International journal of systematic and evolutionary microbiology最新文献

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).

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.

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).

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.

A phylogenetically distinct bacterial strain, designated as DFM-14^T, was isolated in 2022 from marine mud collected in Gochang, Jeollabuk-do, South Korea, and characterized using a polyphasic taxonomic approach. The isolate is Gram-stain-negative, motile, pale white and coccoid-shaped, typically forming clusters. It is facultatively aerobic, and phylogenetic analysis of the 16S rRNA gene placed it within the genus Thaumasiovibrio (family Vibrionaceae, phylum Pseudomonadota). Strain DFM-14^T formed a distinct clade with Thaumasiovibrio subtropicus C4V358^T and Thaumasiovibrio occultus C4II189ᵀ, sharing 16S rRNA gene sequence similarities of 95.6% and 95.2%, respectively. The major fatty acids are C_12 : 0, C_12 : 0 3-OH, C_16 : 0, C_16 : 1  ω9c and C_18 : 1  ω9c, while the predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The draft genome is 4.4 Mb in size, assembled into 56 contigs, and contains 4,445 coding sequences and 110 RNAs (8 rRNAs and 102 tRNAs), with a G+C content of 45.4 mol%. Optimal growth occurs at 25 °C, pH 7.0 and 2% (w/v) NaCl. Based on phenotypic, phylogenetic, chemotaxonomic and genomic evidence, strain DFM-14ᵀ represents a novel species of the genus Thaumasiovibrio, for which the name Thaumasiovibrio clandestinus sp. nov. is proposed. The type strain is DFM-14^T (=KEMB 24352^T=JCM 37837^T=KCTC 8887^T).

During a screening of sulphur-oxidizing bacteria from different Spanish soils, a strain designated AFSI2.2^T was isolated from the rhizosphere soil of a mulberry plant thriving in a sulphur-rich environment. Cells of this strain were Gram-stain-negative motile rods with flagella. Its taxonomic classification was determined through a polyphasic approach. Phylogenetic analysis of the 16S rRNA gene revealed that strain AFSI2.2^T shares high similarity (99.64%) with certain Variovorax species, suggesting that the isolate belongs to this genus. Whole-genome phylogeny showed that the novel strain forms a distinct lineage within the genus Variovorax. Whole-genome analysis of AFSI2.2^T exhibited average nucleotide identity values of 78.37-89.63% and digital DNA-DNA hybridization values of 21.90-38.90% with closely related Variovorax species, both below the established thresholds for species delineation. The predominant cellular fatty acids of strain AFSI2.2^T were C_16 : 0, Summed Feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c) and Summed Feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). Apart from the ability of oxidizing inorganic sulphur compounds, AFSI2.2^T presented further in vitro plant growth-promoting (PGP) activities such as production of indole-3-acetic acid and siderophores and 1-aminocyclopropane-1-carboxylate deaminase activity. Genes associated with these PGP traits, as well as with cytokinin and gamma-aminobutyric acid biosynthesis, were identified in the AFSI2.2^T genome, supporting its potential as a PGP bacterium. In conclusion, phylogenetic, genomic, phenotypic and chemotaxonomic analyses support the classification of the isolate as a novel species within the genus Variovorax, for which the name Variovorax palleresanus sp. nov. is proposed. The type strain is AFSI2.2^T (=CECT 31217^T=CIP 112526^T).

A novel strain, designated Mg75^T, was isolated from a vineyard soil sample collected in Mostaganem, Algeria. This Gram-positive, non-motile strain produces a branched, fragmented substrate mycelium with a yellowish-orange colour and a white aerial mycelium on International Streptomyces Project 2 (ISP2), ISP3 and ISP4. Mg75^T exhibited growth across a temperature range of 15-40 °C, with an optimal range of 28-30 °C. It thrived at pH levels between 5.0 and 10.0, with an optimum at pH 7.0, and tolerated NaCl concentrations ranging from 0% to 3% (w/v), with an optimal concentration range of 0-1% (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence indicated the highest similarity with Saccharothrix yanglingensis Hhs.015^T (98.95%). The G+C content of the genomic DNA of strain Mg75^T was 73.4 mol%. Digital DNA-DNA hybridization (dDDH) between strain Mg75^T and its neighbouring Saccharothrix species ranged from 23.2% to 39.9%. Average nucleotide identity (ANI) ranged from 82.08% to 90.91%, and average amino acid identity (AAI) ranged from 79.8% to 92.57%, way below the thresholds of 70% for dDDH and 95-96% for ANI and AAI used for species delimitation. Strain Mg75^T was found to share a similar chemotaxonomic profile based on genomic chemotaxonomic markers. The phylogenetic and phylogenomic analyses, together with the in silico chemotaxonomic and phenotypic data, indicated that strain Mg75^T (=DSM 118769^T=CECT 31160^T) represented a novel species of the genus Saccharothrix, for which the name Saccharothrix sabaoui sp. nov. is proposed.