- Volume 68, Issue 12, 2018
Volume 68, Issue 12, 2018
- Notification List
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- New Taxa
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- Actinobacteria
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Mycobacterium syngnathidarum sp. nov., a rapidly growing mycobacterium identified in syngnathid fish
More LessTwo closely related isolates, 27335T and 24999, of rapidly growing, non-pigmented mycobacteria, were cultured from two clinically ill fish of the family Syngnathidae. Whole genome sequencing of the two isolates revealed low sequence homology to documented mycobacteria within public databases such as the NCBI. Evaluation of targeted housekeeping genes, including 16S rRNA, ITS, rpoB and hsp65, related the two bacteria distantly to Mycobacterium senegalense CK2 M4421 and Mycobacterium farcinogenes DSM 43637. Phenotypic, biochemical and dDNA–DNA hybridization tests demonstrated that Mycobacterium syngnathidarum is a new species distinct from other recognized rapidly growing mycobacterial species. Phenotypic, chemotaxonomic and phylogenetic data evaluation provided evidence that the two strains represent one novel species. We propose the formal recognition of Mycobacterium syngnathidarum sp. nov., with isolate 27335T as the type strain (=ATCC TSD-89T,=DSM 105112T).
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Actinomyces tangfeifanii sp. nov., isolated from the vulture Aegypius monachus
A novel, Gram-stain-positive, catalase-positive, non-spore-forming, short rod-shaped strain (VUL4_3T) was isolated from rectal swabs of Old World vultures (Aegypius monachus) from the Tibet–Qinghai Plateau, China. Based on the results of biochemical tests and 16S rRNA gene sequence comparison, strain VUL4_3T was determined to be a member of the genus Actinomyces that is closely related to the type strains of Actinomyces liubingyangii (97.7 % 16S rRNA gene sequence similarity) and Actinomyces marimammalium (96.5 %). Optimal growth occurred at 37 °C, pH 6–7 and with 1 % (w/v) NaCl. The typical major cellular fatty acids of strain VUL4_3T were C18 : 1ω9c, C16 : 0 and C18 : 0. The VUL4_3T genome contained 2 207 832 bp with an average G+C content of 51.9 mol%. DNA–DNA hybridization values between strain VUL4_3T and the above two species of the genus Actinomyces showed less than 32 % DNA–DNA relatedness, supporting a novel species status of strain VUL4_3T. Based on the phenotypic data and phylogenetic inference, the novel species Actinomyces tangfeifanii sp. nov. is proposed. The type strain is VUL4_3T (=CGMCC 4.7369T=DSM 103436T).
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Description of a novel species of fast growing mycobacterium: Mycobacterium kyogaense sp. nov., a scotochromogenic strain received as Mycobacterium vaccae
More LessA polyphasic study was undertaken to determine the taxonomic status of a rapidly growing, scotochromogenic organism that had been received as Mycobacterium vaccae NCTC 11659T. The organism was found to have chemotaxonomic and cultural properties in accord with its assignment to the genus Mycobacterium and was distinguished from the type strain of Mycobacterium vaccae and from other closely related reference strains on the basis of concatenated sequences of 16S rRNA, gyrB, hsp65, recA and rpoB genes. It was also distinguished from M. vaccae strain DSM 43292T and from the type strain of Mycobacterium obuense , its nearest phylogenetic neighbour, on the basis of chemotaxonomic and phenotypic data and digital DNA –DNA relatedness values of 22.7 and 68.3 %, respectively. These datasets not only indicate that strain NCTC 11659T had been misclassified as M. vaccae but that it merits recognition as representing a novel species of the genus Mycobacterium . It is proposed that the organism be classified as Mycobacteriumkyogaense sp. nov.
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A description of Mycobacterium chelonae subsp. gwanakae subsp. nov., a rapidly growing mycobacterium with a smooth colony phenotype due to glycopeptidolipids
Three rapidly growing mycobacterial strains, MOTTH4W, MOTT36WT and MOTT68W, were isolated from the sputa of three independent Korean patients co-infected with Mycobacterium yongonense Type II strains. The 16S rRNA gene sequences of all three strains were unique, which were closest to that of Mycobacterium chelonae subsp. bovis KCTC 39630T (99.9 % similarity). Multilocus sequence typing analysis targeting 10 housekeeping genes including hsp65 and rpoB revealed the distinct phylogenetic location of these strains, which were clustered with M. chelonae subsp. chelonae ATCC 35752T and M. chelonae subsp. bovis KCTC 39630T. Phylogenetic analysis based on whole genome sequences revealed a 95.89 % average nucleotide identity (ANI) value with M. chelonae subsp. chelonae , slightly higher than the 95.0 % ANI criterion for determining a novel species. In addition, phenotypic characteristics such as a smooth colony morphology and growth inhibition at 37 °C, distinct MALDI-TOF MS profiles of extracted total lipids due to surface glycopeptidolipids, and distinct drug susceptibility profiles further supported the taxonomic characterization of these strains as representing a novel subspecies of Mycobacterium chelonae . Mycobacterium chelonae subsp. gwanakae subsp. nov. is proposed and the type strain is MOTT36WT (=KCTC 29127T=JCM 32454T).
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Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov
More LessClinical isolates belonging to Corynebacterium diphtheriae biovar Belfanti were characterized by genomic sequencing and biochemical and chemotaxonomic analyses. Phylogenetic analyses indicated that biovar Belfanti represents a branch that is clearly demarcated from C. diphtheriae strains of biovars Mitis and Gravis. The average nucleotide identity of isolates of biovar Belfanti with C. diphtheriae type strain NCTC 11397T (biovar Gravis) was 94.85 %. The inability to reduce nitrate differentiated biovar Belfanti from other strains of C. diphtheriae . On the basis of these results, we propose the name Corynebacterium belfantii sp. nov. for the group of strains previously considered as C. diphtheriae biovar Belfanti. The type strain of C. belfantii is FRC0043T (=CIP 111412T=DSM 105776T). Strains of C. belfantii were isolated mostly from human respiratory samples.
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Microbispora soli sp. nov., isolated from soil of a hot spring
More LessA novel actinomycete, strain RTBAU4-9T, which produced longitudinally paired spores on aerial mycelia, was isolated from a soil sample of a hot spring area. This strain exhibited chemotaxonomic and genotypic properties typical of the genus Microbispora , such as meso-diaminopimelic acid in the cell-wall peptidoglycan, glucose, ribose and trace amount of madurose as the characteristic whole-cell sugars, phosphatidylethanolamine, diphosphatidylglycerol and phosphoglycolipids as the membrane phospholipids, MK-9(H4), MK-9(H2) and MK-9(H0) as the characteristic menaquinones, and iso-C16 : 0 and anteiso-C17 : 0 as the main fatty acids. The G+C content of the genomic DNA was 70.2 mol%. The result of 16S rRNA gene sequence analysis revealed the strain was a member of the genus Microbispora and was most closely related to Microbispora hainanensis 211020T (98.3 % 16S rRNA gene sequence similarity). In addition, the low percentage of DNA–DNA relatedness (<28.1±1.2 %) and several phenotypic differences confirmed that strain RTBAU4-9T should be considered as representing a novel species of the genus Microbispora , for which the name Microbispora soli sp. nov. is proposed. The type strain is RTBAU4-9T (=TBRC 7648T=NBRC 113147T).
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Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces
In the present study, we describe two novel Gram-stain-positive, irregular rod-shaped bacterial strains, 78T and 601, that had been isolated from the faeces of Tibetan antelopes at the Hoh Xil Nature Reserve, Qinghai–Tibet Plateau, China. The cells were aerobic, oxidase-negative and catalase-positive. When cultured on brain–heart infusion agar supplemented with 5 % sheep blood, colonies were cream in colour, circular, smooth and convex. Phylogenetic analysis based on the full-length 16S rRNA sequences revealed that type strain 78T and strain 601 belong to the genus Nocardioides, sharing the highest similarity to Nocardioides solisilvae JCM 31492T (98.3 %), Nocardioides gilvus XZ17T (97.4 %) and Nocardioides daejeonensis JCM 16922T (97.4 %). The average nucleotide identity values between the two novel strains and the three closely related type strains of the genus Nocardioides were lower than the 95–96 % threshold. The DNA G+C content of strains 78T and 601 were 71.2 and 71.3 mol% respectively. MK-8 (H4) was the predominant respiratory quinone and ll-2,6-diaminopimelic acid was the diagnostic diamino acid in its cell-wall peptidoglycan. Its polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The main whole-cell sugars were rhamnose, xylose and galactose and the major fatty acids (>10 %) were C17 : 1ω8c, iso-C16 : 0 and C18 : 1ω9c. These data supported the affiliation of strains 78T and 601 to genus Nocardioides. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named Nocardioides houyundeii sp. nov. The type strain is 78T (=CGMCC 4.7461T=DSM 106424T).
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Arthrobacter silvisoli sp. nov., isolated from forest soil
A novel Gram-stain-positive, strictly aerobic strain, NEAU-SA1T, which showed a rod–coccus growth life cycle, was isolated from forest soil from Zhangjiajie, Hunan Province, China. The isolate grew at 10–40 °C (optimum 28 °C), at pH 5.0–10.0 (optimum pH 7.0) and in the presence of up to 5 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-SA1T belonged to the genus Arthrobacter and was closely related to Arthrobacter cupressi DSM 24664T (98.1 % similarity). Average nucleotide identity values between NEAU-SA1T and A. cupressi DSM 24664T were 88.91 and 87.41 % by ANIm and ANIb analysis, respectively. The in silico DNA–DNA hybridization value between strain NEAU-SA1T and A. cupressi DSM 24664T was 34.20 %, again indicating they belong to different taxa. The genomic DNA G+C content was 66.74 mol%. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The predominant menaquinone was MK-9(H2). The peptidoglycan type was A3α with an interpeptide bridge comprising l-Lys and l-Ala. Glucose, ribose and galactose were the whole-cell sugars. On the basis of morphological, physiological, biochemical and chemotaxonomic analysis, strain NEAU-SA1T was classified as representing a novel species in the genus Arthrobacter , for which the name Arthrobacter silvisoli sp. nov. is proposed. The type strain is NEAU-SA1T (=DSM 106716T=CCTCC AB 2017271T).
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Microbacterium halophytorum sp. nov., a novel endophytic actinobacterium isolated from halophytes
Two actinobacterial strains, YJYP 303T and YZYP 518, were isolated from two species of halophytes collected from the southern edge of the Gurbantunggut Desert. Cells were Gram-stain-positive, aerobic, short rods and without flagella. Growth of the two strains was found to occur at 4–44 °C, pH 6.0–12.0 and in the presence of up to 15 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains are associated with members of the genus Microbacterium . In the phylogenetic tree, the two strains shared a clade with Microbacterium halotolerans YIM 70130T (97.58 % 16S rRNA gene sequence identity) and Microbacterium populi KCTC 29152T (96.54 %). The average nucleotide identity values of strain YJYP 303T and YZYP 518 to M. halotolerans YIM 70130T were determined to be 79.97 and 80.03 %, respectively. The genomic DNA G+C contents of strains YJYP 303T and YZYP 518 were 69.72 and 70.57 %, respectively. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant respiratory quinones was MK-11, followed by MK-10 and MK-12. The muramic acid type of peptidoglycan was N-glycolyl. The whole-cell sugars were mannose, ribose, rhamnose, glucose, galactose and two unidentified sugars. The cell-wall amino acids were glutamic acid, ornithine, glycine and alanine. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. On the basis of the evidence presented in this study, strains YJYP 303T and YZYP 518 are characterized as members of a novel species in the genus Microbacterium , for which the name Microbacterium halophytorum sp. nov. is proposed. The type strain is YJYP 303T (=CGMCC 1.16264T=KCTC 49100T).
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- Archaea
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Halococcus salsus sp. nov., a novel halophilic archaeon isolated from rock salt
More LessTwo pink-pigmented halophilic archaea, designated strains ZJ1T and J81, were isolated from rock salt of Yunnan Salt Mine, China, and commercial salt imported from Bolivia, respectively. Cells were non-motile, coccoid, approximately 0.8–1.6 µm in diameter, stained Gram-negative and often occurred in pairs. Colonies were wet, opaque and smooth-edged. Strain ZJ1T grew optimally with 20 % (w/v) NaCl, at pH 7.5 and at 38–40 °C, which was the same as for strain J81. 16S rRNA gene sequence similarity between strains ZJ1T and J81 was 99.7 %. Sequence similarity searches based on the 16S rRNA gene and cell morphology suggested that strains ZJ1T and J81 belong to the genus Halococcus in the family Halococcaceae . The major polar lipids of the type strain, ZJ1T, were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated diglycosyl-diether-1. The profile of polar lipids, cell shape, motility and lack of lysis of cells in distilled water show that strains ZJ1T and J81 were similar to other members of the genus Halococcus . Strain ZJ1T shared the highest 16S rRNA gene and rpoB′ gene sequence similarities of 99.0 and 95.3 % with Halococcus hamelinensis 100A6T, respectively, followed by less than 94.6 % with sequences of other species in the genus Halococcus . DNA–DNA relatedness between strains ZJ1T and J81 was 90.1±0.7 %, while 27±0.5 % was found between strain ZJ1T and H. hamelinensis JCM 12892T (=100A6T), and 29.0±0.5 % between strains J81 and H. hamelinensis JCM 12892T. The DNA G+C content of strain ZJ1T was 66.5 mol% (T m). The stable phylogenetic position, differential physiological and biochemical properties and extensive sequence divergence suggest that strains ZJ1T and J81 represent a novel species, for which the name Halococcus salsus sp. nov. is proposed. The type strain is ZJ1T (=CGMCC 1.16025T=NBRC 112867T).
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- Bacteroidetes
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Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue
A bacterium, designated strain CM134L-2T, was isolated from a chitin-enriched wheat leaf microbiome in Chengdu, Sichuan province, China. It was Gram-stain-negative, strictly aerobic, non-spore-forming, motile, rod-shaped, and bright yellow in colour. Strain CM134L-2T grew at 4–35 °C, at pH 6.0–9.0 and could use chitin as the only carbon resource. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CM134L-2T was most closely related to Pedobacter nanyangensis Q-4T (97.7 %) and Pedobacter zeaxanthinifaciens TDMA-5T (97.4 %). Digital DNA–DNA hybridization (dDDH) values between strain CM134L-2T with these two type strains were 26.8 and 20.8 %, respectively, and average nucleotide identity (ANI) values were 83.2 and 76.2 %; these values are lower than the proposed and generally accepted species boundaries of 70 % for dDDH and 95–96 % for ANI, which suggests strain CM134L-2T represents a novel species. The genomic DNA G+C content of strain CM134L-2T was 39.3 mol%, menaquinone-7 was the major respiratory quinone, phosphatidylethanolamine was the major polar lipid and the major components of the cellular fatty acids were iso-C15 : 0, and C16 : 1ω7c/C16 : 1ω6c (summed feature 3); these features supported the affiliation of strain CM134L-2T to the genus Pedobacter . Overall, strain CM134L-2T belongs to the genus Pedobacter , but can be classified as a novel species, for which the name Pedobacter chitinilyticus sp. nov. is proposed. The type strain is CM134L-2T (=CGMCC 1.16520T=KCTC 62643T).
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Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert
More LessA Gram-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium, named strain 59N8T, was isolated from Phragmites communis roots in the Kumtag Desert. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the isolate belongs to the genus Zobellella within the family Aeromonadaceae . The analysis showed that strain 59N8T was most closely related to Zobellella taiwanensis ZT1T. The average nucleotide identity value with Zobellella taiwanensis ZT1T was 88.2 %, and the digital DNA–DNA hybridization value was 29.7±2.4 %, which was calculated using the Genome-to-Genome Distance Calculator. The G+C content of strain 59N8T was 62.8 mol%. Strain 59N8T grew at 0–5 % (w/v) NaCl (optimum, 0–4 %), pH 6.0–9.0 (optimum, 7.0–8.0) and at 10–45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0. The major polar lipids in strain 59N8T were phosphatidylethanolamine and phosphatidylglycerol. Based on the chemotaxonomic, phylogenetic and phenotypic data, strain 59N8T represents a novel species in the genus Zobellella , for which the name Zobellella endophytica sp. nov. is proposed. The type strain is 59N8T (=ACCC 60074T=KCTC 62456T).
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Prevotella rara sp. nov., isolated from human faeces
A strain of obligately anaerobic, Gram-stain-negative rods was isolated from human faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed the strain to represent a member of the genus Prevotella , distant from the species with validly published names, with the closest relationship to Prevotella oryzae . The strain was moderately saccharolytic and proteolytic. The predominant menaquinones were MK-13 and MK-12. The major cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 45.7 mol%. On the basis of chemotaxonomic and genotypic properties, it was concluded that the strain represent a novel species within the genus Prevotella , for which the name Prevotella rara sp. nov. is proposed. The type strain of Prevotella rara is 109T (=VKM B-2992T=DSM 105141T).
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Flavobacterium riviphilum sp. nov., isolated from a freshwater creek
More LessA novel bacterium, designated strain TAPY6T, was isolated from a freshwater creek in Taiwan. The strain was Gram-stain-negative, strictly aerobic, motile-by-gliding, rod-shaped and formed translucent yellow colonies. Optimal growth occurred at 20–30 °C, pH 6 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPY6T belonged to the genus Flavobacterium and was most closely related to Flavobacterium succinicans LMG 10402T (97.3 % sequence similarity) and Flavobacterium glycines Gm-149T (96.3 %). Strain TAPY6T contained C15 : 0 and iso-C15 : 0 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, five uncharacterized aminophospholipids, two uncharacterized phospholipids and one uncharacterized aminolipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 39.8 mol%. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Flavobacterium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TAPY6T represents a novel species in the genus Flavobacterium , for which the name Flavobacterium riviphilum sp. nov. is proposed. The type strain is TAPY6T (=BCRC 81007T=LMG 29728T=KCTC 52444T).
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Flavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and Flavobacterium album sp. nov
More LessFour new limnic bacterial strains, namely HYN0048T, HYN0049T, HYN0056T and HYN0059T, were isolated from two lakes in the Nakdong River water system in Korea. 16S rRNA gene sequence analyses indicated that strains HYN0048T, HYN0049T, HYN0056T and HYN0059T belonged to the genus Flavobacterium by showing the highest sequence similarities with the type strains of F. soli (94.9 %), F. keumense (95.1 %), F. dispersum (97.7 %) and F. hauense (97.6 %), respectively. The low sequence similarities and tree topologies implied the novelty of the four isolates, as novel genomic species of the genus Flavobacterium . Numerous physiological and biochemical features also supported the distinctiveness of the isolates from previously known bacterial species. On the basis of the phylogenetic and phenotypic data presented in this study, four novel species are suggested with the following names: Flavobacterium magnum sp. nov. (type strain HYN0048T=KACC 19180T=NBRC 112740T), Flavobacterium pallidum sp. nov. (HYN0049T=KACC 19181T=NBRC 112741T), Flavobacterium crocinum sp. nov. (HYN0056T=KACC 19182T=NBRC 112743T) and Flavobacterium album sp. nov. (HYN0059T=KACC 19183T=NBRC 112744T).
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Flavobacterium sediminis sp. nov., a starch-degrading bacterium isolated from tidal flat sediment
More LessA yellow-pigmented bacterium with the ability to degrade starch, designated MEBiC07310T, was isolated from tidal flat sediment collected in Taean County, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MEBiC07310T was affiliated with the genus Flavobacterium in the phylum Bacteroidetes and showed that the strain was most closely related to Flavobacterium haoranii LQY-7T (96.8 % similarity), followed by Flavobacterium indicum GPTSA 100-9T (95.2 %) and Flavobacterium urocaniciphilum YIT 12746T (94.6 %). Genome-based analysis of the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) of strain MEBiC07310T compared with F. haoranii LQY-7T and F. indicum GPTSA 100-9T yielded ANI values of 77.0 and 73.3 % and DDH values of 18.0±2.7 and 16.1±3.6 %, respectively. The DNA G+C content of strain MEBiC07310T was 35.2 mol%. Cells of the strain were aerobic, Gram-stain-negative and rod-shaped, and negative for flexirubin-type pigments. Growth was observed at 17–43 °C (optimum 32 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–3 % (w/v) NaCl (optimum 1 %). The major fatty acids (>10 %) of strain MEBiC07310T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 1 (iso-C15 : 1 H and/or C13 : 0 3-OH) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was menaquinone MK-6. Based on its phenotypic and genotypic characteristics, strain MEBiC07310T should be classified as representing a novel species of the genus Flavobacterium , for which the name Flavobacterium sediminis sp. nov. is proposed. The type strain is MEBiC07310T (=KCTC 62132T=JCM 32291T).
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- Firmicutes and Related Organisms
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Kyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at São Miguel Island, and emended description of the genus Kyrpidia
A Gram-stain-positive, rod-shaped, non-motile, spore-forming bacterium, strain EA-1T, was isolated from hydrothermal sediment samples from the Azores (São Miguel, Portugal). 16S rRNA gene sequence analysis of the isolated bacterium revealed a phylogenetic affiliation with the genus Kyrpidia . The sequence similarity of the five 16S rRNA gene copies to its closest relative, Kyrpidia tusciae , ranged from 97.79 to 97.85 %. The in silico estimate of DNA–DNA hybridization was 56.0 %. The dominant fatty acids of the novel isolate were anteiso-C17 : 0 (49.9 %), iso-C17 : 0 (23.0 %) and iso-C16 : 0 (13.3 %), while the quinone detected was menaquinone MK-7. Analysis of polar lipids identified phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and additional unidentified compounds comprising two glycolipids, two phospholipids and two lipids. The presence of meso-diaminopimelic acid in the peptidoglycan and mannose, arabinose and ribose in the cell wall of strain EA-1T were detected. The strain was able to grow heterotrophically as well as autotrophically with carbon dioxide as the sole carbon source and with hydrogen and oxygen as electron donor and acceptor, respectively. Based on its chemotaxonomic, physiological and genomic characteristics, the new strain is considered to represent a novel species within the genus Kyrpidia , for which the name Kyrpidia spormannii sp. nov. is proposed. The type strain is strain EA-1T (=DSM 106492T=CCOS1194T).
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Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces
A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0–98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii . The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA–DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7T was 38.6 mol%. The major fatty acids were C16 : 0, C16 : 1 cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7T had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353T. Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353T is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353T=ATCC 27751T) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7T should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7T (=DSM 17630T=KCTC 15707T).
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Jeotgalibacillus proteolyticus sp. nov., a protease-producing bacterium isolated from ocean sediments
A Gram-stain-positive, rod-shaped bacterial strain, 22-7T, was isolated from ocean sediment of Laizhou Bay, China, and was characterized by using a polyphasic approach. Optimal growth was observed at 33 °C on a 2216E agar plate of pH 7.5 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences identified it as a member of the genus Jeotgalibacillus , most similar to Jeotgalibacillus campisalis SF-57T (98.7 % similarity), Jeotgalibacillus marinus DSM 1297T (98.2 %) and Jeotgalibacillus soli P9T (97.1 %). Average nucleotide identity values and digital DNA–DNA hybridization values were less than 74.2 and 18.1 %, respectively, between strain 22-7T and the type strains of closely related species. The major polar lipids were aminophospholipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0; and the major menaquinone was MK-7. The peptidoglycan type of the cell wall was A1α linked through l-lysine as the diamino acid. Combined data from phenotypic, chemotaxonomic and genotypic characterizations demonstrated that strain 22-7T represents a novel Jeotgalibacillus species, for which the name Jeotgalibacillus proteolyticus sp. nov. is proposed. The type strain is 22-7T(=MCCC 1H00228T=KCTC 33930T).
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Lactococcus termiticola sp. nov., isolated from the gut of the wood-feeding higher termite Nasutitermes takasagoensis
More LessA strain of lactic acid bacteria, designated NtB2T, isolated from the gut of the wood-feeding higher termite Nasutitermes takasagoensis, was characterized genetically and phenotypically. Strain NtB2T was related to Lactococcus lacti subsp. tructae JCM 31125T isolated from brown trout, showing 93.2 and 81.0 % similarity in 16S rRNA gene and rpoB gene sequences, respectively. Furthermore, genomic comparisons using pairwise average nucleotide identity analysis and the Genome-to-Genome Distance Calculator between strain NtB2T and L. lacti subsp. tructae JCM 31125T gave values of 81.0 and 23.2 %, respectively. Major cellular fatty acids produced by strain NtB2T were C18 : 1ω9c and C16 : 0. The cell-wall peptidoglycan type of strain NtB2T was A3α, Lys–Gly–Ser–Ala2. Based on the data presented, the isolate represents a novel species of the genus Lactococcus , for which the name Lactococcus termiticola sp. nov. is proposed. The type strain is NtB2T (=JCM 32569T=DSM 107259T).
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Clostridium composti sp. nov., a new anaerobic bacteria isolated from compost
Strain YH-tan31T is a Gram-stain-positive, obligately anaerobic, spore-forming and mesophilic bacterium. The cells are rod-shaped and motile by means of peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium oryzae DSM 28571T (97 % sequence identity), followed by Clostridium cellulovorans DSM 3052T (92.4 %) and Clostridium butyricum KCTC 5387T (92.1 %). The G+C content of the isolate was 30.9 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant fatty acids were C14 : 0, C16 : 0, C16 : 0 DMA,and C19 : 0 cis 11,12 DMA. The major end products of glucose fermentation were butyrate, acetate and lactate. This isolate represents a new species within the genus Clostridium , for which we propose the name Clostridium composti sp. nov. (type strain, YH-tan31T; =KCTC 15630T=JCM 32793T).
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- Other Bacteria
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Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field
A novel anaerobic fermentative bacterium, strain SEBR 4209T, was isolated from a water sample of a Congolese oil field. Strain SEBR 4209T is phylogenetically related to the genus Pleomorphochaeta , in the family Spirochaetaceae . Its closest relatives are Pleomorphochaeta caudata SEBR 4223T (94.5 % 16S rRNA gene sequence similarity) and Pleomorphochaeta multiformis MO-SPC2T (94.3 % similarity). Like the other members of this genus, cells have a pleomorphic morphology, in particular an annular shape and long stalks. Optimal growth was observed at 37 °C, at pH between 6.8 and 7.0, and with 40 g l−1 NaCl. This strain was only able to grow by fermentation of carbohydrates. The fermentation products from glucose utilization were acetate, ethanol, CO2 and H2. Predominant fatty acids were C14 : 0, C14 : 0 DMA, C16 : 0 and C16 : 1ω7c. The major polar lipids were phosphoglycolipids, phospholipids and glycolipids. The G+C content of the DNA was 29.6 mol%. Based on phenotypic characteristics and phylogenetic traits, strain SEBR 4209T is considered to represent a novel species of the genus Pleomorphochaeta , for which the name Pleomorphochaeta naphthae sp. nov. is proposed. The type strain is SEBR 4209T (=DSM 104684T=JCM 31871T).
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Refining the taxonomic structure of the phylum Acidobacteria
More LessThe phylum Acidobacteria was created in 1997 in order to accommodate a large number of 16S rRNA gene sequences retrieved from various environments in cultivation-independent studies. At present, 26 major sequence clades or subdivisions (SDs) are recognized within this phylum, but only seven of them (SDs 1, 3, 4, 6, 8, 10 and 23) are commonly addressed as containing taxonomically described representatives. Here, we examined the currently explored diversity within the Acidobacteria using the candidate taxonomic unit circumscription system. Based on this analysis, 26 subdivisions were assigned to 15 class-level units, five of which contain described members. These include three earlier established classes Acidobacteriia , Blastocatellia and Holophagae , as well as two as-yet-undescribed groups defined by SDs 6 and 23, which we propose to name Vicinamibacteria classis nov. and Thermoanaerobaculia classis nov., respectively. The former assignment of Thermotomaculum hydrothermale to SD10 was found to be incorrect. This bacterium, therefore, was placed in the family Thermotomaculaceae fam. nov., order Thermotomaculales ord. nov. within the class Holophagae . We also propose establishing a number of high-level taxa to accommodate described representatives of SDs 3, 4, 6 and 23. The family Bryobacteraceae of SD3 Acidobacteria is placed in the order Bryobacterales ord. nov. within the taxonomic range of the class Acidobacteriia . The order Vicinamibacteriales ord. nov. is proposed to accommodate the family Vicinamibacteriaceae of SD6 Acidobacteria . Finally, the family Thermoanaerobaculaceae fam. nov., the order Thermoanaerobaculales ord. nov. are proposed to accommodate the only described representative of SD23, Thermoanaerobaculum aquaticum .
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- Proteobacteria
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Bradyrhizobium ripae sp. nov., a nitrogen-fixing symbiont isolated from nodules of wild legumes in Namibia
More LessRoot-nodule bacteria were isolated from wild legumes growing in the Kavango region, Namibia. Using a polyphasic approach, four strains belonging to the genus Bradyrhizobium (WR4T, WR87, T10 and T12) were further characterized to clarify the taxonomic status of this group. On the basis of 16S rRNA gene sequences, the four strains showed highest similarity to Bradyrhizobium elkanii USDA 76T (99.9 %), Bradyrhizobium pachyrhizi PAC48T (identical) and to Bradyrhizobium brasilense UFLA03-321T (identical). Multilocus sequence analysis of concatenated glnII-recA-gyrB-dnaK-rpoB sequences and comparison of the intergenic transcribed spacer (ITS) sequences confirmed that the novel group belongs to a distinct lineage of the genus Bradyrhizobium , with <96.7 % (MLSA) and 97.25 % (ITS) nucleotide identity with B. elkanii USDA 76T. Results from the sequence-based analysis were validated by DNA–DNA hybridization experiments and suggested a novel species. Several phenotypic features including carbon compound utilization and growth characteristics supported the phylogenetic data, thus it is concluded that the strains represent a novel species, for which the name Bradyrhizobium ripae sp. nov. is proposed, with type strain WR4T [LMG 30283, DSM 105795, NTCCM 0019 (Windhoek)].
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Sphingomonas oleivorans sp. nov., isolated from oil-contaminated soil
More LessStrain FW-11T was isolated from oil-contaminated soil from Panjin in Liaoning, China. It was a Gram-stain-negative, aerobic and rod-shaped bacterium. The strain was confirmed to be a member of the genus Sphingomonas based on phylogenetic inference and phenotypic characteristics. The best growth of strain FW-11T occurred at 30 °C and pH 6.0–7.0. The strain was non-spore-forming, catalase-negative and oxidase-negative. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The cell-wall peptidoglycan of strain FW-11T included alanine, glycine, glutamic acid, aspartic acid and meso-diaminopimelate. The predominant isoprenoid quinones were ubiquinone Q-10 (93.2 %) and Q-9 (6.8 %). The fatty acid profile (>5 %) included C18 : 1ω6c (43.1 %), C16 : 0 (14.6 %), C17 : 1ω6c (14.0 %) and C14 : 0 2-OH (11.1 %). The most similar neighbours of FW-11T were Sphingomonas fennica K101T (97.4 %) and Sphingomonas haloaromaticamans A175T (97.0 %). The average nucleotide identity relatedness values between strain FW-11T and the two type strains ( S. fennica K101T and S. haloaromaticamans A175T) were 73.2 and 75.3 %, respectively. The genome size of FW-11T was 3.8 Mbp, comprising 3735 predicted genes with a DNA G+C content of 64.0 mol%. Based on phenotypic, chemotaxonomic and phylogenetic data, strain FW-11T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas oleivorans sp. nov. is proposed. The type strain is FW-11T (=LMG 29274T=HAMBI 3659T).
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Indioceanicola profundi gen. nov., sp. nov., isolated from Indian Ocean sediment
More LessA novel basophilic bacterial strain, designated as SCSIO 08040T, was recovered from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-negative, vibrioid or spiral, light pink, 0.6–1.0 µm wide and 1.0–2.5 µm long. Growth occurred at 20–45 °C, pH 7–11 and <5 % (w/v) NaCl, with optimum growth at 28–37 °C, pH 7 and 0–3 % (w/v) NaCl. Catalase-, oxidase and urease-positive, nitrate reduction-negative. Analysis of 16S rRNA gene sequencing revealed that strain SCSIO 08040T had the highest similarity of 95.3 % to Rhodocista pekingensis 3-pT. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that the novel isolate formed a distinct phylogenetic lineage in the family Rhodospirillaceae . The whole-cell hydrolysate contained meso–diaminopimelic acid, galactose, mannose and xylose. The total cellular fatty acid profile was dominated by C18:1ω7c and C19:0cycloω8c. Q-10 was the predominant ubiquinone. The major phospholipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. The DNA G+C content of strain SCSIO 08040T was 66.82 mol%. Based on these polyphasic data, a new genus, Indioceanicola gen. nov., is proposed in the family Rhodospirillaceae with the type species Indioceanicola profundi sp. nov. and the type strain SCSIO 08040T (=DSM 105146T=CGMCC 1.15812T).
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Hyphobacterium indicum sp. nov., isolated from deep seawater, and emended description of the genus Hyphobacterium
A novel aerobic, Gram-stain-negative bacterium, designated strain 2ED5T, was isolated from a deep seawater sample in the north-west Indian Ocean. Cells of the strain were oval- to rod-shaped, and motile by a polar flagellum or sessile by a prostheca. The strain formed creamy white colonies on 2216E marine agar plates. It grew at 10–40 °C (optimum 28 °C) and pH 5.0–8.0 (optimum pH 6.0–7.0). The strain required 1–6 % (w/v) NaCl for growth and grew optimally in the presence of 2–3 % NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain 2ED5T was affiliated with the genus Hyphobacterium in the family Hyphomonadaceae of the class Alphaproteobacteria , sharing 95.1 % similarity at the 16S rRNA gene sequence level with the type strain of Hyphobacterium vulgare , the only species in the genus Hyphobacterium . The major fatty acids of the strain were C18 : 1ω7c and iso-C17 : 1 ω9c, and the polar lipids included monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol, glucuronopyranosyl diglyceride, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unidentified glycolipid. The strain contained ubiquinone Q-10 as the predominant respiratory quinone. The G+C content of the genomic DNA of the strain was 60.9 mol%. Based on the results of this polyphasic analysis, strain 2ED5T represents a novel species in the genus Hyphobacterium , for which the name Hyphobacterium indicum sp. nov. is proposed. The type strain is 2ED5T (=CGMCC 1.16466T=JCM 32612T).
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Salinimonas sediminis sp. nov., a piezophilic bacterium isolated from a deep-sea sediment sample from the New Britain Trench
More LessA cold-adapted, piezophilic, slightly halophilic bacterium, designated as N102T, was isolated from a deep-sea (4700 m) sediment sample collected from the New Britain Trench. Strain N102T was Gram-stain-negative, rod-shaped, oxidase- and catalase-positive, and grew optimally at 28 °C (range, 4–40 °C), pH 7.0–7.5 (range, 6.0–9.0) and 3–4 %(w/v) NaCl (range, 2–15 %). The optimum pressure for growth was 10 MPa with tolerance up to 70 MPa. 16S rRNA gene sequence analysis showed that strain N102T was most closely related to Alteromonas addita R10SW13T (97.2 %), Alteromonas stellipolaris LMG 21861T (97.1 %), Alteromonas gracilis 9a2T (97.1 %), Salinimonas lutimaris DPSR-4T (96.1 %) and Salinimonas chungwhensis BH030046T (95.4 %). Phylogenetic analyses based on 16S rRNA gene, gyrB gene and whole-genome sequences placed strain N102T within the genus Salinimonas . Genomic comparisons based on average nucleotide identity and tetranucleotide signature frequencies corroborated the results of the phylogenetic analyses. The principal fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1ω6c). The major respiratory quinone was ubiquinone 8. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. The G+C content of the genomic DNA was 48.2 mol%. On the basis of phenotypic, chemotaxonomic and molecular data, we conclude that strain N102T represents a novel species of the genus Salinimonas , for which the name Salinimonas sediminis sp. nov. is proposed (type strain N102T=MCCC 1K03497T=KCTC 62440T).
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Rickettsia fournieri sp. nov., a novel spotted fever group rickettsia from Argas lagenoplastis ticks in Australia
Strain AUS118T was isolated from an Argas lagenoplastis tick collected from the nest of a Petrochelidon ariel (fairy martin) in Australia in 2013. Microscopic observation of infected cell cultures indicated this strain had a morphology and intracellular location typical of Rickettsia species. Phylogenetic analysis of this strain based firstly on multi-locus sequence analysis and subsequently on whole genome analysis demonstrated that AUS118T was most closely related to, but divergent from Rickettsia japonica and Rickettsia heilongjiangensis . We therefore propose the creation of a novel species, Rickettsia fournieri sp. nov, with the type strain AUS118T (DSM 28985 and CSUR R501).
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Alcanivorax indicus sp. nov., isolated from seawater
More LessA Gram-stain-negative, motile, rod-shaped bacterium, designated SW127T, was isolated from a seawater sample collected from the Indian Ocean. Strain SW127T was aerobic, catalase- and oxidase-positive, and grew at 8–42 °C (optimum, 30 °C), at pH 5.5–9.0 (optimum, pH 7.5) and in the presence of 0.5–11.0 % (w/v) NaCl (optimum, 3.0–4.0 %). Comparative analysis of 16S rRNA gene sequences indicated that strain SW127T belonged to the genus Alcanivorax , and closely related to Alcanivorax pacificus MCCC 1A00474T (96.7 % sequence similarity). The predominant cellular fatty acids of strain SW127T were C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Strain SW127T contained phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain SW127T was 62.8 mol%. On the basis of its phenotypic characteristics and phylogenetic data, strain SW127T represents a novel species of the genus Alcanivorax , for which the name Alcanivorax indicus sp. nov. is proposed. The type strain is SW127T (=CGMCC 1.16233T=KCTC 62652T).
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Paracoccus salipaludis sp. nov., isolated from saline–alkaline soil
A Gram-stain-negative, short ovoid- to coccus-shaped, aerobic, non-flagellated, and nonmotile strain, designated WN007T, was isolated from the natural saline–alkali wetland soil. Growth occurred at 10–45 °C (optimum 33–37 °C), pH 6.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 2–4 % NaCl). Catalase- and oxidase-positive. A comparison of the 16S rRNA gene sequence of WN007T showed the highest sequence similarities to Paracoccus chinensis (97.5 %) and Paracoccus niistensis (97.4 %). The major respiratory quinone of strain WN007T was Q10 and the fatty acid profile of strain WN007T contained a predominant amount of summed feature 7 and small quantities of C10 : 0 3OH, C16 : 00 and C18 : 00. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, aminolipid and lipid. The genome revealed that the G+C content was 63.9 mol% and the DNA–DNA relatedness values between strain WN007T and the type strains of P. chinensis CGMCC 1.7655Tand P. niistensis KCTC 22789T were 46.9±2.3 and 42.4±1.7 %, respectively. This was also confirmed by the low average nucleotide identity values (<83.5 %) between strain WN007T and the most closely related recognized Paracoccus species. According to these results, strain WN007T represents a novel species of the genus Paracoccus , for which the name Paracoccus salipaludis sp. nov. is proposed. The type strain is WN007T (=KCTC 52851T=ACCC 19972T).
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Minwuia thermotolerans gen. nov., sp. nov., a marine bacterium forming a deep branch in the Alphaproteobacteria, and proposal of Minwuiaceae fam. nov. and Minwuiales ord. nov.
More LessTwo Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacteria, designated as SY3-15Tand SY3-13, were isolated from a seawater sample of the South China Sea. Colonies were 0.5–1.0 mm in diameter, smooth, circular, convex and translucent after growth on marine agar at 37 °C for 3 days. The strains were found to grow at 20–50 °C (optimum, 42 °C), pH 6.0–8.5 (optimum, pH 6.5–7.5) and with 0.5–6.0 % (w/v) NaCl (optimum, 1.5–2.0 %). Chemotaxonomic analysis showed the sole respiratory quinone to be ubiquinone-10, the major fatty acids (>10 %) were C16 : 0 3-OH, C19 : 0cyclo ω9c, C18 : 1 3-OH and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and the polar lipids were phosphatidylglycerol, two unidentified aminolipids and three unidentified lipids. The DNA G+C content was 67.2–67.4 mol% calculated by genome. The 16S rRNA gene sequences of strains SY3-15T and SY3-13 were identical and related to the genus Lutibaculum with a similarity of 92.1 %. The 16S rRNA gene phylogenetic trees reconstructed with neighbour-joining, maximum-parsimony and minimum-evolution methods showed that the strains constituted a deep and separated branch from other families of Alphaproteobacteria , and the phylogenetic trees based on concatenated 163 protein sequences from genome sequences showed that the clade in which strains SY3-15T and SY3-13 located was separated from the clade of the other orders of Alphaproteobacteria , indicating it may represent a novel family of a novel order. Based on their phenotypic properties and their phylogenetic distinctiveness, we propose strains SY3-15T (=MCCC 1K03467T=KCTC 62335T) and SY3-13 (=MCCC 1K03466=KCTC 62329) to represent a novel species of a novel genus with the name Minwuia thermotolerans gen. nov., sp. nov., and we propose Minwuiaceae fam. nov. and Minwuiales ord. nov. with Minwuia as the type genus.
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Leucothrix arctica sp. nov., isolated from Arctic seawater
More LessA Gram-stain-negative, non-motile, oxidase- and catalase-positive, rod-shaped bacterium was isolated from a coastal seawater sample from the Arctic Circle and designated strain IMCC9719T. On the basis of 16S rRNA gene sequence analysis, it was shown that strain IMCC9719T belonged to the genus Leucothrix and was closely related to the type strains of Leucothrix pacifica (97.6 % similarity) and Leucothrix mucor (95.1 %), while the strain shared <90.6 % sequence similarity with other bacterial species. The average nucleotide identity and genome-to-genome distance values between strain IMCC9719T and L. pacifica JCM 18388T were 71.7 and 16.9 %, respectively. The DNA G+C content of strain IMCC9719T was 43.5 mol%. Optimum growth of strain IMCC9719T was observed at 15 °C, at pH 7.5–8.5 and in the presence of 2.0–2.5 % (w/v) NaCl. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C16 : 0. Cells of strain IMCC9719T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid, an unidentified aminophospholipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-8 (Q-8). Based on the taxonomic data collected in this study, strain IMCC9719T represents a novel species of the genus Leucothrix , for which the name Leucothrix arctica sp. nov. is proposed. The type strain is IMCC9719T (=KACC 18010T=NBRC 110382T).
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Alteromonas indica sp. nov., isolated from surface seawater from the Indian Ocean
More LessA Gram-stain-negative bacterium, designated strain IO390401T, was isolated from a seawater sample from the sulphide region of the Indian Ocean. Phylogenetic trees based on 16S rRNA gene sequences showed that strain IO390401T is a member of the genus Alteromonas , sharing 97.0−97.4 % 16S rRNA gene sequence similarity with Alteromonas addita R10SW13T, A. stellipolaris LMG 21861T, A. naphthalenivorans JCM 17741T, A. gracilis 9a2T and A. australica H17T, and 94.8−96.8 % with the type strains of other species of the genus Alteromonas . Strain IO390401T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone, C16:0 and C16:1 ω7c/C16:1 ω6c as the dominant cellular fatty acids, and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain IO390401T consists of a 4.4 Mb chromosome with a G+C content of 48.2 mol%. Average nucleotide identity values between strain IO390401T and the three closest phylogenetic neighbours, namely A. addita R10SW13T, A. stellipolaris LMG 21861T and A. naphthalenivorans JCM 17741T, were 70.5, 70.4 and 70.6 %, respectively, and the corresponding in silico DNA–DNA hybridization values were 20.6, 20.7 and 21.1 %. Phylogenetic distinctiveness and chemotaxonomic differences, together with phenotypic properties determined in this study, revealed that strain IO390401T could be differentiated from closely related species. It is therefore proposed as representing a novel species in the genus Alteromonas , for which the name Alteromonas indica sp. nov. is suggested. The type strain is IO390401T (=JCM 32638T=CGMCC 1.13554T=CCTCC AB 2018072T).
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Acinetobacter sichuanensis sp. nov., recovered from hospital sewage in China
More LessA novel Acinetobacter strain, WCHAc060041T, was recovered from hospital sewage at West China Hospital in Chengdu, Sichuan Province, China. The strain was Gram-negative coccobacillus, non-spore-forming, non-motile and strictly aerobic. The genomic DNA G+C content was 37.02 mol%. The 16S rRNA and rpoB gene sequences of the strain were ≤98.2 and≤89.5 % identical to the type strains of all known Acinetobacter species, respectively. The strain formed a distinct branch based on the genus-wide comparison of whole-cell mass fingerprints generated by matrix-assisted laser desorption/ionization-time-of flight mass spectrometry. Strain WCHAc060041T was subjected to whole genome sequencing. The average nucleotide identity based on blast (ANIb) and in silico DNA–DNA hybridization (isDDH) values between strain WCHAc060041T and type strains of other Acinetobacter species were ≤82.7 and ≤26.9 %, respectively. Strain WCHAc060041T could be distinguished from all known Acinetobacter species by its ability to assimilate gentisate and levulinate, but not to citrate (Simmons’). Genotypic and phenotypic characteristics from this study indicate that strain WCHAc060041T represents a novel species of the genus Acinetobacter , for which the name Acinetobacter sichuanensis sp. nov. is proposed. The type strain is WCHAc060041T (=CCTCC AB 2018118T=GDMCC 1.1383T=KCTC 62575T).
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Alsobacter soli sp. nov., a novel bacterium isolated from paddy soil, emended description of the genus Alsobacter and description of the family Alsobacteraceae fam. nov.
More LessStrain SH9T, an aerobic bacterium isolated from a paddy soil sample collected in Shanghai, China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, temperatures of 30–35 °C and in the presence of 1 % (w/v) NaCl. Comparative analysis of 16S rRNA gene sequences showed that strain SH9T fell within the genus Alsobacter , forming a clear cluster with the type strain of Alsobacter metallidurans , with which it exhibited a 16S rRNA gene sequence similarity value of 98.5 %. Cells of strain SH9T were Gram-stain-negative, motile, non-spore-forming, rod-shaped, positive for catalase and oxidase activity, and negative for atmospheric nitrogen fixation and nitrate reduction. The strain was a chemo-organotrophic bacterium, incapable of growth on C1 substrates. The chemotaxonomic properties of strain SH9T were consistent with those of the genus Alsobacter: the predominant ubiquinone was Q-10, and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. The DNA G+C content was 68.5 mol%. Strain SH9T exhibited a DNA–DNA relatedness level of 20±2 % with A. metallidurans NBRC 107718T. Based on the data obtained, strain SH9T represents a novel species of the genus Alsobacter , for which the name Alsobacter soli sp. nov. is proposed. The type strain is SH9T (=JCM 32501T=CCTCC AB 2017284T). A new family, Alsobacteraceae fam. nov., is also proposed encompassing strain SH9T and Alsobacter metallidurans NBRC 107718T.
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Litorivita pollutaquae gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae isolated from surface seawater of Xiamen Port, China
More LessA Gram-stain-negative Rhodobacterales strain, designated as FSX-11T, was isolated from surface seawater of Xiamen port in China. Strain FSX-11T showed less than 96.5 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed a distinct monophyletic clade within the family Rhodobacteriaceae and clustered distantly with the genera Thalassobius and Marivita . Cells of strain FSX-11T were non-motile, oval-shaped and facultative anaerobic. Optimal growth occurred at 20–30 °C, at pH 7.0–8.0 and in the presence of 2–3 % NaCl (w/v). The major respiratory quinone was ubiquinone-10. Summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), 11-methyl C18 : 1ω7c and C16 : 0 were the major fatty acids. The DNA G+C content of strain FSX-11T was 58.7 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain FSX-11T represents a novel species in a novel genus within the family Rhodobacteraceae , for which the name Litorivita pollutaquae gen. nov., sp. nov. is proposed. The type strain is FSX-11T (=JCM 32715T=MCCC 1K03503T).
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Halomonas litopenaei sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium isolated from a shrimp hatchery
Two Gram-stain negative, moderately halophilic, exopolysaccharide-producing bacteria, designated strains SYSU ZJ2214T and SYSU XM8, were isolated from rearing water and larvae from shrimp hatcheries, respectively. Cells of the strains were aerobic, motile and short-rod-shaped. They grew at NaCl concentrations of 0.5–22 % (w/v), at 4–45 °C and at pH 6–9. Pairwise comparison of 16S rRNA gene sequences revealed that strains SYSU ZJ2214T and SYSU XM8 were most closely related to Halomonas denitrificans M29T (98.3 and 98.2 % similarity, respectively). Strains SYSU ZJ2214T and SYSU XM8 shared an average nucleotide identity of 99.9 % between them. The DNA G+C contents were calculated at 64.1 % for both strains from the draft genome information. The major cellular fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 3-OH, and the predominant respiratory quinone was ubiquinone Q-9. Their main polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, four unidentified phospholipids and three unidentified lipids. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU ZJ2214T and SYSU XM8 merit recognition as representatives of a novel species of the genus Halomonas , for which the name Halomonas litopenaei sp. nov. is proposed. The type strain is SYSU ZJ2214T (=NBRC 111829T=KCTC 42974T).
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Enterobacter sichuanensis sp. nov., recovered from human urine
More LessAn Enterobacter strain, WCHECL1597T, was recovered from the urine of a patient in China in 2016. Phylogenetic analysis based on its 16S rRNA gene sequence indicated the strain belongs to the genus Enterobacter , while multi-locus sequence analysis of the rpoB, gyrB, infB and atpD housekeeping genes revealed that the strain was distinct from any previously described Enterobacter species. The whole genome sequence of strain WCHECL1597T had a 79.81–91.49 % average nucleotide identity to those of type strains of all known Enterobacter species. In silico DNA–DNA hybridization values between strain WCHECL1597T and the type strains of all known Enterobacter species ranged from 22.8 to 45.2 %. The major cellular fatty acids of strain WCHECL1597T were C16 : 0, C17 : 0cyclo and C18 : 1ω7c, which are in the quantitative range of other Enterobacter species while differentiated by the relatively higher amount (12.3 %) of iso-c16 : 1 I/C14 : 0 3-OH. The genomic DNA G+C content was 55.2 mol%. Strain WCHECL1597T could be distinguished from all known Enterobacter species by its ability to ferment inositol but with a negative l-rhamnose and d-mannitol reaction. Genotypic and phenotypic characteristics from this study indicate that strain WCHECL1597T represents a novel species of the genus Enterobacter , for which the name Enterobacter sichuanensis sp. nov. is proposed. The type strain is WCHECL1597T (=GDMCC1.1217T=CCTCC AB 2017104T=KCTC 52994T).
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Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site
An aerobic, Gram-stain-negative, rod-shaped, non-motile, mesophilic soil bacterium, strain WS5A3pT, was isolated from a pesticide burial site in north-west Poland. The strain grew at 12–37 °C, at pH 8–9 and with 0–2 % (w/v) NaCl. The main fatty acids detected in WS5A3pT were summed feature 3, summed feature 8 and C16 : 0. The major respiratory quinone was Q-10 and major polar lipids were phosphatidylethanolamine, sphingoglycolipid and phosphatidylglycerol. The G+C content of the genome was 65.1 mol%. Phylogenetic pairwise distance analysis of the 16S rRNA gene placed this strain within the genus Sphingopyxis , with the highest similarity to Sphingopyxis witflariensis W-50T (98.8 %), Sphingopyxis bauzanensis BZ30T and Sphingopyxis ginsengisoli Gsoil 250T (98.3 %) and Sphingopyxis granuli NBRC 100800T (98.09 %). Genomic similarity analyses using ANIb and dDDH algorithms indicated levels of similarity of 81.44, 80.84 and 81.16 % between WS5A3pT and S. witflariensis , S. bauzanensis and S. granuli , respectively for average nucleotide identity and 25.90, 25.00 and 26.10 % for digital DNA–DNA hybridization. Based on the phylogenetic and phenotypic data, strain WS5A3pT should be considered as a representative of a novel Sphingopyxis species. The name Sphingopyxis lindanitolerans sp. nov. is proposed with the type strain WS5A3pT (=DSM 106274T=PCM 2932T).
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Mesosutterella multiformis gen. nov., sp. nov., a member of the family Sutterellaceae and Sutterella megalosphaeroides sp. nov., isolated from human faeces
More LessTwo novel, obligately anaerobic, Gram-stain-negative, rod or coccoid-shaped bacteria, designated strains 4NBBH2T and 6FBBBH3T, were isolated from faecal samples of a healthy Japanese woman and man. The 16S rRNA gene sequence analysis showed that these strains represent a distinct lineage within the family Sutterellaceae . Strain 4NBBH2T formed a monophyletic branch between the genera Parasutterella and Sutterella , with sequence similarity to Sutterella stercoricanis CCUG 47620T (92.6 %), followed by Sutterella wadsworthensis WAL 7877 (92.4 %), Sutterella parvirubra YIT 11816T (92.1 %) and Parasutterella secunda YIT 12071T (91.8 %). Strain 6FBBBH3T was affiliated to the genus Sutterella , with highest similarity to S. stercoricanis CCUG 47620T (97.1 %), followed by S. parvirubra YIT 11816T (96.6 %) and S. wadsworthensis WAL 7877 (95.2 %). Strains 4NBBH2T and 6FBBBH3T were asaccharolytic. Analysis of fatty acids revealed that strain 4NBBH2T could be differentiated from Sutterella species (including strain 6FBBBH3T) by the presence of a low concentration of C16 : 1ω7c. The major respiratory quinones of strain 4NBBH2T were menaquinone (MK)-6 and methylmenaquinone (MMK)-6, whereas those of strain 6FBBBH3T were MK-5 and MMK-5. The G+C content of the genomic DNA of strains 4NBBH2T and 6FBBBH3T were 56.9 and 62.8 mol%, respectively. On the basis of the collected data, strain 4NBBH2T represents a novel species in a novel genus of the family Sutterellaceae , for which the name Mesosutterella multiformis gen. nov., sp. nov. is proposed. The type strain is 4NBBH2T (=JCM 32464T=DSM 106860T). We also propose a novel Sutterella species, Sutterella megalosphaeroides sp. nov., for strain 6FBBBH3T (=JCM 32470T=DSM 106861T).
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- Request for Opinion
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Proposal to modify Rules 27 and 30(3)(b) of the International Code of Nomenclature of Prokaryotes
More LessWe propose to modify Rules 27 and 30(3)(b) of the International Code of Nomenclature of Prokaryotes so that the formal description of new taxa (the ‘protologue’) will include a statement about the nomenclatural type, so that this information will be linked to the name of the taxon, the derivation (etymology) of the name, and the properties of the taxon.
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