International journal of systematic and evolutionary microbiology最新文献

Two bacterial strains, designated M3-11^T and M6-14^T, were isolated from paddy field soils in the Republic of Korea. Cells were aerobic, Gram-stain-negative, rod-shaped and non-flagellated but motile. The strains exhibited optimal growth at 28 °C and pH 7.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains M3-11^T and M6-14^T were placed within the genus Flavobacterium, showing the highest similarity to Flavobacterium zhairuonense A5.7^T (97.98%) and Flavobacterium nitrogenifigens NXU-44^T (98.23 %), respectively. The genomic similarity between two strains and their closely related strains was 39.3 and 51.1 % for digital DNA-DNA hybridization and 90.0 and 93.2 % for orthologous average nucleotide identity, both of which were lower than the thresholds recommended for species delineation. The respiratory quinone was menaquinone-6, and the major polar lipids were phosphatidylethanolamine and aminolipid. The major fatty acids (>10 %) were iso-C_15 : 0 and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strains M3-11^T and M6-14^T represent novel species of the genus Flavobacterium, for which the names Flavobacterium oryzagri sp. nov. (type strain M3-11^T=KACC 22761^T=JCM 35942^T) and Flavobacterium oryzicola sp. nov. (type strain M6-14^T=KACC 22763^T=JCM 35943^T) are proposed.

Nine isolates from the gingiva of cheetahs kept in captivity were subjected to genotypic and phenotypic characterization. Sequencing of the 16S rRNA gene documented the highest identity of three representative strains to the type strain of Pasteurella multocida subsp. septica with 95.82%. The highest digital DNA-DNA hybridization predicted from the whole-genome sequence of strain 22721-9-1^T was to Haemophilus felis with 25.0%. The highest average nucleotide identity of strain 22721-9-1^T was also to H. felis with 74.36%, confirming a separate taxonomic status at species level. The phylogenetic comparison of concatenated conserved protein sequences showed a unique position of the taxon investigated, which qualifies for the status of a new genus, since the highest identity was found to Lonepinella koalarum with 83%, well below the upper threshold among genera of 91%. A new genus with one species, Reella acinonychis, is proposed. Production of indole and acid from sucrose and dulcitol separate the genus from most of the other genera of the Pasteurellaceae. Matrix-assisted laser desorption/ionization-time of flight MS analysis of the isolates clustered them close together and clearly separated them from other Pasteurellaceae species, allowing clear discrimination and making this the method of choice for identification. The G+C content of the type strain 22721-9-1^T (=DSM 118580^T=CCUG 77953^T) is 38.53 mol%, calculated from the whole genome.

A novel bacterial strain with chitin-degrading ability, designated strain HSL-7^T, was isolated from a mangrove sediment in Guangxi, PR China. Cells of strain HSL-7^T were Gram-stain-positive, aerobic, rod-shaped bacteria with a single polar flagellum. The strain grew at concentrations of 0-1% (w/v) NaCl (optimum at 0.5%), at pH 6.0-10.0 (optimum at 7.0) and in a temperature range of 15-37 °C (optimum at 20 °C). Strain HSL-7^T shared the highest 16S rRNA gene sequence percentage with Chitinibacter tainanensis BCRC 17254^T (94.4%). Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain HSL-7^T formed a distinct cluster in the family Chitinibacteraceae. The genome-relatedness indices between strain HSL-7^T and other type species of the family Chitinibacteraceae were in the ranges of 75.61-79.73% for average nucleotide identity, 65.50-70.65% for average amino acid identity and 12.7-17.4% for digital DNA-DNA hybridization, which were significantly below the cut-off values for the genus delineation. The genome comprised 3,144,197 bp with a genomic DNA G+C content of 61.5 mol%. The major isoprenoid quinone was ubiquinone-8. The predominant fatty acids were summed feature 3 (C_16:1  ω6c and/or C_16:1  ω7c), summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c) and C_16:0. The polar lipids comprised aminolipid, aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipid and an unidentified lipid. The polyphasic taxonomic properties indicated that the strain represents a novel genus and species in the family Chitinibacteraceae for which the name Chitinirhabdus sediminis gen. nov., sp. nov. is proposed. The type strain is HSL-7^T (=JCM 37906^T=MCCC 1K09933^T).

Emerging evidence supports the role of the nasopharyngeal microbiome in respiratory health, including association with conditions such as asthma and respiratory tract infections. One dominant commensal genus is Corynebacterium, members of which are commonly present in the nasopharynx of infants. These commensal Corynebacterium spp. have been reported to correlate with respiratory health. In this paper, we present isolate MNWGS58^T isolated from the nasopharynx of a South African infant. Genomic analysis of the whole-genome sequence of MNWGS58^T revealed that it is phylogenetically closely related to other Corynebacterium spp. found in the nasopharynx, Corynebacterium propinquum [85% average nucleotide identity (ANI)] and Corynebacterium pseudodiphtheriticum (84% ANI). Bacterial identification using matrix-assisted laser desorption/ionization time-of-flight MS identified MNWGS58^T as C. pseudodiphtheriticum. The API Coryne assay identified the novel isolate as C. propinquum, and the VITEK 2 ANC assay identified the novel isolate as Corynebacterium otitidis. Both genomic analyses and phenotypic analyses show striking similarities to C. propinquum and C. pseudodiphtheriticum. The cell wall is consistent with closely related Corynebacterium spp., albeit with a higher C_17:0 content. The genome is 2.48Mbp with a G+C content of 56.9 mol%. Digital DNA-DNA hybridization values for MNWGS58^T were low when compared to C. pseudodiphtheriticum MNWGS56 and C. propinquum MNWGS51 (27.4 and 28.4%, respectively). Although there are phenotypic similarities, 85% ANI with the closest Corynebacterium spp. strongly supports the classification of a novel species of Corynebacterium, for which we propose the name Corynebacterium drakensteinense sp. nov., with the type strain MNWGS58^T (=TSD-445^T=NCTC 15058^T). It will be important to elucidate the role of this novel species of Corynebacterium in the human nasopharynx and identify additional niches for this species in future studies.

Gram-positive, thermophilic, endospore-forming, yellow, rod-shaped bacteria, D401a^T and D404, were isolated from soil samples of a hot spring in Dikili, Izmir. They can synthesize silver nanoparticles and biotechnologically important thermostable alpha-amylase, alpha-glucosidase and nitrate reductase, which were also confirmed by in silico analyses. 16S rRNA gene phylogenetic analysis revealed that D401a^T was most closely related to D404 (99.9%) and had less than 98.9% similarity to Anoxybacillus flavithermus DSM 2641^T, Anoxybacillus thermarum DSM 7141^T, Anoxybacillus mongoliensis DSM 19169^T and Anoxybacillus ayderensis from the genus Anoxybacillus. Their 2.7 Mb whole-genome analyses indicated that strains D401a^T and D404 represented a novel species within the genus Anoxybacillus, by displaying low average nucleotide identity and in silico DNA-DNA hybridization values between A. ayderensis DSM 14988 (92.9%-50.5%), A. ayderensis DSM 10112^T (92.4%-48.6%), A. thermarum DSM 17141^T (92.6%-48.8%) and Anoxybacillus gonensis NCIMB 13933^T (91.3%-43.8%) below 95% and 70%, respectively. The G+C content of genomic DNA was calculated to be 42.0 mol%. The percentage of conserved protein values of two strains within the genus Anoxybacillus ranged from 89.3% to 85.0% and average amino acid identity values from 95.1% to 91.6%, indicating the overall genus-specific boundaries. In silico chemotaxonomic analysis revealed the presence of complete gene sets encoding iso-C15:0, iso-C17:0 and C16:0 fatty acids, menaquinone-7, polar lipids of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and meso-diaminopimelate-type peptidoglycan were identified. Their genomes encoded type III polyketide synthases that produce biotin. They harboured additional terpene/carotenoid and terpene precursor biosynthetic clusters with secondary metabolites of carotenoids (C30), vitamin E and sesquiterpenes (C15). By morphological, physiological, phylogenetic and phylogenomic features, D401a^T and D404 are assigned to be a new species of the genus Anoxybacillus, which the name Anoxybacillus dikiliensis sp. nov. is proposed (type strain D401a^T=DSM 120222^T=NCIMB 15614^T).

A predatory, motile, Gram-negative bacterium, 22V^T, was isolated from a soil sample collected from Tamaulipas, Mexico, which forms plaques on Vibrio parahaemolyticus prey. It was identified as a member of the genus Bdellovibrio based on its 16S rRNA gene sequence. It has a circular genome of 3,601,631 bp with 3,437 protein-coding genes, one rRNA gene cluster and a G+C (mol%) content of 46.7 mol%. Phylogenetic analysis based on the 16S rRNA gene, concatenated housekeeping genes and core genes placed 22V^T as a member of a new species. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values of <21%, <80% and <78%, respectively, between 22V^T and other known species in the genus Bdellovibrio are below the threshold for species delineation. 22V^T can prey on Gram-negative bacteria, including nine strains from seven genera (Escherichia, Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella and Vibrio). By fluorescence and cryo-electron microscopy, 22V^T was observed as a tiny, motile bacterium that invaded the periplasmic space of host cells to form bdelloplasts, supporting a periplasmic predatory lifestyle. The unique rRNA gene cluster was located on a genomic island near an incomplete prophage. The rRNA gene yielded a phylogeny that conflicts with the phylogeny based on the core genes or housekeeping genes, suggesting that this rRNA gene cluster was obtained by horizontal transfer. Based on the phenotypic and phylogenomic results, 22V^T represents a novel species in the genus Bdellovibrio, for which Bdellovibrio bacteriopascens sp. nov. is proposed. The type strain is 22V^T (=ATCC TSD- 365^T=CM-CNRG 933^T).

Taxonomic positions of Streptomyces albosporeus subsp. labilomyceticus, Streptomyces lavendulae subsp. grasserius, Streptomyces asiaticus subsp. ignotus, Streptomyces antimycoticus subsp. sporoclivatus and Streptomyces althioticus subsp. attaecolombicae were reviewed according to analyses of 16S rRNA gene and whole-genome sequences and phenotypic comparisons. The rank of S. albosporeus subsp. labilomyceticus was elevated to an independent species, for which Streptomyces labilomyceticus comb. nov. was proposed. S. lavendulae subsp. grasserius was considered a later heterotypic synonym of Streptomyces colombiensis. S. colombiensis and Streptomyces lavendulae can be united under one species as subspecies. Therefore, S. colombiensis was reclassified as a subspecies of S. lavendulae, for which Streptomyces lavendulae subsp. colombiensis comb. nov. was proposed. S. asiaticus subsp. ignotus was closely related to Streptomyces rhizosphaericus. Streptomyces asiaticus was reclassified as a later heterotypic synonym of S. rhizosphaericus. According to the reclassification of the parent taxa, the scientific name of S. asiaticus subsp. ignotus was updated to Streptomyces rhizosphaericus subsp. ignotus comb. nov. S. antimycoticus subsp. sporoclivatus NBRC 100767^T showed 88.6% DNA-DNA relatedness to Streptomyces antimycoticus subsp. antimycoticus NBRC 12839^T, suggesting that they belong to the same subspecies. In contrast, Streptomyces mordarskii JCM 5052^T showed DNA-DNA relatedness of 75.6% to Streptomyces antimycoticus NBRC 12839^T, suggesting that they are two subspecies of the same species. Therefore, S. mordarskii was considered as a subspecies of S. antimycoticus, for which Streptomyces antimycoticus subsp. mordarskii comb. nov. was proposed. Although the genus Streptomyces included inappropriate scientific names of subspecies, they were correctly updated through these reclassifications. Additionally, Streptomyces labedae, Streptomyces gancidicus and Streptomyces albaduncus were reclassified as later heterotypic synonyms of Streptomyces griseoincarnatus, Streptomyces pseudogriseolus and Streptomyces griseoloalbus, respectively.

Two halophilic archaeal strains, AD34^T and PAK95, were isolated from a salt mine in Yunnan and rock salt in Jiangsu, two provinces in China that are 2,000 km apart, respectively. Cells of strain AD34^T were spherical while those of PAK95 were rod-shaped. Strains AD34^T and PAK95 were Gram-stain-negative, aerobic and able to grow at 1.4-4.8 M NaCl (with optimum at 3.1 M NaCl), pH 5.0-9.0 (optimum, pH 7.5) and 20-60 °C (optimum, 37 °C and 40 °C, respectively). Their 16S rRNA gene sequences showed the closest similarity to Haloparvum sedimenti DYS4^T, with similarities of 95.11% (AD34^T) and 95.46% (PAK95). The rpoB' gene sequences of strains AD34^T and PAK95 showed the highest similarity to species of Haloparvum alkalitolerans MK62-1^T with 91.40% (PAK95) and 91.53% (AD34^T) identity. Comprehensive phylogenetic analyses revealed that strains AD34^T and PAK95 form a robust, monophyletic clade with 100% bootstrap support, clearly distinct from related genera, particularly from the genus Haloparvum. From whole-genome sequencing, the DNA G+C content of AD34^T and PAK95 is 66.5 and 66.4 mol%, respectively, while that of DYS4^T and MK62-1^T is 68.3 and 69.1 mol%, respectively. The average nucleotide identity between AD34^T, PAK95 and the family Haloferacaceae ranged from 66.5 to 79.2%. The digital DNA-DNA hybridization values ranged from 19.6 to 32.8%, while the average amino acid identity (AAI) values were between 58.0 and 72.0%. Strains AD34^T and PAK95 may represent a novel species of a novel genus within the family Haloferacaceae, as judged by the AAI cutoff value (≤72.1%) proposed for differentiating genera within this family. The major polar lipids of strain AD34^T were phosphatidylglycerol (PG), PG phosphate methyl ester, PG sulphate and sulphated mannosyl glucosyl diether. Based on the phenotypic and phylogenetic analyses, it is proposed that strains AD34^T (=MCCC 4K00176^T=KCTC 4324^T) and PAK95 (=MCCC 4K00231=CGMCC 1.62791=KCTC 4376) represent a novel genus and species within the family Haloferacaceae, for which the name Halosubterraneus shenae gen. nov., sp. nov. is proposed. The type strain is AD34^T.

Four strains (LYQ92^T, LYQ131, LYQ121^T and LYQ103) were isolated from the faeces of Anser anser and Anser indicus in the Qinghai, PR China. Phylogenetic analyses based on 16S rRNA gene and genome sequences demonstrated that strains LYQ92^T and LYQ131 were adjacent to Serinicoccus profundi MCCC 1A05965^T and Serinicoccus sediminis KCTC 49173^T, while strains LYQ121^T and LYQ103 were most closely related to Ornithinimicrobium kibberense DSM 17687^T, Ornithinimicrobium avium KCTC 49180^T, Ornithinimicrobium tianjinense CGMCC 1.12160^T and Ornithinimicrobium cerasi CPCC 203383^T. Four novel strains were Gram-stain positive, oxidase-negative, catalase-positive, aerobic, non-motile and coccoid- and rod-shaped. Strains LYQ92^T and LYQ131 grew at 10-37 °C, pH 6.0-10.0 and 0-13.0% (wt/vol) NaCl, while strains LYQ121^T and LYQ103 grew at 10-35 °C, pH 7.0-9.0 and 0-7.0% (wt/vol) NaCl. Both strains LYQ92^T and LYQ121^T had MK-8(H4) as the primary respiratory quinone and contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Major fatty acids of strains LYQ92^T and LYQ131 were iso-C_16:0, iso-C_15:0, anteiso-C_17:0, anteiso-C_15:0 and summed feature 9 (10-methyl C_16:0 and/or iso-C_17:1 ω9c), while those of strains LYQ121^T and LYQ103 were iso-C_16:0, iso-C_15:0 and summed feature 9. Strain LYQ92^T contained ribose, glucose and galactose as major sugars and alanine, glutamic acid, serine, glycine, aspartic acid and ornithine as major amino acids. Strain LYQ121^T had a similar composition but lacked galactose and serine. Based on polyphasic characterization, these strains represent two novel species within the family Ornithinimicrobiaceae, proposed as Serinicoccus shuyuelongi sp. nov. (type strain LYQ92^T=GDMCC 1.5391^T=KCTC 59547^T) and Ornithinimicrobium jinqii sp. nov. (type strain LYQ121^T=GDMCC 1.5402^T=KCTC 59549^T), respectively.

Four Gram-positive, aerobic, non-motile cocci-shaped bacteria were isolated from the coal mine dust samples collected in Yuncheng City, Shanxi Province, and subjected to polyphasic taxonomic characterization. Whole-genome sequencing revealed that genomic sizes ranged from 3.7 to 4.2 Mb, with G+C contents of 67.0-69.5 mol%. Comparative analysis of 16S rRNA gene sequences revealed that strains Y1685^T, Y1700, Y2011^T and Y2014 shared the highest similarity (95.12-95.33%) with Enemella dayhoffiae NML 130396^T. Phylogenetic analysis based on 16S rRNA gene sequences and 552 core genes consistently placed the 4 strains within a distinct clade, separate from recognized genera in the family Propionibacteriaceae. The strains Y1685^T, Y1700, Y2011^T and Y2014 exhibited optimal growth on brain heart infusion agar supplemented with 5% defibrinated sheep blood medium at 30 °C, forming convex, opaque, smooth colonies with spherical cells. All strains were oxidase-negative and catalase-positive. MK-9 (H₄) was the sole menaquinone in type strains Y1685^T and Y2011^T. The major fatty acids of strain Y1685^T were iso-C_15 : 0, anteiso-C_15 : 0 and iso-C_16 : 0, while the major fatty acids of strain Y2011^T were iso-C_15 : 0 and anteiso-C_15 : 0. The cell-wall sugars of strain Y1685^T were ribose and rhamnose, and the cell-wall amino acids were alanine, glutamic acid, glycine and ll-diaminopimelic acid. In contrast, strain Y2011^T contained arabinose, glucose and galactose as cell wall sugars, with alanine, glutamic acid and glycine as the principal amino acids. Genomic and phenotypic data collectively support the classification of these isolates as representing two novel species within a new genus of the family Propionibacteriaceae. We proposed the genus Carbonicoccus gen. nov., with the type species Carbonicoccus zhangzhihongae sp. nov. (type strain Y1685^T=KCTC 59535^T=GDMCC 1.5547^T) and Carbonicoccus niuqiaonis sp. nov. (type strain Y2011^T=KCTC 59536^T=GDMCC 1.5548^T).