- Volume 73, Issue 3, 2023
Volume 73, Issue 3, 2023
- New Taxa
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- Bacteroidota
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Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov., isolated from marine sediment
More LessTwo Gram-stain-negative, strictly aerobic, chemoheterotrophic, short-rod-shaped and non-motile strains, forming yellow colonies and designated F47161T and F64183T, were isolated from marine sediment of Xiaoshi Island, Wei Hai, PR China. Strain F47161T grew at 15–37 °C (optimally at 30 °C) and pH 6.0–9.0 (optimally at pH 7.5) and in the presence of 1–9 % (w/v) NaCl (optimally at 3 %). Strain F64183T grew at 10–37 °C (optimally at 30 °C) and pH 6.0–8.5 (optimally at pH 7.0) and in the presence of 1–8 % (w/v) NaCl (optimally at 3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that F47161T and F64183T were related to members of the genus Aequorivita . The strains shared 97.4 % 16S rRNA gene sequence similarity to each other. F47161T and F64183T shared highest 16S rRNA gene sequence similarity to Aequorivita sinensis JCM 19789T, and the values were 97.5 % and 98.4 %, respectively. The predominant cellular fatty acids of both F64183T and F47161T were iso-C15 : 0 and iso-C17 : 0 3-OH, but the predominant fatty acids of F47161T also included anteiso-C15 : 0. The sole respiratory quinone of F47161T and F64183T was menaquinone 6 (MK-6), consistent with that observed for all related strains. Between F47161T and F64183T, the average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values were 75.8 % and 20.5 %, respectively, and between the novel isolates (F47161T and F64183T) and A. sinensis JCM 19789T they were 76.0 % and 94.2 % and 20.6 % and 57.1 %, respectively. The genomic DNA G+C contents of F47161T and F64183T was 37.3 % and 34.5 %, respectively. The polar lipid profiles of F47161T and F64183T contained phosphatidylethanolamine, two aminolipids, one glycolipid, one phosphoglycolipid and two unidentified polar lipids. Differential phenotypic and genotypic characteristics of the two strains indicated that the two strains should be classified as representing two novel species of the genus Aequorivita, for which the names Aequorivita vitellina sp. nov. and Aequorivita xiaoshiensis sp. nov. are proposed. The type strains are F47161T (=MCCC 1H00509T=KCTC 92017T) and F64183T (=MCCC 1H00507T=KCTC 92016T), respectively.
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- Bacillota
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Insulambacter thermoxylanivorax sp. nov., a thermophilic xylanolytic bacterium isolated from compost
We isolated and analysed a Gram-negative, facultatively thermophilic, xylan-degrading bacterium that we designated as strain DA-C8T. The strain was isolated from compost from Ishigaki Island, Japan, by enrichment culturing using beech wood xylan as the sole carbon source. The strain showed high xylan degradation ability under anaerobic growth conditions. The isolate grew at 37–60 °C (optimum, 55 °C) and pH 4.0–11.0 (optimum, pH 9.0). As well as xylan, strain DA-C8T could use polysaccharides such as arabinoxylan and galactan as carbon sources. Comparison of 16S rRNA gene sequences indicated that strain DA-C8T was most closely related to Paenibacillus cisolokensis LC2-13AT (93.9 %) and Paenibacillus chitinolyticus HSCC596 (93.5 %). In phylogenetic analysis, strain DA-C8T belonged to the same lineage as Xylanibacillus composti K13T (92.5 %), but there was less statistical support for branching (70 %). Digital DNA–DNA hybridization, average nucleotide identity values and average amino acid sequence identity between strain DA-C8T and P. cisolokensis LC2-13AT were 21.8, 68.3 and 58.2 %, respectively. Those between strain DA-C8T and X. composti K13 were 23.7, 67.7 and 57.6 %, respectively. The whole-genome DNA G+C content of strain DA-C8T was 52.3 mol%. The major cellular fatty acids were C16 : 0 (42.9 %), anteiso-C15 : 0 (20.0 %) and anteiso-C17 : 0 (16.7 %), the major quinone was menaquinone 7, and the major polar lipids were unidentified glycolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, a novel genus is proposed—Insulambacter gen. nov.—for the novel species Insulambacter thermoxylanivorax sp. nov. The type strain is DA-C8T (=JCM 34211T=DSM 111723T).
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Crassaminicella indica sp. nov., a novel thermophilic anaerobic bacterium isolated from a deep-sea hydrothermal vent
A novel moderately thermophilic heterotrophic bacterium, designated strain 143-21T, was isolated from a deep-sea hydrothermal chimney sample collected from the Central Indian Ridge at a depth of 2 440 m. Phylogenetic analysis indicated that strain 143-21T belongs to the genus Crassaminicella . It was most closely related to Crassaminicella thermophila SY095T (96.79 % 16S rRNA gene sequence similarity) and Crassaminicella profunda Ra1766HT (96.52 %). Genomic analysis showed that strain 143-21T shares 79.79–84.45 % average nucleotide identity and 23.50–29.20 % digital DNA–DNA hybridization with the species of the genus Crassaminicella , respectively. Cells were rod-shaped, non-motile, Gram-positive-staining. Terminal endospores were observed in stationary-phase cells when strain 143-21T was grown on Thermococcales rich medium. Strain 143-21T was able to grow at 30–60 °C (optimum, 50 °C), pH 6.5–8.5 (optimum, pH 7.0) and in 1.0–7.0 % NaCl (w/v; optimum 2.0 %, w/v). Strain 143-21T utilized fructose, glucose, maltose, mannose, ribose, N-acetyl-d-(+)-glucosamine and casamino acids, as well as amino acids including glutamate, lysine, histidine and cysteine. The main fermentation products from glucose were acetate (2.07 mM), H2 and CO2. It did not reduce elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe (III). The predominant cellular fatty acids were C14 : 0 (48.8 %), C16 : 0 (12.9 %), and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 10.2 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, as well as two unidentified phospholipids and four unidentified aminolipids. No respiratory quinones were detected. Based on its phylogenetic analysis and physiological characteristics, strain 143-21T is considered to represent a novel species of the genus Crassaminicella , for which the name Crassaminicella indica sp. nov. is proposed. The type strain is strain 143-21T (=DSM 114408T= MCCC 1K06400T).
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Ligilactobacillus ubinensis sp. nov., a novel species isolated from the wild ferment of a durian fruit (Durio zibethinus)
A Gram-stain-positive, rod-shaped, non-spore-forming, catalase-negative, urease-negative, homofermentative and facultatively anaerobic strain, named WILCCON 0076T, was isolated from a wild ferment of pieces of a ‘Kampung’ durian fruit collected on the island of Ubin (Pulau Ubin), Singapore. The durian had fallen to the ground from a durian tree (Durio zibethinus), on which a group of long-tailed macaques had been observed picking and eating the fruits. Comparative analyses of 16S rRNA gene sequences indicated that WILCCON 0076T potentially represented a novel species within the genus Ligilactobacillus , with the most closely related type strain being Ligilactobacillus agilis DSM 20509T (16S rRNA gene sequence similarity of 97.2 %). Average nucleotide identity and digital DNA–DNA hybridization prediction values were only 86.0% and 18.9 %, respectively. On the basis of the results of a polyphasic approach that included phylogenomic, chemotaxonomic and morphological analyses, we propose a novel species with the name Ligilactobacillus ubinensis sp. nov. (type strain WILCCON 0076T=DSM 114293T=LMG 32698T).
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Chordicoccus furentiruminis, gen. nov., sp. nov., a novel succinic acid producing bacterium isolated from a steer on a high grain diet
More LessThis study presents MP1D12T (=NRRL B-67553T=NCTC 14480T), an isolate from the ruminal content of an Angus steer fed a high grain diet. Phenotypic and genotypic traits of the isolate were explored. MP1D12T was found to be a strictly anaerobic, catalase-negative, oxidase-negative, coccoid bacterium that frequently grows in chains. Analysis of metabolic products as a result of carbohydrate fermentation showed succinic acid as the major organic acid produced with lactic acid and acetic acid as minor products. Phylogenetic analysis of MP1D12T based on 16S rRNA nucleotide sequence and amino acid sequences from the whole genome presents a divergent lineage from other members in the family Lachnospiraceae . 16S rRNA sequence comparison, whole genome average nucleotide identity digital DNA–DNA hybridization and average amino acid identity results suggest that MP1D12T represents a novel species in a novel genus within the family Lachnospiraceae . We propose the creation of the genus Chordicoccus in which MP1D12T represents the type strain for the novel species Chordicoccus furentiruminis.
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Cytobacillus citreus sp. nov., isolated from citrus rhizosphere soil
A Gram-stain-positive, rod-shaped and motile strain, designated FJAT-49705T, was isolated from the citrus rhizosphere soil sample. Strain FJAT-49705T grew at 20–40 °C (optimum, 30 °C) and pH 6.0–11.0 (optimum, pH 7.0) with 0–5 % (w/v) NaCl (optimum, 2 %). Strain FJAT-49705T showed high 16S rRNA gene sequence similarity to ‘Bacillus dafuensis’ FJAT-25496T (99.7 %) and Cytobacillus solani FJAT-18043T (98.0 %). In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees (based on 71 bacterial single-copy genes), strain FJAT-49705T clustered with the members of the genus Cytobacillus . MK-7 was the only isoprenoid quinone present. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 36.9 %. The average nucleotide identity (ANI) values between FJAT-49705T and ‘B. dafuensis’ FJAT-25496T and C. solani FJAT-18043T were below the cut-off level (95–96 %) recommended as the ANI criterion for interspecies identity. Based on the above results, strain FJAT-49705T represents a novel species of the genus Cytobacillus , for which the name Cytobacillus citreus sp. nov. is proposed. The type strain is FJAT-49705T (=CCTCC AB 2019243T= LMG 31580T).
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Lacticaseibacillus parakribbianus sp. nov., isolated from a pig farm faeces dump
A lactic acid bacterium isolated from pig faeces was characterized using a polyphasic approach. The strain was Gram-stain-positive, rod-shaped, and facultative anaerobic. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus . The multi-locus sequence tree revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus kribbianus. The main fatty acids were C16 : 0 and C18 : 1ω9c. The average nucleotide identity value, average amino acid identity, and genome-to-genome distance for YH-lacS6T and its most closely related strain, L. kribbianus, were 85.4, 85.2 and 29.2 %, respectively. The G+C content of the genomic DNA was 61.6 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lacS6T (=KCTC 21186T=JCM 34954T) represents a novel species. The name Lacticaseibacillus parakribbianus sp. nov. is proposed.
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Paenibacillus mangrovi sp. nov., a novel endophytic bacterium isolated from bark of Kandelia candel
A endospore-forming bacterium, designated strain KQZ6P-2T, was isolated from surface-sterilized bark of the mangrove plant Kandelia candel, collected from Maowei Sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, China. Strain KQZ6P-2T was able to grow at NaCl concentrations in the range of 0–3 % (w/v) with optimum growth at 0–1 % (w/v) NaCl. Growth occurred at 20–42 °C (optimal growth at 30–37 °C) and pH 5.5–6.5 (optimal growth at pH 6.5). The 16S rRNA gene sequence similarity between strain KQZ6P-2T and its closest phylogenetic neighbour Paenibacillus chibensis JCM 9905T was 98.2 %. Phylogenetic analyses using 16S rRNA gene sequences showed that strain KQZ6P-2T formed a distinct lineage with Paenibacillus chibensis JCM 9905T. The draft genome of strain KQZ6P-2T was 5 937 633 bp in size and its DNA G+C content was 47.2mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values among strain KQZ6P-2T and its related species were below the cut-off levels of 95, 70 and 95.5%, respec-tively. The cell-wall peptidoglycan of strain KQZ6P-2T contained meso-diaminopimelic acid as the diagnostic diamino acid. Major cellular fatty acids were anteiso-C15:0 and C16:0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, four unidentified phospholipids, an unidentified aminolipid and five unidentified lipids. Based on phylogenetic, phenotypic and chemotaxonomic data, strain KQZ6P-2T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus mangrovi sp. nov. is proposed. The type strain is KQZ6P-2T (=MCCC 1K07172T =JCM 34931T).
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Metabacillus arenae sp. nov., isolated from seashore sand
More LessA Gram-stain-positive, non-motile, rod-shaped, facultatively anaerobic bacterium, designated as IB182487T, was isolated from a seashore sand sample collected from Zhaoshu Island, PR China. Strain IB182487T grew at pH 6.0–10.0 (optimum, pH 8.0), 4–45 °C (optimum, 25–30 °C) and with 0–17 % (w/v) NaCl (optimum, 2–10 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IB182487T belonged to the genus Metabacillus and was closely related to Metabacillus idriensis SMC 4352-2T, (96.6 %), Metabacillus indicus LMG 22858T (96.5 %), Metabacillus niabensis DSM 17723T (96.3 %) and Metabacillus halosaccharovorans DSM 25387T (96.1 %). Strain IB182487T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and contained menaquinone MK-7 as the predominant isoprenoid quinone. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and three unidentified glycolipids. The major cellular fatty acids of strain IB182487T were iso-C15 : 0 and anteiso-C15 : 0. The whole genome average nucleotide identity and digital DNA–DNA hybridization analysis between the isolate and its closely related type strains demonstrated that the strain significantly differed from other Metabacillus species. The genomic DNA G+C content of strain IB182487T was 37.4 mol%. On the basis of phenotypic and chemotaxonomic properties, phylogenetic relatedness as well as genomic characteristics, strain IB182487T represents a novel species of the genus Metabacillus , for which the name Metabacillus arenae sp. nov. is proposed. The type strain of M. arenae is IB182487T (=MCCC 1K04629T=JCM 34523T).
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Vagococcus luciliae sp. nov., isolated from the common green bottle fly Lucilia sericata
More LessThe genus Vagococcus belongs to the family Enterococcaceae (order Lactobacillales) and is closely related to the genus Enterococcus . Currently, 19 species of the genus have been validly named. In this study, we isolated strain G314FT from the common green bottle fly Lucilia sericata collected in Germany. Sequencing of its almost-complete 16S rRNA gene revealed that the isolate belongs to the genus Vagococcus , being closely related to Vagococcus bubulae SS1994T with high sequence identity (99.50 %), followed by Vagococcus martis D7T301T (98.86 %), Vagococcus vulneris SS1995T (98.71 %), Vagococcus teuberi DSM 21459T (98.64 %), Vagococcus silagei 2B-2T (98.64 %) and Vagococcus penaei CD276T (98.64 %). Genome sequencing of strain G314FT was performed by a combination of Illumina and Oxford Nanopore technology, yielding a circular genome with a size of 2 139 468 bp and an 11 kb plasmid. Average nucleotide identity and digital DNA–DNA hybridization values were calculated between G314FT and its closest-related taxa, and found to be <91 % and <40 %, respectively, thus strongly supporting that strain G314FT represents a novel species of the genus Vagococcus . Phylogenetic and core protein-based phylogenomic trees revealed that G314FT was closely related to a group of three species, V. bubulae SS1994T, V. martis D7T301T and V. teuberi DSM 21459T. Comparatively, the genome of G314FT is the smallest in the group of the four related species, and the biochemical pathway comparison using BlastKOALA revealed that G314FT has lost some amino acid biosynthetic proteins; however, it has gained enzymes for carbohydrate metabolism. Phenotypically, G314FT was consistent with other species of the genus Vagococcus including a negative catalase reaction and non-motility. Using the polyphasic approach, our data supports that the isolate represents a new species, for which we propose the name Vagococcus luciliae G314FT (=DSM 112651T= CCM 9164T).
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Brevibacillus humidisoli sp. nov., a moderately thermoalkaliphilic and halotolerant species isolated from riverside soil
More LessA Gram-stain-positive, aerobic, rod-shaped, motile, and endospore-forming bacterial strain designated MMS20-4M-10-YT was isolated from riverside soil and subjected to taxonomic characterization. Strain MMS20-4M-10-YT was moderately thermophilic, alkaliphilic and halotolerant, as the strain grew at 25–50 °C (optimum, 45 °C), at pH 7.0–10.0 (optimum, pH 8.0) and in the presence of 0–6 % NaCl (optimum, 0 %). Analysis of 16S rRNA gene sequences indicated that MMS20-4M-10-YT fell into a phylogenetic cluster belonging to the genus Brevibacillus . Strain MMS20-4M-10-YT showed the highest 16S rRNA gene sequence similarity to Brevibacillus marinus SCSIO 07484T (96.7 %). Based on the reults of orthologous average nucleotide identity analysis, MMS20-4M-10-YT was again mostly related to B. marinus SCSIO 07484T with 78.0 % identity, which also shared the highest average nucleotide identity of 68.0 %. In contrast, the digital DNA–DNA relatedness analysis indicated that Aneureibacillus migulanus DSM 2895T was the closest species with 29.5 % similarity. The genome-based analyses indicated that all compared species showed low genomic relatedness with MMS20-4M-10-YT. The major fatty acids of the strain were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0, the major respiratory quinone was MK-7, the diagnostic polar lipids were phosphatidyl-N-methylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and diagnostic cell-wall diamino acid was meso-diaminopimelic acid, which was consistent with the general chemotaxonomic features of the genus. The total length of the genome was 4.91 Mbp and the DNA G+C content was 51.8 mol%. Based on both phenotypic and phylogenetic evidence, strain MMS20-4M-10-YT should be classified as representing a novel species of the genus Brevibacillus , for which a name Brevibacillus humidisoli sp. nov. (type strain=MMS20-4M-10-YT=KCTC 43333T=LMG 32359T) is proposed.
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Neobacillus terrae sp. nov., isolated from mountain soil
More LessA Gram-stain-positive, spore-forming and facultative aerobic bacterium, designated C11T, was isolated from mountain soil collected in the Republic of Korea. The cells were motile rods with peritrichous flagella, and positive for catalase and oxidase activities. Strain C11T grew at 15–45 °C (optimum, 30–37 °C) and pH 6.0–8.0 (optimum, pH 6.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0.5 %). Strain C11T contained menaquinone-7 as the sole isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were the major polar lipids. The G+C content of the genomic DNA was 38.8 mol%. Strain C11T was most closely related to Neobacillus drentensis IDA1967T and Mesobacillus foraminis CV53T, with 98.0 and 97.7 %, 71.7 and 69.9 %, and 20.1 and 20.3 % 16S rRNA gene sequence similarity, average nucleotide identity, and digital DNA–DNA hybridization values, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain C11T was included in a phyletic lineage with members of the genus Neobacillus but was distinct from members of the genus Mesobacillus . Phenotypic, chemotaxonomic and molecular properties suggested that strain C11T represents a novel species of the genus Neobacillus , for which the name Neobacillus terrae sp. nov. is proposed. The type strain is C11T (=KACC 21661T=JCM 33943T).
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- Pseudomonadota
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Citrobacter meridianamericanus sp. nov., isolated from a soil sample
A Gram-stain-negative strain, designated BR102T, isolated from a soil sample in Brazil was characterized by a polyphasic approach. Comparative 16S rRNA gene sequences indicated that strain BR102T belonged to the genus Citrobacter . The recN- and whole-genome-based phylogeny, and multilocus sequence analysis based on concatenated partial fusA, leuS, pyrG and rpoB sequences strongly supported a clade encompassing strain BR102T and a strain from public database that was distinct from currently recognized species of the genus Citrobacter . Average nucleotide identity and digital DNA–DNA hybridization values between strain BR102T and the closest relative Citrobacter freundii ATCC 8090T were 91.8 and 48.8 %, respectively. The ability to metabolize different compounds further discriminated strain BR102T from other closely related species of the genus Citrobacter . The novel variants bla CMY-179 and qnrB97, which encoded a CMY-2-like β-lactamase and a QnrB-type protein, respectively, were identified in strain BR102T. BR102T was resistant to ampicillin, amoxicillin/clavulanate and cefoxitin. The DNA G+C content of strain BR102T is 51.3 mol%. Based on these results, strain BR102T represents a novel species of the genus Citrobacter , for which the name Citrobacter meridianamericanus sp. nov. is proposed. The type strain is BR102T (=MUM 22.55T=IMI 507229T).
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Description of Alkalimarinus coralli sp. nov., isolated from tissue of the coral Pocillopora damicornis
More LessThree novel strains, SCSIO 12582T, SCSIO 12638 and SCSIO 12817, were isolated from tissue of the coral Pocillopora damicornis collected from Hainan province, PR China. The results of phylogenetic analysis based on 16S rRNA genes revealed that these three isolates showed nearly identical 16S rRNA gene sequences (99.86 %−99.93 %), forming a separate monophyletic cluster within the genus Alkalimarinus and closely related to Alkalimarinus sediminis FA028T. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) relatedness values among the three strains were 99.94 %−99.96 % and 100 %, respectively, indicating that these three isolates were affiliated with the same species. Analysis of the 16S rRNA gene sequence revealed that SCSIO 12582T (representative of the novel isolates) exhibited 98.49 % sequence similarity to A. sediminis FA028T. The ANI and dDDH values between SCSIO 12582T and A. sediminis FA028T were 74.81 % and 18.90 % respectively. These three isolates were facultatively anaerobic, Gram-stain-negative, rod shaped and catalase- and oxidase-positive. The DNA G+C content of SCSIO 12582T was 45.82 %. The major respiratory quinone was Q-9. The main cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 1ω9c. The polar lipids present were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of the results of the phylogenetic, chemotaxonomic, phenotypic and genomic analysis, it was evident that isolates SCSIO 12582T, SCSIO 12638 and SCSIO 12817 represent a novel species of the genus Alkalimarinus , for which the name Alkalimarinus coralli sp. nov. is proposed. The type strain is SCSIO 12582T (=JCM35228T=GDMCC1.3061T).
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Bradyrhizobium zhengyangense sp. nov., isolated from effective nodules of Arachis hypogaea L. in central China
Three slow-growing rhizobial strains (WYCCWR 12678, WYCCWR 12774 and WYCCWR 13023T) isolated from effective nodules of Arachis hypogaea L. (cultivated peanut) sampled in Zhengyang County, Henan Province, central China were characterized using a polyphasic approach. The three strains were assigned to the genus Bradyrhizobium based on phylogenetic analysis of their 16S rRNA sequences. Phylogenetic analysis based on their concatenated recA-glnII-gyrB-dnaK-rpoB gene sequences placed the strains into a distinct lineage. Whole-genome average nucleotide identity (ANI) values between WYCCWR 13023T and WYCCWR 12774 and WYCCWR 12678 were 99.43 and 99.31% respectively. ANI values between WYCCWR 13023T and the most closely related strains were all below 93 %. The digital DNA–DNA hybridization (dDDH) values between WYCCWR 13023T and ‘ B. guangzhouense ’ CCBAU 51670T, B. manausense BR 3351T and B. guangdongense CCBAU 51649T, the three most closely related type strains, were 50.40, 43.50 and 39.20% respectively. Phenotypic characterization also allowed the differentiation of the novel strains from their most closely related type strains. Based on the genotypic and phenotypic features, we conclude that the three strains represent a novel species for which the name Bradyrhizobium zhengyangense sp. nov. is proposed, with WYCCWR 13023T (=GDMCC 1.3180T=HAMBI 3760T) as the type strain.
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Croceibacterium selenioxidans sp. nov., isolated from seleniferous soil
A Gram-negative, aerobic bacterial strain, designated LX-88T, was isolated from seleniferous soil in Enshi, Hubei Province, PR China. Strain LX-88Toxidized elemental selenium to selenite, and produced carotenoids but not bacteriochlorophyll. The isolate grew optimally at 28 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysies of the organism’s 16S rRNA and bacterial core gene set sequences indicated that LX-88T belongs to the genus Croceibacterium , and has the highest degree of 16S rRNA gene sequence similarity to Croceibacterium soli MN-1T (97.4 %). The LX-88T genome was 3.4 Mbp and had a G+C content of 63.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values showed low relatedness (below 95 and 70 %, respectively) between strain LX-88T and other strains in the genus Croceibacterium . Ubiquinone-10 was the predominant quinone. The polar lipid profile was dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). These physiological and biochemical tests facilitated the differentiation of strain LX-88T from other members of the genus Croceibacterium . The results of this multifaceted taxonomic study indicate that strain LX-88T represents a novel species in the genus Croceibacterium , for which the name Croceibacterium selenioxidans sp. nov. is proposed. The type strain is LX-88T (=MCCC 1K08007T=LMG 32570T).
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Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens
A Gram-stain-negative, spiral bacterium (PAGU 1991T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close relationship between the two human isolates (PAGU 1991T and PAGU 1750) and the horse strain. However, a phylogenetic analysis based on 16S rRNA showed that the two human isolates formed a lineage that was distinct from the horse strain (less than 99.2 % similarity). In silico whole-genome comparisons based on digital DNA–DNA hybridization, average nucleotide identity based on blast and orthologous average nucleotide identity using usearch between the two human isolates and the type strain of H. equorum showed values of less than 52.40, 93.47, and 93.50 %, respectively, whereas those between the two human isolates were 75.8, 97.2, and 97.2 %, respectively. These data clearly demonstrated that the two human isolates formed a single species, distinct from H. equorum . Morphologically, the human isolates could be distinguished by the type of flagella; the human isolates showed a bipolar sheathed flagellum, whereas that of H. equorum was monopolar. Biochemically, the human isolate was characterized by growth at 42 °C under microaerobic conditions and nitrate reduction unability. We conclude that the two human isolates, obtained from geographically and temporally distinct sources, were a novel species, for which we propose the name Helicobacter kumamotonensis sp. nov., with the type strain PAGU 1991T (=GTC 16810T=CCUG 75774T).
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Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey
A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming and yellow-pigment-producing bacterium, designated as Sx8-5T, was isolated from stem tissue of Kaempferia marginata Carey in Kanchanaburi Province, Thailand. The strain exhibited tricalcium phosphate solubilizing activity. Its taxonomic position was investigated using a polyphasic approach. Sx8-5T grew at 25–37 °C (optimum 30 °C), pH 6–9 (optimum 7) and with 0 and 1% NaCl (optimum 0 %). According to the 16S rRNA gene phylogeny, Sx8-5T represents a member of genus Novosphingobium and shared the highest sequence similarities to Novosphingobium barchaimii LL02T of 99.4 % and shared sequence similarities with other species of the genus Novosphingobium of less than 99.4 %. The whole-genome size was 5.7 Mb, comprised of one contig, with a DNA G+C content of 66 %. The average nucleotide identity using BLASTn (ANIb) or MUMMER (ANIm) values for whole genome comparisons between Sx8-5T and Novosphingobium barchaimii LL02T and six closely related type strains were 72.33–82.14 % and 83.82–87.38 %, respectively, and the digital DNA–DNA hybridization (dDDH) values ranged from 21.0 to 28.6% when compared with the type strains of the members of the genus Novosphingobium . Major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), respectively. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unidentified phospholipids and unidentified polar lipids. The major isoprenoid quinone was Q-10. According to results obtained using a polyphasic approach, Sx8-5T represents a novel species of the genus Novosphingobium , the name Novosphingobium kaempferiae sp. nov. is proposed. The type strain is Sx8-5T (=JCM 35076T =TBRC 15600T).
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Marinagarivorans cellulosilyticus sp. nov., a cellulolytic bacterium isolated from the deep-sea off Noma-misaki, Japan
Cells from strain GE09T, isolated from an artificially immersed nanofibrous cellulose plate in the deep sea, were Gram-stain-negative, motile, aerobic cells that could grow with cellulose as their only nutrient. Strain GE09T was placed among members of Cellvibrionaceae , in the Gammaproteobacteria , with Marinagarivorans algicola Z1T, a marine degrader of agar, as the closest relative (97.4 % similarity). The average nucleotide identity and digital DNA–DNA hybridization values between GE09T and M. algicola Z1T were 72.5 and 21.2 %, respectively. Strain GE09T degraded cellulose, xylan and pectin, but not starch, chitin and agar. The different carbohydrate-active enzymes encoded in the genomes of strain GE09T and M. algicola Z1T highlights their differences in terms of target energy sources and reflects their isolation environments. The major cellular fatty acids of strain GE09T were C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c. The polar lipid profile showed phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. Based on these distinct taxonomic characteristics, strain GE09T represents a new species in the genus Marinagarivorans , for which we propose the name Marinagarivorans cellulosilyticus sp. nov. (type strain GE09T=DSM 113420T=JCM 35003T).
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Frateuria soli sp. nov. and Frateuria edaphi sp. nov., isolated from greenhouse soil
More LessTwo bacterial strains, designated 5GH9-11T and 5GH9-34T, were isolated from greenhouse soil sampled in Wanju-gun, Jeollabuk-do, Republic of Korea. Both strains formed yellow colonies and were aerobic, rod-shaped and flagellated. The 16S rRNA gene sequence similarity between 5GH9-11T and 5GH9-34T was 98.6 %. Strain 5GH9-11T showed the highest sequence similarities to Dyella thiooxydans ATSB10T (98.1 %) and Frateuria aurantia DSM 6220T (97.7 %) while strain 5GH9-34T revealed the highest sequence similarity to F. aurantia DSM 6220T (98.3 %) and D. thiooxydans ATSB10T (98.3 %). Phylogenetic analysis on the basis of the 16S rRNA gene sequence showed that strains 5GH9-11T and 5GH9-34T formed a robust cluster with Frateuria flava MAH-13T and Frateuria terrea NBRC 104236T. The phylogenomic tree also showed that strains 5GH9-11T and 5GH9-34T formed a robust cluster with F. terrea DSM 26515T and F. flava MAH-13T. Strain 5GH9-11T showed the highest orthologous average nucleotide identity (OrthoANI; 88.5 %) and digital DNA–DNA hybridization (dDDH) values (35.5 %) with F. flava MAH-13T, and strain 5GH9-34T revealed highest OrthoANI (88.1 %) and dDDH (34.2 %) values with F. flava MAH-13T. The orthoANI and dDDH values between strain 5GH9-11T and 5GH9-34T were 87.7 and 33.9 %, respectively. Their major respiratory quinone was ubiquinone 8, and the major cellular fatty acids were iso-C16 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The major polar lipids of both strains were composed of large or moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified aminophospholipid. Based on these data, strains 5GH9-11T and 5GH9-34T should represent two independent novel species of Frateuria , for which the names Frateuria soli sp. nov. (type strain 5GH9-11T=KACC 16943T=JCM 35197T) and Frateuria edaphi sp. nov. (type strain 5GH9-34T=KACC 16945T=JCM 35198T) are proposed.
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