frigoriresistens sp. nov., isolated from saline lake sediment
More LessCells of members of the family Clostridiaceae , phylum Firmicutes , are generally obligate anaerobic rods. Strains D2Q-14T and D2Q-11T were isolated from sediment of the saline lake Manisi in the Xinjiang Uygur Autonomous Region, PR China. In this study, we employed a polyphasic approach and whole genome analysis of the two isolates. Cells of both isolates were Gram-stain-positive rods that were motile by means of flagella and could utilize sulphate, thiosulphate, elemental sulphur and nitrate as electron acceptors. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences indicated that strains D2Q-14T and D2Q-11T constituted a coherent cluster affiliated to the family Clostridiaceae . In addition, genome analysis revealed that strain D2Q-14Tharboured one nonribosomal peptide synthetase gene cluster, making up 1.4 % of the entire genome. The genome-based analysis, including average nucleotide identity, average amino acid identity and in silico DNA–DNA hybridization, biochemical, phenotypic and chemotaxonomic characterization, indicated that strains D2Q-14T and D2Q-11T represented two novel species of a novel genus in the family Clostridiaceae , for which we propose the names Anaeromonas gelatinilytica gen. nov., sp. nov. and Anaeromonas frigoriresistens sp. nov., with the type strains D2Q-14T (=KCTC 15986T=MCCC 1K04634T) and D2Q-11T (=KCTC 15985T=MCCC 1K04391T), respectively.
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Vagococcus allomyrinae sp. nov. and Enterococcus larvae sp. nov., isolated from larvae of Allomyrina dichotoma
More LessThe taxonomic positions of two novel strains isolated from larvae of an insect (Allomyrina dichotoma) collected in Jeju, Republic of Korea, were determined by a polyphasic approach. Strain BWB3-3T was closely related to the type strain of Vagococcus salmoninarum , having 97.2 % 16S rRNA gene sequence similarity, whereas strain BWM-S5T formed an independent cluster within the genus Enterococcus in the 16S rRNA gene phylogeny and the closest relative was the type strain of Enterococcus canis (98.1 % sequence similarity). The core gene analysis supported the phylogenetic positions of the isolates revealed by 16S rRNA gene phylogeny. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain BWB3-3T and the type strain of V. salmoninarum were 73.2 and 20.0 %, respectively, whereas strain BWM-S5 T showed an ANI value of 70.9 % with the type strain of Enterococcus canis . The dDDH values between strain BWM-S5T and all the type strains of Enterococcus species were ≤25.1 %. On the basis of the results obtained here, the two isolates are considered to constitute two novel species of the family Enterococcaceae , for which the names Vagococcus allomyrineae sp. nov. and Enterococcus larvae sp. nov. are proposed, with the type strains BWB3-3T (=KCTC 43277T=CCM 9080T) and BWM-S5T (=KACC 22156T=CCM 9075T), respectively.
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Furfurilactobacillus milii sp. nov., isolated from fermented cereal foods
More LessGenomic characterization of Furfurilactobacillus rossiae revealed that strains which were previously identified as F. rossiae are genetically heterogeneous. The 16S rRNA gene sequences of strains FUA3430, FUA3583, C5, FUA3115 and FUA3119, were 99.6 % identical to F. rossiae but the core genome analysis revealed that these strains share less than 93 % average nucleotide identity (ANI) with the F. rossiae type strain DSM 15814T. Because the ANI value is below the threshold for delineation of bacterial species, we propose the novel species Furfurilactobacillus milii sp. nov. with the type strain FUA3430T (=DSM 113338T=LMG 32478T). Strains of F. milii have smaller genomes than F. rossiae , lack the pdu-cbi-cob-hem cluster which is responsible for 1,2-propanediol utilization in F. rossiae , and lack genes involved in ethanolamine utilization. Two strains of the novel species (FUA3430T and FUA3583) were compared to F. rossiae FUA3214. Analysis of the cellular fatty acid composition and metabolite analysis did not reveal significant differences between F. milii sp. nov. and F. rossiae FUA3124. Although the growth requirements with respect to temperature and pH were very similar, only the strain of F. rossiae utilized melibiose and d-xylose. Morphological differences were also seen in the colony and cell size of the novel compared to F. rossiae .
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Apilactobacillus zhangqiuensis sp. nov. and Apilactobacillus xinyiensis sp. nov., isolated from the gut of honeybee (Apis mellifera)
More LessThree Gram-stain-positive bacterial strains (designated F502-1T, F575-4T and F582-1) were isolated from the gut of honeybee (Apis mellifera). These strains were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain F502-1T was phylogenetically related to the type strains of Apilactobacillus kunkeei , Apilactobacillus nanyangensis and Apilactobacillus apinorum , having 98.7–99.9 % 16S rRNA gene sequence similarities, 84.6–92.5 % pheS sequence similarities and 95.2–99.0 % rpoA sequence similarities, and that strains F575-4T and F582-1 were closely related to the type strain of Apilactobacillus ozensis , having 99.7 and 99.4 % 16S rRNA gene sequence similarities, respectively. Strains F575-4T and F582-1 had less than 88.7 % pheS and 96.4 % rpoA sequence similarities to strain F502-1T and type strains of all Apilactobacillus species. The average nucleotide identity and digital DNA–DNA hybridization values between strains F502-1T, F575-4T, F582-1 and type strains of all Apilactobacillus species were less than 91.3 and 43.5 %, respectively, confirming that they represent two novel species within the genus Apilactobacillus . Based upon the data obtained in the present study, two novel species, Apilactobacillus zhangqiuensis sp. nov. and Apilactobacillus xinyiensis sp. nov., are proposed and the type strains are F502-1T (=JCM 34500T=CCTCC AB 2021026T) and F575-4T (=JCM 34501T=CCTCC AB 2021028T), respectively.
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- Other Bacteria
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A new family for ‘termite gut treponemes’: description of Breznakiellaceae fam. nov., Gracilinema caldarium gen. nov., comb. nov., Leadbettera azotonutricia gen. nov., comb. nov., Helmutkoenigia isoptericolens gen. nov., comb. nov., and Zuelzera stenostrepta gen. nov., comb. nov., and proposal of Rectinemataceae fam. nov.
More LessThe intestinal tracts of termites are abundantly colonized by a diverse assemblage of spirochetes. Most of them belong to ‘termite cluster I’, a monophyletic group within the radiation of the genus Treponema that occurs exclusively in termite guts. Phylogenomic analysis revealed that members of the genus Treponema are extremely diverse and represent two separate, family-level lineages: the Treponemataceae sensu stricto, which comprise the majority of the validly described Treponema species, and a second lineage that comprises the remaining members of the genus Treponema , including all members of ‘termite cluster I’ from termites and the recently isolated Breznakiella homolactica from cockroaches. Here, we present the formal description of Breznakiellaceae fam. nov. and of the new genera required to accommodate the misplaced Treponema species in the new family as new combinations ( Leadbettera azotonutricia , Gracilinema caldarium , Helmutkoenigia isoptericolens and Zuelzera stenostrepta). To avoid paraphyly of Treponemataceae , we propose Rectinemataceae fam. nov. to include the genus Rectinema .
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- Proteobacteria
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Helicobacter turcicus sp. nov., a catalase-negative new member of the Helicobacter genus, isolated from Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey
More LessEleven Gram-negative, curved and S-shaped, oxidase activity positive, catalase activity negative bacterial isolates recovered from faeces of Anatolian ground squirrel (Spermophilus xanthoprymnus) in the city of Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR revealed that these isolates belonged to the genus Helicobacter . The 16S rRNA gene sequence analysis revealed that the 11 isolates had over 99 % sequence identity with each other and were most closely related to Helicobacter ganmani CMRI H02T with 97.0–97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter . Faydin-H64 and Faydin-H70T strains were subjected to gyrA and atpA gene and whole genome sequence analyses. These two Helicobacter strains formed separate phylogenetic clades, divergent from other known Helicobacter species. The DNA G+C content and genome size of the strain Faydin-H70T were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Faydin-H70T and its close phylogenetic neighbour H. winghamensis ATCC BAA-430T were determined as 81.7 and 34.9 %, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02T however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430T. The data obtained from the polyphasic taxonomy approach, including phenotypic characterization and whole-genome sequences, revealed that these strains represent a novel species within the genus Helicobacter , for which the name Helicobacter turcicus sp. nov., is proposed with Faydin-H70T as the type strain (=DSM 112556T=LMG 32335T).
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Pontibrevibacter nitratireducens gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone
More LessTwo Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacteria, strains h42T and ALG8, were isolated individually from the Indian Ocean and intertidal zone of Zhoushan, China. The results of 16S rRNA gene sequence analysis showed that the sequence similarity between strains h42T and ALG8 was 99.7 %, and the closest related strains were Monaibacterium marinum C7T (97.77 and 97.62 %) and Pontivivens insulae GYSW-23T (95.31 and 95.45 %). Phylogenetic analysis based on 16S rRNA gene sequences shows that these two novel strains belong to a distinct new lineage of the family Rhodobacteraceae in the order Rhodobacterales . The average nucleotide identity and in silico DNA–DNA hybridization values between the two novel strains and M. marinum C7T and P. insulae GYSW-23T were 72.73–78.15 % and 19.70–20.80 %, respectively. The DNA G+C content of strains h42T and ALG8 was 62.36 % and 62.17 mol %. The major fatty acids (>10 %) in strain h42T were C18 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), and in strain ALG8 were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1 ω7c). The predominant isoprenoid ubiquinone of the two novel strains was Q-10; their major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids, an unidentified aminoglycolipid, an unidentified phospholipid and an unidentified lipid. Based on the results of the morphological, physiological, chemotaxonomic and phylogenetic analysis of these two strains, a novel species of a new genus in the family Rhodobacteraceae is proposed, named as Pontibrevibacter nitratireducens gen. nov., sp. nov. The type strain and non-type strain of P. nitratireducens are h42T (=KCTC 72875T=CGMCC 1.17849T=MCCC 1K04735T) and ALG8 (=KCTC 82194=MCCC 1K04733).
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Ottowia testudinis sp. nov., isolated from the cloaca of a giant Asian pond turtle (Heosemys grandis)
More LessA bacterial strain designated 27CT isolated from the cloaca of a giant Asian pond turtle was subjected to polyphasic taxonomic characterization. The strain was Gram-stain negative and oxidase- and catalase-positive. It had highest 16S rRNA gene sequence similarity to Ottowia beijingensis GCS-AN-3T (97.6 %) and Ottowia flava GY511T 96.0% and less than 96.0 % to other established species including Ramlibacter rhizophilus YS3.2.7T, Ottowia konkukae SK3863T, Acidovorax caeni E-24608T and Ottowia thiooxydans DSM 14619T. Phylogenetically, strain 27CT formed a branch with O. beijingensis GCS-AN-3T within the Ottowia clade. The genome size was 4.32 Mbp and the G+C content was 65.7 mol%. Strain 27CT shared highest ANIb values with O. beijingensis GCS-AN-3T (82.71/82.73 %) followed by O. oryzae KADR8-3T (78.9/79.0 %) and O. caeni BD-1T (73.3/75.2 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the quinone system was ubiquinone Q-8. Predominant compounds in the polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. Major polyamines were 2-hydroxyputrescine and putrescine. In the fatty acid profile, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C14 : 0, C10 : 0 3-OH and C16 : 0 2-OH were detected. All these data identify strain 27CT as representing a novel species of the genus Ottowia and hence we propose the name Ottowia testudinis sp. nov. The type strain is 27CT (=CCM 9138T=LMG 32213T).
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Hydrogenophilus thiooxidans sp. nov., a moderately thermophilic chemotrophic bacterium unable to grow on hydrogen gas, isolated from hot spring microbial mats
More LessA novel thermophilic chemotrophic bacterium, strain SS56T, was isolated from Nakabusa Hot Spring, Japan. The isolate was a rod-shaped (1.5–2.1×0.6–0.8 µm), Gram-stain-negative bacterium. The cells of this strain grew chemoheterotrophically under aerobic and anaerobic conditions. Autotrophic growth was observed with thiosulphate and elemental sulphur under aerobic conditions but not with H2 as the electron donor. Heterotrophic growth in the presence of O2 occurred on yeast extract, tryptone, polypeptone and organic acids. Strain SS56T used nitrite as an alternative electron acceptor under anaerobic chemoheterotrophic conditions. The isolate grew between 35 and 65 °C, with the optimum at 55 °C. The pH range for growth was pH 6.0–9.0; optimal growth occurred at pH 7.0–8.0. The 16S rRNA gene sequence of strain SS56T was 98.9% identical to that of Hydrogenophilus thermoluteolus TH-1T. The draft genome sequence of 2401804 bp for strain SS56T gave values of 53.7% for digital DNA–DNA hybridization, 92.9% for average nucleotide identity and 93.6% for average amino acid identity compared with the genome sequence of 2223143 bp for H. thermoluteolus TH-1T. Based on the information described above, strain SS56T (=DSM 111892T=JCM 34254T) is proposed as the type strain of a novel species, Hydrogenophilus thiooxidans sp. nov.
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Pseudomonas insulae sp. nov., isolated from island soil
More LessA novel Gram-stain-negative, rod-shaped, aerobic and motile bacterium designated strain UL073T was isolated from a forest soil of an island, and subjected to taxonomic characterization. Strain UL073T grew at 10–37 °C (optimum, 30 °C), at pH 5.0–10.0 (optimum, pH 7.0) and in the presence of 0–3 % NaCl (optimum, 0 %), respectively. Strain UL073T showed the highest sequence similarity to Pseudomonas lalkuanensis PE08T based on 16S rRNA gene analysis with a sequence similarity of 98.08 %, which was well below the suggested cutoff for species distinction. The 16S rRNA gene tree as well as the multilocus sequence analysis and genome-based trees indicated the independent taxonomic position of strain UL073T, and the orthologous average nucleotide identity and in silico DNA–DNA hybridization values between strain UL073T and related species were no higher than 84.7 and 28.3% respectively, thus confirming the distinctive taxonomic position of the strain. The chemotaxonomic properties were consistent with those of the genus, as the major fatty acids of the strain were a summed feature consisting of C18 : 1 ω7c/C18 : 1 ω6c (31.4 %), another summed feature consisting of C16 : 1 ω7c/C16 : 1 ω6c (23.1 %), and C16 : 0 (22.0 %), the major respiratory quinone was ubiquinone 9, and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genome size and DNA G+C content of strain UL073T were 4.87 Mbp and 65.9 mol%. On the basis of phenotypic and phylogenetic evidence, strain UL073T should be classified as representing a novel species of Pseudomonas , for which the name Pseudomonas insulae sp. nov. (type strain=UL073T=KCTC 82407T=JCM 34511T) is proposed.
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Marinomonas lutimaris sp. nov., isolated from a tidal flat sediment of the East China Sea
More LessA Gram-stain-negative bacterial strain, designated as E165T, was isolated from a tidal flat sediment of the East China Sea. Strain E165T grew optimally at pH 6, at 32 °C and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence similarity results revealed that strain E165T was most closely related to Marinomonas rhizomae IVIA-Po-145T, Marinomonas polaris CK13T, Marinomonas foliarum IVIA-Po-155T, Marinomonas hwangdonensis HDW-15T, Marinomonas pontica 46-16T, Marinomonas mangrovi B20-1T and Marinomonas shanghaiensis DSL-35T with values of 97.0–98.5 %. The digital DNA–DNA hybridization and average nucleotide identity values between strain E165T and the reference strains were 21.9–34.3 % and 77.6–87.3 %, respectively. The DNA G+C content of the isolate was 42.9 mol%. Strain E165T contained Q-8 as the sole ubiquinone and C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as the major fatty acids. The major polar lipids of strain E165T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid and aminophospholipid. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas lutimaris sp. nov., is proposed with E165T (=MCCC 1K06241T=KCTC 82809T) as the type strain.
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Undibacter mobilis gen. nov., sp. nov. isolated from an artificial wetland in Okcheon, Korea
More LessStrain GY_HT was isolated from an artificial wetland in Okcheon, Chungcheongbuk-do Province, Republic of Korea. Strain GY_HT was closely related to Pseudolabrys taiwanensis CC-BB4T based on 16S rRNA gene sequences (94.7 % similarity) and clustered within the family Nitrobacteraceae . Cells of the isolate were Gram-stain-negative, catalase-negative and oxidase-positive, and colonies were white or pale transparent. A flagellum was observed, and the isolate could respire both aerobically and anaerobically. Growth of GY_ HT was observed in the following conditions: 10–45 °C, pH 5–11 and 0–4 % NaCl. The optimal conditions for growth were 25 °C, pH 6.5–7.5 and 0.5–1.5 % NaCl. The major fatty acids were C19 : 0 cyclo ω8c (35.8 %) and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 27.4 %). The major quinone was found to be ubiquinone-10. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The G+C content of the genome of GY_HT was 63.3 mol%. Based on its phylogenomic, physiological and biochemical attributes, strain GY_HT represents a novel species of a novel genus of the family Nitrobacteraceae . We propose the name as Undibacter mobilis gen. nov., sp. nov. The type strain is GY_HT (=KCTC 62792T=JCM 32856T).
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Phenylobacterium glaciei sp. nov., isolated from Vestrebroggerbreen, a valley glacier in Svalbard, Arctic
More LessA Gram-stain-negative, rod-shaped bacterial strain designated as 20VBR1T was isolated from a valley glacier (Vestrebroggerbreen) snout ice sample from Ny-Ålesund, Svalbard, Arctic. The colonies were smooth, circular and light creamish on half-strength R2A agar and grew at 10–35 °C (optimum, 20 °C), at pH 6.5–8.0 (optimum, 7.0) and with 0–2.5 % (w/v) NaCl (optimum, 0.5 %). 16S rRNA gene sequence analysis revealed that strain 20VBR1T belonged to the genus Phenylobacterium and was most closely affiliated to Phenylobacterium aquaticum W2-3-4T (97.65 % similarity), Phenylobacterium haematophilum LMG 11050T (97.57 %) and Phenylobacterium koreense Slu-01T (96.91 %). 20VBR1T has a genome size of 4.24 Mb, comprising 4185 predicted genes with a DNA G+C content of 67.86 mol%. DNA–DNA hybridization experiments indicated that the DNA–DNA relatedness between strain 20VBR1T and P. aquaticum KACC 18306T was 41.95±4.36 %, well below the threshold (<70 %) to delineate bacterial species. Genome relatedness indexes revealed that the average nucleotide identity and digital DNA–DNA hybridization values between 20VBR1T and its closest phylogenomic relative, P. aquaticum KACC 18306T, were 78.97 and 22.10 %, respectively. The predominant isoprenoid quinone was ubiquinone (Q-10) and the major polar lipids were phosphatidylglycerol, one unknown phospholipid, one unknown glycolipid and four unidentified polar lipids. The major fatty acids (>10 %) of strain 20VBR1T were summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. Based on the physiological, biochemical, chemotaxonomic, phylogenetic and phylogenomic analyses, isolate 20VBR1T is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium glaciei sp. nov. is proposed. The type strain is 20VBR1T (=JCM 33227 T=DSM 111428 T=MCC 4220 T).
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Microvenator marinus gen. nov., sp. nov., isolated from marine sediment, and description of Microvenatoraceae fam. nov. and Lujinxingiaceae fam. nov.
More LessA Gram-stain-negative, facultatively anaerobic, oxidase-negative and catalase-positive predatory bacillus, designated strain V1718T, was isolated from Xiaoshi Island, PR China. Strain V1718T was found to be closely related to Lujinxingia sediminis SEH01T, with 89.8 % similarity in the 16S rRNA gene sequence, followed by Bradymonas sediminis FA350T with a similarity of 88.4 %. Strain V1718T had the ability to prey on other bacteria, and selective predation on members of Algoriphagus , Nocardioides and Bacillus occurred with the strain. Growth was observed within the range of 20–45 °C (optimal at 37 °C), pH 6.5–9.0 (optimal at pH 8.0) and 1–10 % NaCl (optimal at 3–4 %, w/v). The predominant cellular fatty acids in strain V1718T were iso-C15 : 0 (53.0 %) and C16 : 0 (19.1 %). The major polar lipids present in the strain were phosphatidylglycerol and phosphatidylethanolamine, and the respiratory quinone was menaquinone MK-7. The complete genome sequence of strain V1718T was 5 847 748 bp with a G+C content of 55.2 mol%. The topology of the phylogenomic tree indicated that strain V1718T forms a separate branch in the same clade with the genus Lujinxingia and the family Bradymonadaceae . The average nucleotide identity and average amino acid identity values were 66.4 and 48.6 %, respectively, with Bradymonas sediminis FA350T (type species of Bradymonas ) and 66.8 % and 48.9 % with Lujinxingia litoralis B210T (type species of Lujinxingia ). The genes related to biosynthesis pathways of several important chemical compounds could not be found in the genome of strain V1718T, which was predicted to be the intrinsic reason for predation in this group. The physiological, biochemical and phylogenetic properties of strain V1718T suggest that it belongs to a novel family distinct from other culturable bradymonabacteria. The name Microvenator marinus gen. nov., sp. nov. is proposed, with strain V1718T (=KCTC 72082T=MCCC 1H00380T) as type strain; the name Microvenatoraceae fam. nov. is also proposed. Meanwhile, the genus Lujinxingia can also be taxonomic classified as Lujinxingiaceae fam. nov. Thus, two novel families and a novel genus of the order Bradymonadales are proposed in this paper.
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Wielerella bovis gen. nov., sp. nov. a member of the family Neisseriaceae associated with bovine endocarditis
Seven bacterial strains isolated from bovine endocarditis in six animals from different geographic regions were investigated in a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences placed all seven isolates on a distinct, monophyletic cluster in the family Neisseriaceae with closest similarity to type strains of Alysiella filiformis (97.06 %) and Kingella kingae (96.34 %). Whole genome sequence analysis of isolates confirmed their species status, with an average nucleotide identity >96 % between isolates and <80 % to other type species of genera of Neisseriaceae while digital DNA–DNA hybridization values were >80 % and<18 %, respectively. The DNA G+C content was 42.5–43.0 mol%. Whole genome sequence based phylogeny showed the isolates being monophyletic and separated from established genera, thereby forming a new genus within the family Neisseriaceae . Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates close together and clearly separated from other genera, making this the method of choice for identification. Biochemical markers based on classical as well as commercial identification schemes allowed separation from closely related Neisseriaceae genera, even though the new taxon is biochemically not very active. Major fatty acids are C12 : 0, C14 : 0 and C16 : 0. The major quinone is ubiquinone Q-8. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospholipid were predominant. We propose the novel genus Wielerella with the type species Wielerella bovis gen. nov., sp. nov. The type strain is CCUG 44465T (=DSM 113289T=JF 2483T) isolated post mortem from a cow with endocarditis in Switzerland.
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Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant
Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7T grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus Novosphingobium . The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of Novosphingobium species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1 ω7c, C18 : 0, C16 : 1 ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of Novosphingobium , for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.
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Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China
More LessA novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20T, was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20T was affiliated with the genus Sphingomonas , and was most closely related to Sphingomonas gei ZFGT-11T (99.0 %), Sphingomonas naasensis KIS18-15T (97.8%) and Sphingomonas kyeonggiensis THG-DT81T (97.2 %). The average nucleotide identity values between strain Cra20T, S. gei ZFGT-11T, S. naasensis KIS18-15T and S. kyeonggiensis THG-DT81T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20T were summed feature 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c, 67.3 %) and C14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20T (=CGMCC 1.15510T=NBRC 112697T).
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Pseudophaeobacter flagellatus sp. nov., isolated from coastal water
A Gram-stain-negative, aerobic, motile, rod-shaped novel bacterial strain, designated as MA21411-1T, was isolated from the Korean coast. The colonies were white-yellow-coloured, smooth, convex and entire, spherical and 1.0–1.8 mm in diameter. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MA21411-1T is closely related to species of the genus Pseudophaeobacter . The 16S rRNA gene sequence similarities between strain MA21411-1T and Pseudophaeobacter arcticus DSM 23566T, Phaeobacter porticola DSM 103148T and Pseudophaeobacter leonis DSM 25627T were 98.31, 97.80 and 97.28 %, respectively. Strain MA21411-1T has a draft genome size of 4 294 042 bp, annotated with 4125 protein-coding genes, and 53 tRNA, three rRNA and one tmRNA genes. The genomic DNA G+C content was 59.2 mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values among strain MA21411-1T and other related species were below the cut-off levels of 95, 70 and 95.5 %, respectively. The growth temperature range for growth was 15–28 °C (optimum, 25 °C), pH range was 6.0–9.0 (optimum, pH 6.0), and salt tolerance range was 0.5–4 % (optimum 0.5 %). Ubiquinone-10 was the sole quinone present in MA21411-1T and all three closely related strains. The major cellular fatty acid (>10 %) of the strain was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and four unidentified polar lipids. Based on the phylogenetic tree, as well as phenotypic, chemotaxonomic and genomic features, strain MA21411-1T represents a novel species of the genus Pseudophaeobacter , for which the name Pseudophaeobacter flagellatus sp. nov. is proposed. The type strain is MA21411-1T (=KCTC 92095T=GDMCC 1.2988T).
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Sessilibacter corallicola gen. nov., sp. nov., a sessile bacterium isolated from coral Porites lutea
A Gram-stain-negative, non-spore-forming, motile, aerobic bacterium (strain C21T) was isolated from coral and identified using polyphasic identification approach. Global alignment of 16S rRNA gene sequences indicated that strain C21T shares 95.7 % sequence identity to its closest neighbour, Marinibactrum halimedae NBRC 110095T, followed by other type strains with identities of lower than 95 %. The average nucleotide identity and average amino acid identity values between strain C21T and M. halimedae NBRC 110095T were 69.6 and 64.8 %, respectively, indicating that strain C21T may represent a new species in a new genus. Phylogenetic analysis based on 16S rRNA gene and phylogenomic results indicated that strain C21T forms a distinct branch in the family Cellvibrionaceae . Cellular fatty acids and polar lipids could also readily distinguish strain C21T from closely related type strains. Therefore, strain C21T is suggested to represent a new species in a new genus, for which the name Sessilibacter corallicola gen. nov., sp. nov. is proposed. The type strain is C21T (=MCCC 1K03260T=KCTC 62317T).
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Thalassolituus alkanivorans sp. nov., a hydrocarbon-utilizing bacterium isolated from the Mariana Trench
More LessTwo strains, TMPB967T and TTPB476, were isolated from two different locations in the Mariana Trench. Cells of strains TMPB967T and TTPB476 were Gram-negative, curved rod-shaped (0.35–0.6 µm×2–4 µm) with flagella. Both strains were catalase- and oxidase-positive. Strains TMPB967T and TTPB476 could grow at 4–37 °C (optimum, 37 °C), at pH 6–9 (optimum, pH 6–7) and in the presence of 0–8 % (w/v) NaCl (optimum, 5 %). Both strains could grow with tetradecane or hexadecane as the sole carbon source. The predominant isoprenoid quinone was ubiquinone 9. The major cellular fatty acids of strains TMPB967T and TTPB476 were C18 : 1 ω9c, C16 : 0 and summed feature 3 (C16 : 1 ω7c or ω6c). The polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown aminolipid. The DNA G+C contents of strains TMPB967T and TTPB476 were 53.1 and 53.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species were Thalassolituus marinus IMCC1826T (97.1 % similarity) and Thalassolituus oleivorans MIL-1T (95.9 % similarity). Digital DNA–DNA hybridization results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 99.9, 20.9 and 20.2 %, respectively. Average nucleotide identity results of strain TMPB967T with TTPB476, T. marinus IMCC1826T and T. oleivorans MIL-1T were 100, 75.8 and 72.0 %, respectively. On the basis of the phenotypic, chemotaxonomic and molecular features, strains TMPB967T and TTPB476 belong to a novel species within the genus Thalassolituus , for which the name Thalassolituus alkanivorans sp. nov. is proposed. The type strain is TMPB967T (=KCTC 82621T=MCCC 1K05476T).
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- Eukaryotic Micro-Organisms
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Hyphopichia xiaguanensis f.a., sp. nov., an ascomycetous yeast species isolated from plant leaves
More LessTwo strains representing a novel yeast species were isolated from plant leaves collected in the Baotianman Nature Reserve in Henan Province, central China. Phylogenetic analysis based on the concatenated sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S–ITS2) and the D1/D2 domain of the large subunit rRNA gene revealed that the novel species belonged to the genus Hyphopichia, although the formation of ascospores was not observed. The novel species was related most closely to Hyphopichia paragotoi CBS 13913T but they differed by 0.9 % sequence divergence (five substitutions) in the D1/D2 domain and by 3.7 % sequence divergence (seven substitutions and eight gaps) in the ITS region. Furthermore, the novel species can also be differentiated from the closely related species in some biochemical and physiological characteristics. The species name of Hyphopichia xiaguanensis f.a., sp. nov. (Holotype CBS 16668, Mycobank MB 842425) is proposed to accommodate strains NYNU 20899T and NYNU 20914.
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- Combined Taxa
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Reclassification of Brevibacterium frigoritolerans as Peribacillus frigoritolerans comb. nov. based on phylogenomics and multiple molecular synapomorphies
More LessThe taxonomic assignment of Brevibacterium frigoritolerans together with the in-house environmental isolate EB93 was reassessed in this study using phylogenetic and phylogenomic approaches, and the detection of multiple molecular synapomorphies. Results from the reconstructed phylogenetic trees based on the 16S rRNA gene sequences, the concatenated protein sequences of GyrA-GyrB-RpoB-RpoC, and the whole-genome sequences revealed the consistent exclusion of B. frigoritolerans and the environmental isolate EB93 from the cluster formed by the type strains of the genus Brevibacterium . In addition, B. frigoritolerans and the environmental isolate EB93 were both observed to form a clade together with the type strains of the genus Peribacillus . The results from the analysis of the digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the difference in the G+C content also corroborated with the phylogenetic inference, and that B. frigoritolerans and the environmental isolate EB93 were of the same species. Furthermore, the presence of the molecular synapomorphies in the protein sequences noted in the description of the genus Peribacillus were also observed in B. frigoritolerans , further strengthening its taxonomic affiliation in the genus. Based on the evidence from the multiple lines of analyses, we propose the reclassification of Brevibacterium frigoritolerans as a member of the genus Peribacillus and assume the name Peribacillus frigoritolerans comb. nov. (type strain DSM 8801 T=ATCC 25097T=CCUG 43489T=CIP 67.20T=JCM 11681T).
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- Evolution, Phylogeny and Biodiversity
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Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber
More LessAlthough 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus Streptomyces . Gene sequences of atpD, gyrB, recA, rpoB and trpB are generally used in MLSA for Streptomyces species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of atpD gene sequences was not necessarily able to distinguish closely related species. In contrast, trpB gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in trpB gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that Streptomyces anthocyanicus and Streptomyces tricolor are synonyms of Streptomyces violaceoruber .
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Characterization of a new Blastobotrys navarrensis strain indicates that it is not a later synonym of Blastobotrys proliferans
More LessThe species Blastobotrys navarrensis Sesma and Ramirez was delineated based on the description of the single strain CBS 139.77T. Based on its phenotypic similarities to Blastobotrys proliferans, B. navarrensis CBS 139.77T was later considered a synonym of B. proliferans. In the present study, we isolated the yeast strain IST 508 (=PYCC 8784=CBS 16671) from the soil surrounding an olive tree in Ferreira do Alentejo, Portugal. The phylogenetic analysis of D1/D2 domain and ITS sequences from strain IST 508 indicates that is closely related to B. navarrensis and B. proliferans. Although strain IST 508 differs from B. navarrensis CBS 139.77T by 14 substitutions and 20 indels (6.6 % divergence) in the ITS sequence, no divergence was detected at the level of D1/D2 domain, mitochondrial small subunit rDNA, and cytochrome oxidase II sequences. On the other hand, strains IST 508 and CBS 139.77 differ from B. proliferans NRRL Y-17577T by eight substitutions (1.4 % divergence) in the D1/D2 domain sequence, by 16 substitutions (2.7 % divergence) in the cytochrome oxidase II sequence, and by 16 substitutions (3.7 % divergence) in the mitochondrial small subunit rDNA sequence. Due to the high number of variable phenotypic tests in B. proliferans and B. navarrensis, strains from the two species are difficult to distinguish. Contrasting with what is described for other Blastobotrys species, no differences were detected at the level of micromorphology between the two species. Nevertheless, based on the molecular differences between the two strains, CBS 139.77 and IST 508, and B. proliferans NRRL Y-17577T and their phylogenetic analysis, strains CBS 139.77 and IST 508 are from B. navarrensis and this species should be considered as an independent species and not a later synonym of B. proliferans. We propose an emended description of B. navarrensis.
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- ICSP Matters
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Judicial Commission of the International Committee on Systematics of Prokaryotes: Minutes of the Meeting on 3 March 2022
More LessThe minutes of the online meeting of the Judicial Commission of the International Committee on Systematics of Prokaryotes that was held on 3 March 2022 per video conference are presented.
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- Corrigenda
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- Errata
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 58 (2008)
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Volume 45 (1995)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 8 (1958)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)