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Volume 73,
Issue 9,
2023
Volume 73, Issue 9, 2023
- Validation Lists
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- Notification Lists
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- New Taxa
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Reclassification of Streptomyces griseostramineus as a synonym of Streptomyces griseomycini based on a polyphasic taxonomic approach
More LessIn the present work, the taxonomic relationship between Streptomyces griseomycini and Streptomyces griseostramineus was reevaluated by a comprehensive comparison of phenotypic, chemotaxonomic and genomic characteristics, as well as phylogeny. Phylogenetic analysis based on 16S rRNA gene sequences and whole-genome sequences indicated that Streptomyces griseostramineus JCM 4385T was clustered together with Streptomyces griseomycini JCM 4382T, suggesting they were closely related to each other. However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between their genomes were 99.7 and 97.5 %, respectively, much larger than the recommended threshold values of 96.7 % ANI and 70 % dDDH for Streptomyces species delineation. In addition, the morphological, cultural, physio-biochemical and chemotaxonomic features of these two species further demonstrated that they belonged to the same genome species. Based on the above data and the principle of priority in nomenclature, it is proposed that S. griseostramineus (Preobrazhenskaya et al. 1957) Pridham et al. 1958 (Approved Lists 1980) is a later heterotypic synonym of S. griseomycini (Preobrazhenskaya et al. 1957) Pridham et al. 1958 (Approved Lists 1980).
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- Actinomycetota
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Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant
In 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615T (Tom532T) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values <93 % and <50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter . In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532T = CFBP 8615T = ICMP 22100T as type strain.
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Streptomyces fuscus sp. nov., a brown-black pigment producing actinomycete isolated from dry mudflat sand
A novel Gram-stain-positive, aerobic actinobacterial strain, designated GXMU-J15T, was isolated from dry mudflat sand. A polyphasic approach was employed for its taxonomic characterization. The strain developed extensively branched yellowish white to light yellow substrate mycelia and white aerial mycelia, and produced smooth cylindrical spores in a loose straight spore chain on International Streptomyces Project 2–7 agar media. Strain GXMU-J15T grew at 20–50 °C (optimum, 35 °C), at pH 5.0–8.0 (optimum, pH 7.0) and in the presence of 0–8 % (w/v) NaCl. Analysis of 16S rRNA gene sequences indicated that strain GXMU-J15T represents a member of the genus Streptomyces . Strain GXMU-J15T showed the highest 16S rRNA gene sequence similarity to Streptomyces lusitanus CGMCC 4.1745T (99.1 %) and Streptomyces thermocarboxydus CGMCC 4.1883T (98.8 %). Phylogenetic tree analysis based on multilocus sequence analysis (MLSA) and whole genome sequence construction revealed that strain GXMU-J15T was most closely related to Streptomyces cupreus PSKA01T, Streptomyces cinnabarinus DSM 40467T and Streptomyces davaonensis JCM 4913T. The MLSA and genome-to-genome distances between strain GXMU-J15T and its relatives were 0.0418, 0.0443 and 0.0485 and 0.1237, 0.1188 and 0.1179, respectively. The results of orthologous average nucleotide identity and digital DNA–DNA hybridization analysis corroborated the results of the MLSA and whole genome sequence evolution analysis, indicating that the novel isolate represents a distinct species of the genus Streptomyces . The whole-cell sugars of strain GXMU-J15T were xylose, glucose and galactose. The characteristic diamino acid in the cell-wall hydrolysate was ll-diaminopimelic acid. The lipids contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol, phosphatidylglycerides, phosphatidylcholine, two phospholipids of an unknown structure containing glucosamine, one unknown phospholipid and two unknown lipids. The major cellular fatty acid components were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The main respiratory quinone types were MK-9(H6) and MK-9(H8). The whole genome size of strain GXMU-J15T was 8.68 Mbp, with 71.23 mol% G+C content. Genomic analysis indicated that strain GXMU-J15T has the potential to synthesize polyketides, terpenes and a series of important antibiotics besides the gene cluster for melanin synthesis. Based on these genotypic and phenotypic data, strain GXMU-J15T is proposed to represent a new species of the genus Streptomyces named Streptomyces fuscus sp. nov. The type strain is GXMU-J15T (=MCCC 1K08211T=JCM 35917T).
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Microbacterium plantarum sp. nov. and Microbacterium thalli sp. nov., two endophytic metal-resistant bacteria isolated from Sphaeralcea angustifolia (Cav.) G. Don and Prosopis laevigata (Humb. et Bonpl. ex Willd) M.C. Johnston
Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA–DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).
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Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora
More LessTwo novel Gram-positive bacteria designated as strains STR2T and STR3T were isolated from the rhizosphere of a Pinus densiflora sample collected from Goyang-si, Republic of Korea. Strains STR2T and STR3T were aerobic, rod shaped, non-sporulated, catalase negative, oxidase negative and non-motile bacteria. They grew at 15–37 °C (optimum, 25–30 °C), at pH 6.0–11.0 (optimum, pH 7.0) and in the presence of 0–2% NaCl (optimum, 0 %, w/v). The chemotaxonomic and morphological characteristics of the novel strains were consistent with those of the members of Nocardioides . The phylogenetic analysis of the 16S rRNA gene sequences revealed that STR2T was closely related to N. cavernae YIM A1136T (99.3 %) and N. flavus Y4T (99.1 %), and STR3T was closely related to N. exalbidus DSM 22017T (99.0 %), N. baculatus G10T (98.8 %) and N. hwasunensis HFW-21T (98.7 %). The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of STR2T and STR3T with the most closely related strains that have publicly available whole genomes were 83.1–89.8 %, 80.9–89.6% and 26.2–39.1 %, respectively. The cell-wall peptidoglycan of strain STR2T and STR3T contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids in STR2T and STR3T were iso-C16 : 0 and C17 : 1 ω8c, and the predominant quinone was MK-8(H4). Their polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and other polar lipids. The draft genome sequences showed that the genomic DNA G+C content of STR2T and STR3T were both 72.2 mol%. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that STR2T and STR3T could represent novel Nocardioides species. Their proposed names were as follows: Nocardioides pini sp. nov. for strain STR2T (=KACC 22784T=TBRC 16336T) and Nocardioides pinisoli sp. nov. for strain STR3T (= KACC 22785T=TBRC 16337T).
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Streptomyces silvisoli sp. nov., a polyene producer, and Streptomyces tropicalis sp. nov., two novel actinobacterial species from peat swamp forests in Thailand
More LessTwo novel actinobacterial strains, designated RB6PN23T and K1PA1T, were isolated from peat swamp soil samples in Thailand and characterized using a polyphasic taxonomic approach. The strains were filamentous Gram-stain-positive bacteria containing ll -diaminopimelic acid in their whole-cell hydrolysates. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strain RB6PN23T was most closely related to Streptomyces rubrisoli (99.1 % sequence similarity) and Streptomyces ferralitis (98.5%), while strain K1PA1T showed 98.8 and 98.7% sequence similarities to Streptomyces coacervatus and Streptomyces griseoruber , respectively. However, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values were below the species-level thresholds (95–96 % ANI and 70 % dDDH). The genomes of strains RB6PN23T and K1PA1T were estimated to be 7.88 Mbp and 7.39 Mbp in size, respectively, with DNA G+C contents of 70.2 and 73.2 mol%. Moreover, strains RB6PN23T and K1PA1T encode 37 and 24 putative biosynthetic gene clusters, respectively, and in silico analysis revealed that these new species have a high potential to produce unique natural products. Genotypic and phenotypic characteristics confirmed that strains RB6PN23T and K1PA1T represented two novel species in the genus Streptomyces . The names proposed for these strains are Streptomyces silvisoli sp. nov. (type strain RB6PN23T=TBRC 17040T=NBRC 116113T) and Streptomyces tropicalis sp. nov. (type strain K1PA1T=TBRC 17041T=NBRC 116114T). Additionally, a giant linear polyene compound, neotetrafibricin A, exhibiting antifungal activity in strain RB6PN23T, was identified through HPLC and quadrupole time-of-flight MS analysis. The crude extract from the culture broth of strain RB6PN23T exhibited strong antifungal activity against Fusarium verticillioides, Fusarium fujikuroi and Bipolaris zeicola. This finding suggests that strain RB6PN23T could be a promising candidate for biological control of fungal diseases.
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- Archaea
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Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., halophilic archaea isolated from salt lakes and soda lakes
Shun Tan, Mu Cheng, Xin-Xin Li, Yao Hu, Xue Ma, Jing Hou and Heng-Lin CuiFive halophilic archaeal strains (AGai3-5T, KZCA101T, CGA3T, WLHS1T and WLHSJ1T) were isolated from salt lakes and soda lakes in PR China. These strains had low 16S rRNA gene similarities (91.3–96.0 %) to closely related species of the family Natrialbaceae and may represent a new genus of the family. Phylogenetic and phylogenomic analyses revealed that these strains formed a distinct clade, separate from the nearby genera Natronobiforma and Saliphagus . The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity (AAI) values among these five strains and the current members of the family Natrialbaceae were 72–90, 20–42 and 62–91 %, respectively, clearly below the threshold values for species demarcation. According to the critical value of AAI (≤76 %) proposed to differentiate genera within the family Natrialbaceae , it was further indicated that these strains represented a novel genus within the family. These strains could be distinguished from the related genera according to differential phenotypic characteristics. The major lipids of these strains were phosphatidic acid (PA), phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, mannosyl glucosyl diether (DGD-PA), sulphated DGD-1 (S-DGD-PA) and sulphated galactosyl mannosyl glucosyl diether. The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains AGai3-5T (=CGMCC 1.16078T=JCM 33549T), KZCA101T (=CGMCC 1.17431T=JCM 35074T), CGA3T (=CGMCC 1.17463T=JCM 34318T), WLHS1T (=CGMCC 1.13780T=JCM 33562T) and WLHSJ1T (=CGMCC 1.13784T=JCM 33563T) represent five novel species of a new genus within the family Natrialbaceae , named Natronosalvus halobius gen. nov., sp. nov., Natronosalvus caseinilyticus sp. nov., Natronosalvus vescus sp. nov., Natronosalvus rutilus sp. nov. and Natronosalvus amylolyticus sp. nov., respectively.
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- Bacteroidota
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Five novel Hymenobacter species isolated from air: Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov.
Five Hymenobacter strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus Hymenobacter . Digital DNA–DNA hybridization values and average nucleotide identities values for species delineation (70 and 95–96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus Hymenobacter for which we propose the names, Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov., with strains 5116 S-3T (=KACC 21925T=JCM 35216T), 5116 S-27T (=KACC 21926T=JCM 35217T), 5413 J-13T (=KACC 21928T=JCM 35219T), 5516 S-25T (=KACC 21931T=JCM 35222T) and 5420 S-77T (=KACC 21932T=JCM 35223T) as the type strains, respectively.
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Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China
Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and ‘ Chryseobacterium formosus ’ CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and ‘ C. formosus ’ CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium , for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).
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Kaistella polysaccharea sp. nov., isolated from Antarctic intertidal sediment produces a novel extracellular polymeric substance
More LessAn exopolysaccharide-producing bacterial strain GW4-15T, belonging to the genus Kaistella , was isolated from intertidal sediment from King George Island, Antarctic. The strain was Gram-stain-negative, aerobic, rod-shaped, non-motile and yellow-pigmented. The strain was able to grow in the presence of 0–2 % (w/v) NaCl (optimum, 0 %), at 4–30 °C (optimum, 20–28 °C) and at pH 5.0–10.0 (optimum, pH 8.0). A phylogenetic tree based on 16S rRNA gene sequences showed that strain GW4-15T formed a lineage within the genus Kaistella with the closest phylogenetic neighbours Kaistella carnis NCTC 13525T (98.3 %), Kaistella gelatinilytica G5-32T (97.7 %), Kaistella antarctica LMG 24720T (97.4 %) and Kaistella yonginensis HMD1043T (96.9 %). Digital DNA–DNA hybridization values of strain GW4-15T with K. carnis NCTC 13525T, K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 22.8, 22.0, 21.7 and 21.6 %, respectively. The average nucleotide identity values between strain GW4-15T and K. carnis NCTC 13525T , K. antarctica LMG 24720T, K. gelatinilytica G5-32T and K. yonginensis HMD1043T were 79.3, 78.6, 77.5 and 77.2 %, respectively. The G+C content of the genome was 36.2 mol%. The major phospholipids were phosphatidylethanolamine and aminophospholipid. The predominant menaquinone was MK-6. The major fatty acids were anteiso-C15 : 0 (28.7 %), iso-C16 : 0 3-OH (15.7 %), iso-C16 : 0 H (10.0 %), iso-C16 : 0 (5.4 %), summed feature 9 (comprising iso-C17 : 1 ω9c and/or 10-methyl C16 : 0; 5.2 %) and iso-C15 : 0 (5.1 %). The monosaccharide composition of the new type of extracellular polymeric of GW4-15T was Glc, GalN, GlcN, Rha, Man and Gal with a molar ratio of 3.14 : 3.83 : 8.38 : 5.16 : 1 : 2.82. Based on phenotypic, phylogenetic and genotypic data, a novel species, Kaistella polysaccharea sp. nov., is proposed with the type strain GW4-15T (=CGMCC 1.19368T=KCTC 92753T).
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Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment
More LessTwo novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus Winogradskyella and the phylogenetic similarities to their closest relative, Winogradskyella aquimaris , were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03–OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus Winogradskyella , for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.
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Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov., isolated from tree barks
More LessTwo Gram-staining-negative, aerobic, rod-shaped, bacteria that formed pale-pinkish colonies, designated HMF7056T and HMF7647T were isolated from Ginkgo (Ginkgo biloba) and Korean cornel dogwood (Cornus offcinalis), respectively. Phylogenetic analyses based on sequences of 16S rRNA genes and 92 core genes indicated that two strains represent novel species within the family Sphingobacteriaceae . HMF7056T and HMF7647T showed high 16S rRNA sequence similarities to Daejeonella lutea N7d-4T (93.9 % and 95.7 %, respectively). The genomes of HMF7056T and HMF7647T were 5.2 and 4.8 Mbp in size with 50.5 and 42.5 % DNA G+C contents, respectively. Menaquinone-7 was the main respiratory quinone. The predominant fatty acids of HMF7056T and HMF7647T were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipid of both strains was phosphatidylethanolamine. The average nucleotide identity and digital DNA–DNA hybridization values of HMF7056T, HMF7647T and related species were well below the threshold limit for species delineation (<68.9 and <20.8 %, respectively). The average amino acid identity values of HMF7056T, HMF7647T with related type strains were below 67.8 and 68.3 %, respectively. On the basis of the results of phenotypic and phylogenetic characterizations, the two strains are considered to represent members of a novel genus of the family Sphingobacteriaceae , for which the names Hufsiella ginkgonis gen. nov., sp. nov. and Hufsiella arboris sp. nov. are proposed. The type strains are HMF7056T (=KCTC 72282T =NBRC 113964T) and HMF7647T (=KCTC 72283T =NBRC 113965T), respectively.
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Muricauda meishanensis sp. nov., a facultative anaerobic bacterium belonging to the family Flavobacteriaceae isolated from marine sediment in the East China Sea
A facultative anaerobic, Gram-strain-negative, rod-shaped bacterium (strain NBU2970T) was isolated by using modified ichip in situ cultivation from a marine sediment sample collected from Meishan Island in the East China Sea. Strain NBU2970T grew optimally at 37 °C, with a NaCl concentration of 2.0 % (w/v) and at pH 7.0. The 16S rRNA gene sequence analyses revealed that strain NBU2970T represents a novel species with the genus Muricauda , sharing highest sequence identities with Muricauda beolgyonensis BB-My12T (96.1 %), Muricauda alvinocaridis SCR12T (96.0 %), Muricauda taeanensis 105T (96.0 %) and Muricauda ruestringensis B1T (95.6 %). Phylogenetic analyses also indicated that strain NBU2970T clustered with the genus Muricauda and was closely related to M. beolgyonensis BB-My12T and M. ruestringensis B1T. The draft genome sequence of strain NBU2970T was composed of six contigs with a size of 3.2 Mbp, containing 3045 protein-coding genes and 38 RNA genes. The DNA G+C content was 43.8 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NBU2970T and related species of the genus Muricauda were well below the threshold limit for prokaryotic species delineation. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The only respiratory quinone was MK-6. The major polar lipid was phosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU2970T is considered to be a representative of a novel species in the genus Muricauda , for which the name Muricauda meishanensis sp. nov. is proposed. The type strain is NBU2970T (=KCTC 82915T=MCCC 1K06394T).
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- Bacillota
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Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov.
Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14T, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14T showed the highest 16S rRNA gene sequence similarity to Sellimonas monacensis Cla-CZ-80T (97.5 %) and ‘Lachnoclostridium phocaeense’ Marseille-P3177T (97.2 %). Strain 12BBH14T was also closely related to Eubacterium sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14T, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with Eubacterium sp. c-25. Near this monophyletic cluster, S. monacensis Cla-CZ-80T and ‘L. phocaeense’ Marseille-P3177T formed a cluster and did not form a cluster with other Sellimonas species. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14T, 9CFEGH4, 10CPCBH12 and Eubacterium sp. c-25 were higher than the cut-off values of species demarcation (>88 % dDDH and >98 % ANI), indicating that these four strains are the same species. On the other hand, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<29 % dDDH and <76 % ANI). Moreover, the average amino acid identity values among these strains were higher than the genus boundary. These results indicate that the isolates should be considered to belong to a new genus of the family Lachnospiraceae . Based on the collected data, strains 12BBH14T, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name Claveliimonas bilis gen. nov., sp. nov. is proposed. The type strain of C. bilis is 12BBH14T (=JCM 35899T=DSM 115701T). Eubacterium sp. c-25 belongs to C. bilis. In addition, S. monacensis is transferred to the genus Claveliimonas as Claveliimonas monacensis comb. nov.
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Peptoniphilus equinus sp. nov., a novel Gram-stain-positive anaerobic coccus isolated from the faeces of a thoroughbred racehorse
A novel, anaerobic, Gram-stain-positive coccoid strain, CBA3646T, was isolated from the faeces of a thoroughbred racehorse. Phylogenetic analysis based on 16S rRNA gene sequencing yielded results indicative of CBA3646T representing a member of the genus Peptoniphilus , with the species most closely related to it being Peptoniphilus asaccharolyticus DSM 20463T, with a similarity of 94.79 %. DNA–DNA relatedness and average nucleotide identity values between CBA3646T and P. asaccharolyticus DSM 20463T were 21.4 and 67.6 %, respectively. CBA3646T has a circular chromosomal genome of 1 709 189 bp (45.5 mol% DNA G+C content), containing 1652 genes in total, 1584 predicted protein-coding genes, 3 complete rRNA loci and 47 tRNA genes. The cells were non-motile diplococci, catalase-positive and oxidase-negative. Growth of CBA3646T was observed at 20–40 °C (optimal temperature, 35 °C) and in the presence of 0–4 % (w/v) NaCl (optimum concentration, 1 %). The major fatty acids (>10 %) of CBA3646T were C16 : 0, C18 : 1ω9c and C18 : 1ω9c dimethyl acetal, with its major polar lipids being diphosphatidylglycerol and phosphatidylglycerol. The elucidated phylogenetic, physiological, chemotaxonomic and molecular properties are indicative of strain CBA3646T representing a novel species of the genus Peptoniphilus , or which the name Peptoniphilus equinus sp. nov. is proposed. The type strain is CBA3646T (= KACC 22890T = JCM 35845T).
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Taxonomic considerations on Aerococcus urinae with proposal of subdivision into Aerococcus urinae, Aerococcus tenax sp. nov., Aerococcus mictus sp. nov., and Aerococcus loyolae sp. nov
Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as Aerococcus urinae , an emerging uropathogen, discriminates at least six unique genomic taxa. The whole genome analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification and phylogenetic organization of Aerococcus species. The newly described species can be differentiated by matrix-assisted laser desorption ionization time-of-flight analysis of protein signatures. We propose the emendation of the description of A. urinae (type strain ATCC 51268T = CCUG 34223T=NCFB 2893) and the names of Aerococcus tenax sp. nov. (ATCC TSD-302T = DSM 115700T = CCUG 76531T=NR-58630T), Aerococcus mictus sp. nov. (ATCC TSD-301T = DSM 115699T = CCUG 76532T=NR-58629T), and Aerococcus loyolae sp. nov. (ATCC TSD-300T = DSM 115698T = CCUG 76533T=NR-58628T) for three of the newly identified genomic taxa.
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- Other Bacteria
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Methylacidiphilum kamchatkense gen. nov., sp. nov., an extremely acidophilic and moderately thermophilic methanotroph belonging to the phylum Verrucomicrobiota
More LessThe thermo-acidophilic aerobic methanotrophic Verrucomicrobia bacterium, designated strain Kam1T was isolated from an acidic geothermal mud spring in Kamchatka, Russia. Kam1T is Gram-stain-negative, with non-motile cells and non-spore-forming rods, and a diameter of 0.45–0.65 µm and length of 0.8–1.0 µm. Its growth is optimal at the temperature of 55 °C (range, 37–60 °C) and pH of 2.5 (range, pH 1–6), and its maximal growth rate is ~0.11 h−1 (doubling time ~6.3 h). Its cell wall contains peptidoglycan with meso-diaminopimelic acid. In addition to growing on methane and methanol, strain Kam1T grows on acetone and 2-propanol. Phylogenetically, it forms a distinct group together with other Methylacidiphilum strains and with the candidate genus Methylacidimicrobium as a sister group. These findings support the classification of the strain Kam1T as a representative of a novel species and genus of the phylum Verrucomicrobiota . For this strain, we propose the name Methylacidiphilum kamchatkense sp. nov. as the type species within Methylacidiphilum gen. nov. Strain Kam1T (JCM 30608T=KCTC 4682T) is the type strain.
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Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils
Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T, W786T, Red222T, Red802T, Red803T, and Red804T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T, Red802T, Red803T, and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains. The former four strains shared 97.95–99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix , whereas the latter two strains 94.86–95.49% similarities. The average amino acid identity of strains W79T and W786T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79T, W786T, Red222T, Red803T, and Red804T) except for strain Red802T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota / Holophagae / Holophagales / Holophagaceae , comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.
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