ABSTRACT
Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5â% (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8âmol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8â% (19.0 and 21.6â% for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1â% (74.4 and 78.3â% for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6â% (25.7â%). The corresponding ANI value was 85.7â% (85.5â% for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1â%) and 82/190 (43.2â%) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Sphingobacterium , Vitamin K 2 , RNA, Ribosomal, 16S/genetics , Fatty Acids/analysis , Sphingobacterium/genetics , Sphingobacterium/classification , Sphingobacterium/isolation & purification , DNA, Bacterial/genetics , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , China , Animals , TibetABSTRACT
Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65â% 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89â% 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5âmol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5â% as well as digital DNA-DNA hybridization values between 20.1 and 40.8â%, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16â:â0, C17â:â1 ω8c or C18â:â1 ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).
Subject(s)
Antelopes , Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Feces , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Soil Microbiology , RNA, Ribosomal, 16S/genetics , Tibet , Fatty Acids/analysis , Fatty Acids/chemistry , DNA, Bacterial/genetics , Feces/microbiology , Antelopes/microbiology , Animals , China , Actinomycetales/genetics , Actinomycetales/isolation & purification , Actinomycetales/classification , Peptidoglycan , Phospholipids/analysisABSTRACT
Six novel bacterial strains, designated N016T, N017, N022T, N028, N056T, and N064, were isolated from soil sampled on the Qinghai-Tibet Plateau. Cells were aerobic, orange or yellow, globular or rod-shaped, non-motile, non-spore-forming, Gram-stain-positive, catalase-positive and oxidase-negative. All the isolates were salt-tolerant and could grow in the range of 4-42â°C. Results of phylogenomic analyses based on 16S rRNA gene sequences and core genomic genes showed that the three pairs of strains (N016T/N017, N022T/N028, and N056T/N064) were closely related to the members of the genus Planococcus, and clustered with Planococcus ruber, Planococcus glaciei, and Planococcus chinensis. The digital DNA-DNA hybridization and average nucleotide identity values of the six novel strains with other members of the genus Planococcus were within the ranges of 18.7-53â% and 70.58-93.49â%, respectively, all below the respective recommended thresholds of 70.0â% and 95-96â%. The genomic DNA G+C content of the six strains ranged from 43.5 to 46.0 mol%. The major fatty acids of the six strains were anteiso-C15â:â0, iso-C14â:â0, and C16â:â1 ω7c alcohol. The predominant polar lipids of strains N016T, N022T, and N056T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Menaquinones 7 and 8 were the respiratory quinones. The results of the above analyses indicated that the six strains represent three novel species of the genus Planococcus, for which the names Planococcus shenhongbingii sp. nov. (type strain N016T=GDMCC 1.4062T=JCM 36224T), Planococcus shixiaomingii sp. nov. (type strain N022T=GDMCC 1.4063T=JCM 36225T), and Planococcus liqunii sp. nov. (type strain N056T=GDMCC 1.4064T=JCM 36226T) are proposed.
Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Nucleic Acid Hybridization , Phylogeny , Planococcus Bacteria , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Soil Microbiology , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Fatty Acids/analysis , Tibet , Planococcus Bacteria/genetics , Planococcus Bacteria/isolation & purification , Planococcus Bacteria/classification , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Phospholipids/analysisABSTRACT
Six facultative anaerobic, Gram-stain-positive, oxidase-negative, rod-shaped bacteria (strains zg-B89T, zg-B12, zg-Y338T, zg-Y138, zg-Y908T and zg-Y766), were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. The 16S rRNA gene sequence analysis showed that zg-B89T showed highest similarity to Cellulomonas iranensis NBRC 101100T (99.5â%), zg-Y338T to Cellulomonas cellasea DSM 20118T (98.7â%), and zg-Y908T to Cellulomonas flavigena DSM 20109T (99.0â%). Phylogenetic and phylogenomic analysis based on 16S rRNA gene and 881 core genes revealed that these six strains formed three separate clades in the genus Cellulomonas. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between these three novel species and all members of the genus Cellulomonas were below species thresholds (95-96â% for ANI and 70â% for dDDH). The DNA G+C contents of zg-B89T, zg-Y338T and zg-Y908T were 73.6, 72.9 and 74.5â%, respectively. Strains zg-B89T and zg-Y908T had anteiso-C15â:â0, C16â:â0 and anteiso-C15â:â1 A, and zg-Y338T had anteiso-C15â:â0, C16â:â0 and iso-C16â:â0 as the main fatty acids. All novel type strains had MK-9 (H4) as the predominant respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as the major polar lipids, and rhamnose, ribose and glucose as the cell-wall sugars. The peptidoglycan amino acids of zg-B89T, zg-Y338T and zg-Y908T contained ornithine, alanine, glutamic acid and aspartic acid (except for zg-Y338T). Based on genotypic, phenotypic, phylogenetic and biochemical properties, the six uncharacterized strains represent three novel species in the genus Cellulomonas, for which the names Cellulomonas xiejunii sp. nov. (type strain zg-B89T=GDMCC 1.2821T=KCTC 49756T), Cellulomonas chengniuliangii sp. nov. (type strain zg-Y338T=GDMCC 1.2829T=KCTC 49754T) and Cellulomonas wangsupingiae sp. nov. (type strain zg-Y908T=GDMCC 1.2820T=KCTC 49755T) are proposed, respectively.
Subject(s)
Cellulomonas , Fatty Acids , Animals , Fatty Acids/chemistry , Phospholipids/chemistry , Gastrointestinal Contents , Marmota , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Sequence Analysis, DNA , Base Composition , Bacterial Typing TechniquesABSTRACT
A polyphasic taxonomic characterization of two novel strain pairs (designated zg-579T/zg-578 and zg-536T/zg-ZUI104) isolated from the faeces of Marmota himalayana was conducted based on phylogenetic analysis of the nearly full-length 16S rRNA gene and genome, digital DNA-DNA hybridization, ortho-average nucleotide identity (Ortho-ANI), and phenotypic and chemotaxonomic traits. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed that strain zg-579T was most closely related to Nocardioides dokdonensis FR1436T (97.57â%) and Nocardioides deserti SC8A-24T (97.36â%), whereas strain zg-536T had the highest similarity to Nocardioides caeni MN8T (98.33â%), Nocardioides convexus W2-2-3T (98.26â%) and Nocardioides daeguensis 2C1-5T (98.19â%). Low levels of DNA-DNA relatedness and Ortho-ANI values (19.8-31.0â%/78.6-88.2â%, zg-579T; 19.9-31.3â%/78.8-86.2â%, zg-536T) between the two new type strains and previously known species within the genus Nocardioides support the hypothesis that the four newly characterized strains could be considered to represent two novel species within this genus. The dominant cellular fatty acids found in strain pair zg-536T/zg-ZUI104 were iso-C16â:â0 and C18â:â1 ω9c, whereas C17â:â1 ω8c was major component in zg-579T/zg-578. Galactose and ribose were the main cell-wall sugars in these two new strain pairs. Diphosphatidylglycerol (DPG), phosphatidylcholine, phosphatidylglycerol (PG) and phosphatidylinositol (PI) were the major polar lipids in zg-579T, whereas DPG, PG and PI predominated in zg-536T. Both strain pairs had MK8(H4) as the major respiratory quinone and ll-diaminopimelic acid as the major cell-wall peptidoglycan. The optimal growth conditions for the two novel strain pairs were 30 °C, pH 7.0 and 0.5â% NaCl (w/v). Based on these polyphasic characterizations, two novel species within the genus Nocardioides are proposed, i.e. Nocardioides marmotae sp. nov. and Nocardioides faecalis sp. nov., with zg-579T (=CGMCC 4.7663T=JCM 33892T) and zg-536T (=CGMCC 4.7662T=JCM 33891T) as the type strains.
Subject(s)
Actinomycetales , Fatty Acids , Fatty Acids/chemistry , Phospholipids/chemistry , Nocardioides , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Base Composition , Sequence Analysis, DNA , Bacterial Typing Techniques , CardiolipinsABSTRACT
Six Gram-stain-positive, facultative anaerobic, nonmotile and rod-shaped strains, designated zg-Y50T, zg-Y1362, zg-Y1379T, zg-Y869, zg-629T and zg-Y636, were isolated from the intestinal contents of Marmota himalayana in Qinghai Province, PR China. Strains zg-Y50T, zg-Y1379T and zg-629T exhibited the highest 16S rRNA gene sequence similarities of 99.2, 98.9 and 98.8â% to Aeromicrobium choanae 9 H-4T, Aeromicrobium ginsengisoli JCM 14732T and Aeromicrobium flavum TYLN1T, respectively. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and genomic sequences, respectively, revealed that the six strains formed three distinct clades within the genus Aeromicrobium. The genome sizes of strains zg-Y50T, zg-Y1379T and zg-629T were 3.1-3.7 Mb, with DNA G+C contents of 69.6-70.4âmol%. Average nucleotide identity and digital DNA-DNA hybridization values between each novel strain and available members of the genus Aeromicrobium were all below species thresholds. All novel strains contained MK-9 (H4) as the major menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the polar lipids. The predominant fatty acid of the six isolates was C18â:â1 ω9c. The cell-wall peptidoglycan contained ÊÊ-diaminopimelic acid as the diagnostic diamino acid. Based on the results from this polyphasic taxonomic study, three novel species in the genus Aeromicrobium are proposed, namely, Aeromicrobium duanguangcaii sp. nov. (zg-Y50T=GDMCC 1.2981T=KCTC 49764T), Aeromicrobium wangtongii sp. nov. (zg-Y1379T=GDMCC 1.2982T=KCTC 49765T) and Aeromicrobium senzhongii sp. nov. (zg-629T=CGMCC 1.17414T=JCM 33888T).
Subject(s)
Actinomycetales , Fatty Acids , Animals , Base Composition , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , MarmotaABSTRACT
Two Gram-stain-negative, non-spore-forming, rod-shaped, and obligately aerobic bacteria, designated strains CX-624T and cx-311, were isolated from soil samples in Qinghai Province, China. The two strains grew best at 28 °C on the plate with Tryptone soya agar (TSA). Cells formed circular, convex, translucent, smooth, and orange colonies with approximately 1.0 mm diameter after 2 days of incubation on TSA at 28 °C. The strains were oxidase-negative and catalase-positive. The predominant cellular fatty acids were iso-C15â:â0 and anteiso-C15â:â0, and major polar lipids included phosphatidylethanolamine, an unidentified aminophospholipid, four unidentified lipids and an aminolipid. MK-6 was the sole menaquinone in strain CX-624T. Comparative analysis of the nearly full-length 16S rRNA gene sequences showed strains CX-624T and cx-311 were member of the family Weeksellaceae, with the highest similarity to Kaistella haifensis H38T (96.66â%), Epilithonimonas pallida DSM 18015T (96.59â%), and Chryseobacterium gambrini DSM 18014T (96.53â%). Both phylogenetic analysis of the 16S rRNA gene and 177 core genes revealed that strains CX-624T and cx-311 formed an independent clade. Average nucleotide identity values (< 72.64â%), average amino-acid identity values (<72.61â%) and digital DNA-DNA hybridization (< 21.10â%) indicated that the strains CX-624T and cx-311 should constitute a novel genus. The DNA G+C contents of strains CX-624T and cx-311 were 43.0 mol% and 42.7 mol%. According to the data obtained in this study, strain CX-624T represents a novel species belonging to a novel genus of the Weeksellaceae, for which the name Marnyiella aurantia gen. nov., sp. nov. is proposed. The type strain is CX-624T (=GDMCC 1.1714T = JCM 33925T).
Subject(s)
Fatty Acids , Flavobacteriaceae , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Base Composition , Bacterial Typing Techniques , Sequence Analysis, DNA , Vitamin K 2ABSTRACT
Four Gram-stain-negative, oxidase-positive, non-motile, cocci-shaped bacteria strains (ZJ106T, ZJ104, ZJ785T and ZJ930) were isolated from marmot respiratory tracts. Phylogenetic analyses based on 16S rRNA genes, 53 ribosomal protein sequences and 441 core genes supported that all four strains belonged to the genus Neisseria with close relatives Neisseria weixii 10022T and Neisseria iguanae ATCC 51483T. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the species-level thresholds (95-96â% for ANI, and 70â% for dDDH). The major fatty acids of all four strains were C16â:â1 ω7c /C16â:â1 ω6c, C16â:â0 and C18â:â1 ω9c. Major polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. MK-8 was the major menaquinone. Based on Virulence Factor Database analysis, the four strains were found to contain NspA and PorB H-factor binding proteins that promote evasion of host immunity. Strains ZJ106T and ZJ104 contained structures similar to the capsule synthesis manipulator of Neisseria meningitidis. Based on phenotypic and phylogenetic evidence, we propose that strains ZJ106T and ZJ785T represent two novel species of the genus Neisseria, respectively, with the names Neisseria lisongii sp. nov. and Neisseria yangbaofengii sp. nov. The type strains are ZJ106T (=GDMCC 1.3111T=JCM 35323T) and ZJ785T (=GDMCC 1.1998T=KCTC 82336T).
Subject(s)
Fatty Acids , Marmota , Animals , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , DNA, Bacterial/genetics , Bacterial Typing Techniques , Base Composition , Neisseria/genetics , Respiratory System , NucleotidesABSTRACT
Currently, the genus Paracoccus comprises 76 recognized species. Members of Paracoccus are mostly isolated from environmental, animal, and plant sources. This report describes and proposes a novel species of Paracoccus isolated from clinical specimens of the human ocular surface. We isolated two aerobic, Gram-stain-negative, non-spore-forming, coccoid or short rod-shaped, and non-motile strains (designated DK398T and DK608) from conjunctival sac swabs of two healthy volunteers. The results showed that the strains grew best under the conditions of 28°C, pH 7.0, and 1.0â% (w/v) NaCl. Sequence analysis based on the 16S rRNA gene showed that strains DK398T and DK608 were members of Paracoccus, most similar to Paracoccus laeviglucosivorans 43PT (98.54 and 98.62â%), Paracoccus litorisediminis GHD-05T (98.34 and 98.41â%), and Paracoccus limmosus NB88T (98.21 and 98.29â%). Phenotypic analysis showed that DK398T and DK608 were positive for catalase and oxidase, negative for producing N-acetyl-ß-glucosaminic acid, arginine dihydrolase, and ß-glucuronidase but positive for leucine arylamidase. The predominant isoprenoid quinone was Q-10, and the major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and an unidentified glycolipid. The major fatty acids (>10%) were summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c) and C16â:â0. The meso-diaminopimelic acid was found in the cell wall peptidoglycan of DK398T. The major cell wall sugars were ribose and galactose. Based on the results of phylogenetic analyses, low (<83.22â%) average nucleotide identity, digital DNA-DNA hybridization (<26.0%), chemotaxonomic analysis, and physiological properties, strain DK398T represents a novel species of the genus Paracoccus, for which the name Paracoccus shanxieyensis sp. nov. is proposed. The type strain is DK398T (=CGMCC 1.17227T=JCM 33719T).
Subject(s)
Fatty Acids , Paracoccus , Animals , Humans , Fatty Acids/chemistry , Phospholipids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Ubiquinone/chemistry , Bacterial Typing Techniques , DNA, Bacterial/genetics , Base CompositionABSTRACT
A novel Gram-stain-negative, aerobic, rod-shaped bacterium named T808T was isolated from an alpine soil in Qamdo, Tibet, PR China. Strain T808T grew at 5-30â, pH 5.0-9.0 (optimum, 25â and pH 7.0-8.0) with 0-2% (w/v) NaCl (optimum, 0%). The 16S rRNA gene sequences of strain T808T showed the highest similarity with Pararhizobium herbae CCBAU83011T (98.8%), followed by Pararhizobium polonicum F5.1T (98.7%), Pararhizobium giardinii H152T (98.5%), Rhizobium gei ZFJT-2 T (98.4%), and Pararhizobium antarcticum NAQVI59T (97.5%). The highest digital DNA-DNA hybridization (dDDH), core-proteome average amino acid identity (cpAAI) and average nucleotide identity (ANI) values between strain T808T and related strains were estimated as 28.0%, 92.1% and 84.4%, respectively. Phylogenetic analysis based on 16S rRNA, core-proteome and whole-genome indicated that strain T808T belonged to the genus Pararhizobium. The genome size was 6.24 Mbp with genomic DNA G + C content of 60.1%. The major cellular fatty acids were Summed feature 8 (C18:1 ω7c or C18:1 ω6c), C16:0 and C19:0 cyclo ω8c. The polar lipids were diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline and unidentified aminophospholipid. The isoprenoid quinone were ubiquinone-10 and ubiquinone-9. Based on phenotypic, phylogenetic, and genotypic data, strain T808T is considered to represent a novel species of the genus Pararhizobium, for which the name Pararhizobium qamdonense sp. nov. is proposed. The type strain is T808T (= JCM 36247 T = CICC 25216 T). According to phylogenetic coherence based on 16S rRNA, core-proteome and whole-genome, it is also proposed that the type strain Rhizobium gei Shi et al. 2016 should be reclassified as Pararhizobium gei comb. nov., the type strain is ZFJT-2 T (= CCTCC AB 2013015 T = KCTC 32301 T = LMG 27603 T).
Subject(s)
DNA , Proteome , Tibet , RNA, Ribosomal, 16S/genetics , Phylogeny , PhosphatidylglycerolsABSTRACT
Two Gram-stain-positive, aerobic and rod-shaped actinomycetes (strains CY18T and CY8) were isolated from the sputum of two patients with pulmonary infections, and their taxonomic status was investigated. The 16S rRNA gene sequences and the results of phylogenetic analyses indicated that CY18T and CY8 were identical (100â%) and were most closely related to Nocardia beijingensis CGMCC 4.1521T (99.9â%) and Nocardia araoensis NBRC 100135T (99.5â%). The predominant cellular fatty acids of CY18T and CY8 were C16â:â0, C18â:â0, C18â:â1ω9c and summed feature 3 (comprising C16â:â1É·7c and/or C16â:â1É·6c), and the major menaquinone was MK-8(H4ω-cycl).The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The whole-cell hydrolytic sugar pattern consisted of arabinose and glucose. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified glycolipids and two unidentified lipids.The DNA G+C contents of CY18T and CY8 were 67.9 and 68.0â% respectively. The digital DNA-DNA hybridization and average nucleotide identity values between the two novel strains and closely related species were well under the 70â% and 95-96â% thresholds, respectively, but these values between the two novel strains were 95.5â% and 99.5â%, respectively. On the basis of morphological and chemotaxonomic characteristics and the results of phylogenetic analyses, strains CY18T and CY8 represent a novel species of the genus Nocardia, for which the name Nocardia sputi sp. nov. is proposed. The type strain is CY18T (=GDMCC 1.3318T = JCM 33932T).
Subject(s)
Nocardia , Soil Microbiology , Humans , RNA, Ribosomal, 16S/genetics , Phylogeny , Base Composition , Sputum , Fatty Acids/chemistry , DNA, Bacterial/genetics , Bacterial Typing Techniques , Sequence Analysis, DNA , Phospholipids/chemistryABSTRACT
Four mesophilic actinobacteria (HY002T, HY442, HY366T and HY285) isolated from the faeces of bats collected in southern China were found to be strictly aerobic, non-motile, rod-shaped, oxidase-negative, Gram-stain-positive and catalase-positive. Strains HY002T and HY366T contained meso-diaminopimelic acid as the diagnostic diamino acid and MK-9(H2) the sole respiratory quinone. Arabinose, galactose and ribose were detected in the whole-cell hydrolysates of both type strains. The main cellular fatty acids (> 10.0%) of all strains were C16â:â0, C18â:â1 ω9c, 10-methyl-C18â:â0 and summed feature 3. Strains HY002T and HY366T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidyl inositol mannosides as the major polar lipids. The phylogenetic/phylogenomic analyses based on 16S rRNA gene and genomic sequence comparison revealed that the four strains belong to the genus Gordonia, most closely related to G. neofelifaecis NRRL B-59395T(98.2-98.3% sequence similarity) on the EzBioCloud database. The G+C contents of strains HY002T and HY366T based on genomic DNA were 66.5 and 66.9%, respectively. The DNA-DNA relatedness values between the two types strains and members of the genus Gordonia were far below 70â% (18.6-23.1â%). All genotypic and phenotypic data indicated that the four strains are representatives of two novel separate species, for which the names Gordonia zhenghanii sp. nov. and Gordonia liuliyuniae sp. nov. are proposed, with HY002T (=CGMCC 4â7757T=JCM 34â878T) and HY366T (=CGMCC 1â19146T=JCM 34â879T) as the respective type strains.
Subject(s)
Chiroptera , Animals , RNA, Ribosomal, 16S/genetics , Phylogeny , Base Composition , Phosphatidylethanolamines , Catalase/genetics , Diaminopimelic Acid/chemistry , Cardiolipins , Arabinose , Galactose , Ribose , Bacterial Typing Techniques , DNA, Bacterial/genetics , Fatty Acids/chemistry , Sequence Analysis, DNA , Phospholipids/chemistry , Nucleic Acid Hybridization , Feces , Phosphatidylinositols/analysis , Quinones , MannosidesABSTRACT
Six Gram-stain-positive, aerobic or facultative anaerobic, catalase-positive, urease- and oxidase-negative, rod-shaped bacteria (zg-ZUI157T/zg-ZUI40, zg-ZUI222T/zg-ZUI199 and zg-ZUI188T/ zg-ZUI168) were characterized by a polyphasic approach. Optimal growth of the six strains was observed at pH 7.0 and 28 °C. Phylogenetic analyses based on the 16S rRNA gene and 247 core genes revealed that they belong to genus Cellulomonas. The three type strains have low digital DNA-DNA hybridization (19.3-30.1%) and average nucleotide identity values (78.0-85.5%) with all available genomes in the genus Cellulomonas, and a DNA G+C content range of 73.0-74.6 mol%. The major fatty acids detected in strain pairs zg-ZUI157T/zg-ZUI40 and zg-ZUI 222T/zg-ZUI199 were C16:0, anteiso-C15:0 and anteiso A-C15:1, and C16:0, anteiso-C15:0, anteiso A-C15:1 and anteiso-C17:0 in strain pair zg-ZUI188T/zg-ZUI168. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides were the major polar lipids detected in the three novel species. MK-9(H4) was the predominant quinone detected in strains zg-ZUI222T (87.4â%) and zg-ZUI188T (91.4â%), and MK-9(H4) (49.1â%) and MK-8 (43.4â%) in strain zg-ZUI157T. The cell-wall sugars detected in the three novel species mainly contained rhamnose. The cell-wall peptidoglycan type of the three novel species was A4ß, with an inferred l-Orn-d-Asp interpeptide bridge for strains zg-ZUI157T and zg-ZUI222T, and l-Orn-d-Glu for strain zg-ZUI188T. Based on the results of the phenotypic, phylogenetic, genomic hybridization, average nucleotide identity and chemotaxonomic analyses, the six strains should be classified as belonging to three novel Cellulomonas species, for which the names Cellulomonas dongxiuzhuiae sp. nov. (zg-ZUI157T=GDMCC 1.2559T=KCTC 49678T), Cellulomonas wangleii sp. nov. (zg-ZUI222T=GDMCC 1.2501T=KCTC 49675T) and Cellulomonas fengjieae sp. nov. (zg-ZUI188T=GDMCC 1.2563T=KCTC 49674T) are proposed.
Subject(s)
Cellulomonas , Animals , RNA, Ribosomal, 16S/genetics , Phylogeny , Marmota , Catalase/genetics , Base Composition , Peptidoglycan/chemistry , Gastrointestinal Contents , Cardiolipins , Urease/genetics , Rhamnose , DNA, Bacterial/genetics , Bacterial Typing Techniques , Sequence Analysis, DNA , Fatty Acids/chemistry , Phosphatidylinositols , Nucleotides , Sugars , Quinones , MannosidesABSTRACT
Six Gram-stain-positive, aerobic and irregular-rod-shaped actinobacteria (ZJ1313T, ZJ1307, MC1495T, Y192, 603T and X2025) were isolated from the Qinghai-Tibet Plateau of China and were characterized using a polyphasic taxonomic method. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the six new strains formed three distinct clusters within the genus Nocardioides, and strains ZJ1313T and ZJ1307 were most closely related to N. solisilvae JCM 31492T (16S rRNA gene sequence similarity, 98.0â%), MC1495T and Y192 to N. houyundeii 78T (98.5â%), and 603T and X2025 to N. dokdonensis JCM 14815T (97.6â%). The digital DNA-DNA hybridization values of strains ZJ1313T, MC1495T and 603T among each other and with type strains of their closest relatives were all below the 70â% cut-off point, but values within each pair of new strains were all higher than the threshold. The major fatty acids of these strains were iso-C16â:â0, C17â:â1 ω8c or C18â:â1 ω9c. MK-8(H4) was the predominant respiratory menaquinone and ÊÊ-2,6-diaminopimelic acid was the diagnostic diamino acid. All the strains shared diphosphatidylglycerol (predominant), phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol as the common polar lipids, with minor difference in the types of unidentified phospholipids, glycolipids and lipids. The G+C contents based on genomic DNA of strains ZJ1313T, MC1495T and 603T were 72.5, 72.1 and 73.2 mol%, respectively. The above results suggested that strain pairs ZJ1313T/ZJ1307, MC1495T/Y192 and 603T/X2025 represent three new species of genus Nocardioides, for which the names Nocardioides ochotonae sp. nov. (ZJ1313T=GDMCC 4.177T=KCTC 49537T=JCM 34185T), Nocardioides campestrisoli sp. nov. (MC1495T=GDMCC 4.176T=KCTC 49536T=JCM 34307T) and Nocardioides pantholopis sp. nov. (603T=CGMCC 4.7510T=DSM 106494T) are proposed accordingly.
Subject(s)
Cardiolipins , Nocardioides , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Glycolipids , Phosphatidylcholines , Phosphatidylinositols , Phospholipids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/chemistryABSTRACT
Four novel bacterial strains (zg-ZUI122T/zg-ZUI10 and zg-ZUI227T/zg-ZUI100) were isolated from the intestinal contents of Marmota himalayana and characterized using a polyphasic approach. Cells were Gram-stain- and catalase-positive, urease- and oxidase-negative. Strains grew optimally at 28-30 °C, pH 7.0, with 0.5â% NaCl (w/v). A comparative analysis of 16S rRNA gene sequences revealed that strain pairs zg-ZUI122T/zg-ZUI10 and zg-ZUI227T/zg-ZUI100 belonged to the genus Arthrobacter and were most closely related to Arthrobacter citreus DSM 20133T, with similarities of 99.6 and 99.5â%, respectively. This was further confirmed by phylogenetic analyses based on the 16S rRNA gene and genome sequences. The digital DNA-DNA hybridization and average nucleotide identity values between the two new type strains (zg-ZUI122T and zg-ZUI227T) and other species in the genus Arthrobacter were 20.0-24.4/77.2-83.4% and 19.9-25.1/77.1-83.4%, all below the thresholds. The major cellular fatty acids detected in the two novel species included iso-C15â:â0 and anteiso-C15â:â0; the predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. MK-8(H2) (77.3%) was the predominant respiratory quinone detected in strain zg-ZUI122T, while MK-8(H2) (53.7%) and MK-9(H2) (46.3%) were detected in strain zg-ZUI227T. The shared cell-wall amino acids detected in the two novel species were alanine, glutamic acid and lysine; the shared whole cell wall sugars consisted of galactose, mannose and ribose. All these analyses concluded that these four strains represent two different novel species in the genus Arthrobacter, for which the names Arthrobacter sunyaminii sp. nov. (zg-ZUI122T = GDMCC 1.2502T = KCTC 49677T) and Arthrobacter jiangjiafuii sp. nov. (zg-ZUI227T = GDMCC 1.2500T = KCTC 49676T) are proposed.
Subject(s)
Arthrobacter/classification , Marmota/microbiology , Phylogeny , Animals , Arthrobacter/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Intestines/microbiology , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
In the present study, four bacterial strains, two (S-713T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531T and 1598) from leaves of dandelion collected on the Qinghai-Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713T/406 and S-531T/1598 form two independent branches belonging to the genus Nocardioides, and are closest to Nocardioides lianchengensis, Nocardioides dokdonensis, Nocardioides salarius, Nocardioides marinisabuli, Nocardioides psychrotolerans and Nocardioides szechwanensis. Although sharing MK8-(H4) as their major isoprenoid quinone, strains S-713T and S-531T contained C18â:â1 ω9c (24.64 and 16.34â%) and iso-C16â:â0 (9.74 and 29.38â%), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713T and S-531T were 4â207â844 bp (G+C content, 73.0 mol%) and 4â809â817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides, for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713T (=JCM 33698T=CGMCC 4.7660T) and S-531T (=JCM 33468T=CGMCC 4.7659T) as the respective type strains.
Subject(s)
Antelopes/microbiology , Nocardioides/classification , Phylogeny , Taraxacum/microbiology , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Feces/microbiology , Nocardioides/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , Plant Leaves/microbiology , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistryABSTRACT
Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141T and HF-106) was most closely related to Bacteroides xylanisolvens XB1AT (98.0-98.3â% similarity) and Bacteroides ovatus ATCC 8483T (97.3-97.5â%), whereas cluster II (strains HF-5287T and HF-5300) exhibited a similarity range of 96.8-97.0â% to Bacteroides finegoldii JCM 13345T, 96.7-96.9â% to Bacteroides faecis MAJ27T and 96.4-96.5â% to Bacteroides xylanisolvens XB1AT. The DNA G+C contents of type strains HF-5141T and HF-5287T were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C15â:â0 as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus Bacteroides. However, the average nucleotide identity and digital DNA-DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus Bacteroides. Therefore, strains HF-5141T and HF-5287T represent two novel species in the genus Bacteroides, for which the names Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. are proposed, with HF-5141T (=CGMCC 1.16787T=GDMCC 1.1591T=JCM 33480T) and HF-5287T (=CGMCC 1.16724T=GDMCC 1.1590T=JCM 33481T) as type strains.
Subject(s)
Bacteroides/classification , Feces/microbiology , Phylogeny , Bacterial Typing Techniques , Bacteroides/isolation & purification , Base Composition , China , DNA, Bacterial/genetics , Fatty Acids/chemistry , Humans , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/chemistryABSTRACT
Four Gram-stain-positive, non-motile and asporous bacilli (strains ZJ-599T, ZJ-621, MC1420T and MC1482), isolated from animal tissue and environmental samples collected on the Qinghai-Tibet Plateau, PR China, were taxonomically characterized. Based on the results of 16S rRNA gene sequence analyses, the closest relatives of strains ZJ-599T and ZJ-621 were Corynebacterium endometrii LMM-1653T (97.5â%), Corynebacterium phocae M408/89/1T (96.5â%) and Corynebacterium flavescens OJ8T (96.3â%), whereas strains MC1420T and MC1482 were closest to Corynebacterium sanguinis CCUG 58655T (98.9â%), Corynebacterium mycetoides DSM 20632T (98.4â%) and Corynebacterium lipophiloflavum DSM 44291T (97.9â%). The results of rpoB gene sequence similarity analysis indicated that C. phocae M408/89/1T and C. sanguinis CCUG 58655T were closest to strains ZJ-599T/ZJ-621 (83.5â%) and MC1420T/MC1482 (91.8â%), respectively. The two novel type strains shared a similarity of 95.2â% in 16S rRNA and 81.3â% in rpoB gene sequences. The TAP-PCR DNA fingerprint and MALDI-TOF MS spectrum patterns clearly differentiated the novel isolates within and between each pair of strains. Strain ZJ-599T had 21.9-22.4â% digital DNA-DNA hybridization (dDDH) scores with C. endometrii LMM-1653T, C. phocae M408/89/1T and C. flavescens OJ8T, and 72.3-72.9â% of average nucleotide identity (ANI) with them. Similarly, strain MC1420T had 22.9-23.7â% dDDH values with C. sanguinis CCUG 58655T, C. mycetoides DSM 20632T and C. lipophiloflavum DSM 44291T, and 80.4-81.3â% ANI scores with them. Strain ZJ-599T had a 23.1â% dDDH value and 70.5â% ANI score with strain MC1420T, both below the corresponding thresholds for species delineation. Strains ZJ-599T and MC1420T both contain mycolic acids and have MK-8(H2) and MK-9(H2) as the predominant respiratory quinones, meso-diaminopimelic acid as the diagnostic diamino acid, and C18â:â1 ω9c as the main fatty acid. C17â:â1 ω8c and C15â:â1 ω8c were predominant in strain ZJ-599T in contrast to C17â:â1 ω7c being predominant in strain MC1420T. The main polar lipids in strain ZJ-599T were diphosphatidylglycerol, phosphatidylinositol and one unidentified glycolipid, while strain MC1420T had diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid as the major components. Since the two pairs of novel strains (ZJ-599T/ZJ-621, MC1420T/MC1482) distinctly differ from each other and from their nearest relatives, two novel species of the genus Corynebacterium are proposed, namely Corynebacterium lizhenjunii (type strain ZJ-599T=GDMCC 1.1779T=JCM 34341T) and Corynebacterium qintianiae (type strain MC1420T=GDMCC 1.1783T=JCM 34340T), respectively.
Subject(s)
Corynebacterium/classification , Lung/microbiology , Marmota/microbiology , Phylogeny , Respiratory System/microbiology , Sheep/microbiology , Animals , Bacterial Typing Techniques , Base Composition , China , Corynebacterium/isolation & purification , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Vitamin K 2/chemistryABSTRACT
Four mesophilic and Gram-stain-positive strains (zg-686T/zg-691 and HY186T/HY189) isolated from Tibetan Plateau wildlife (PR China) belong to the genus Gordonia according to 16S rRNA gene and genomic sequence-based phylogenetic/genomic results. They have a DNA G+C content range of 67.4-68.3 mol% and low DNA relatedness (19.2-27.6â%) with all available genomes in the genus Gordonia. Strains zg-686T/zg-691 and HY186T/HY189 had C18â:â1ω9c, C18â:â0 10-methyl, C16â:â1 ω7c/C16â:â1ω6c and C16â:â0 as major cellular fatty acids. The polar lipids detected in strains zg-686T and HY186T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl inositol mannoside and phosphatidylinositol. The respiratory quinones comprised MK8(H2) (10.8â%) and MK9(H2) (89.2â%) for strain zg-686T, and MK6 (7.7â%), MK8(H2) (8.4â%), MK8(H4) (3.1â%) and MK9(H2) (80.8â%) for strain HY186T. Optimal growth conditions were pH 7.0, 35-37 °C and 0.5-1.5â% NaCl (w/v) for strains pair zg-686T/zg-691, and pH 7.0, 28 °C and 1.5â% (w/v) NaCl for strains pair HY186T/HY189. Based on these genotypic and phenotypic results, these four strains could be classified as two different novel species in the genus Gordonia, for which the names Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov. are proposed. The type strains are zg-686T (=GDMCC 1.1715T =JCM 33890T) and HY186T (=CGMCC 4.7607T =JCM 33466T), respectively.
Subject(s)
Animals, Wild/microbiology , Gordonia Bacterium/classification , Phylogeny , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Gordonia Bacterium/isolation & purification , Nucleic Acid Hybridization , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Tibet , Vitamin K 2/chemistryABSTRACT
Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60T, HY54, HY82T and HY89) were isolated from bat faeces of Hipposideros and Rousettus species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to Microbacterium agarici CGMCC 1.12260T (97.6-97.7â% similarity), Microbacterium humi JCM 18706T (97.3-97.5â%) and Microbacterium lindanitolerans JCM 30493T (97.3-97.4 %). The 16S rRNA gene sequence similarity was 98.3â% between strains HY60T and HY82T, and identical within strain pairs HY60T/HY54 and HY82T/HY89. The DNA G+C contents of strains HY60T and HY82T were 61.9 and 63.3 mol%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70â% and 95-96â% thresholds for species delimitation, respectively. All four novel strains contained anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0 as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus Microbacterium, for which the names Microbacterium chengjingii sp. nov. [type strain HY60T (=CGMCC 1.17468T=GDMCC 1.1951T=KACC 22102T)] and Microbacterium fandaimingii sp. nov. [type strain HY82T (=CGMCC 1.17469T=GDMCC 1.1949T=KACC 22101T)] are proposed, respectively.