International journal of systematic and evolutionary microbiology最新文献

Six novel actinobacterial strains (BH034^T, BH055, BH097, BH104, BH105 and BH106^T) were isolated from developing brood in nests of the solitary bee species Anthophora bomboides from Bodega Bay, California, USA. Phylogenetic analysis based on a five-gene multilocus sequence alignment and whole-genome data positions all six strains within the genus Streptomyces, with close relation to Streptomyces endophyticus YIM 65594^T and Streptomyces fractus MV32^T. Through genetic and chemotaxonomic analysis, five of the isolates (BH034^T, BH055, BH097, BH104 and BH105) were found to be a clade representing one species [>96% average nucleotide identity (ANI)], whereas BH106^T was a distinct species (<93% ANI with each of the other isolate genomes). Within this species (BH034^T-BH105), the genomes comprised on average 9.6 Mb (±0.4 Mb), encoded 8,640 (±349) predicted genes and had a G+C content of 70.9 (±0.07) mol%. The type strain, BH034^T, contained iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_15 : 0 as major fatty acids and contained ll-diaminopimelic acid in the cell wall. The remaining strain, BH106^T, represents a distinct species; its genome comprised 9.4 Mb, encoded 8,426 predicted genes and had a G+C content of 70.7 mol%; the major fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0, iso-C_17 : 0 and iso-C_15 : 0, and the cell wall also contained ll-diaminopimelic acid. Functional genomic analysis revealed multiple secondary metabolite gene clusters in the bee-associated Streptomyces strains, several of which were found to be absent in closely related Streptomyces species. Based on genotypic, phenotypic and chemotaxonomic analyses, strains BH034-BH105 and BH106 represent two novel species within the genus Streptomyces, for which the names Streptomyces anthophorae sp. nov. (type strain BH034^T=NRRL B-65741^T=DSM 119658^T) and Streptomyces nidicola sp. nov. (type strain BH106^T=NRRL B-65742^T=DSM 119659^T) are proposed.

A marine bacterium capable of degrading alginate, designated as strain TSD2052^T, was isolated from a tidal flat sediment sample collected in Taean County, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TSD2052^T belonged to the genus Agarivorans, showing 96.2-97.8% sequence similarity. The whole genome of strain TSD2052^T was 4.62 Mb, with a DNA G+C content of 44.3 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain TSD2052^T and all genome-sequenced species of the genus Agarivorans were below 76.7%, 81.7% and 20.6%, respectively, indicating values lower than the standard cut-off for species delineation. Growth was observed at 10-35 °C (optimum 25 °C), pH 6-10 (optimum pH 8) and 1-5% (w/v) NaCl (optimum 3%). The major fatty acids (>10%) were C_12:0, C_16:0, summed feature 3 (C_16 : 1 ω6c and/or C_16 : 1ω7c) and summed feature 8 (C_18 : 1 ω6c and/or C_18:1ω7c). The respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and four unidentified lipids. Based on the results of phenotypic characterization, phylogenetic analysis and genome-based comparisons, strain TSD2052^T represents a novel species in the genus Agarivorans, for which we propose the name Agarivorans sediminis sp. nov. (=KCTC 92288^T=JCM 35392^T).

A Gram-stain-negative, aerobic, motile, short rod-shaped methanotrophic bacterium, designated CM2^T, was isolated from a reservoir pond in Korea. Cells of strain CM2^T possessed a single polar flagellum, intracytoplasmic membrane stacks characteristic of type I methanotrophs, and contained electron-dense granules. The strain grew only on methane and methanol as carbon and energy sources. Growth occurred at 20-35 °C (optimum, 30 °C), pH 5.5-8.5 (optimum, 6.5) and with 0-0.5% (w/w) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain CM2^T within the genus Methylomonas, with sequence similarities to known species ranging from 94.5 to 98.3%. The major cellular fatty acids were C_16:1 and C_14:0, and the predominant respiratory quinone was ubiquinone-8. The genome of strain CM2^T is 5.06 Mb in size with a G+C content of 56.8 mol%. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values between the genome of strain CM2^T and those of Methylomonas species were 19.2-21.3 %, 73.5-77.5 % and 72.3-76.7 %, respectively. Genome analysis identified genes encoding two distinct particulate forms and one soluble form of methane monooxygenase. Based on a polyphasic characterization, strain CM2^T is considered to represent a novel species of Methylomonas, for which the name Methylomonas stagni sp. nov. is proposed. The type strain is CM2^T (KCTC 8468^T=JCM 36702^T).

A novel member of the phylum Bacillota was isolated from Tengchong Hot Spring sediments (Yunnan, China). Cells are Gram-stain-negative, anaerobic, rod-shaped bacteria (0.3-0.5 µm wide and 1.5-3.5 µm long) and flagellated. Optimal growth occurs anaerobically at 60 °C (range 50-70 °C), pH 7.0 (range 6.0-8.0) and 0 g l^-1 NaCl (range 0-50 g l^-1). Substrate utilization encompassed cellobiose, sucrose, soluble starch, casein, glucose, xylan, ethanol, ribose, yeast extract, mannose and tryptone. Comparative 16S rRNA gene-sequence analysis revealed 93.6% similarity to Biomaibacter acetigenes SK-G1^T. The genome is 2.86 Mbp with a DNA G+C content of 46.5 mol%. Phylogenetic analyses based on the 16S rRNA gene and the whole genome placed strain DL9XJH-110^T within the family Tepidanaerobacteraceae. The predominant cellular fatty acids (>10%) were C_15 : 0, iso-C_15 : 0, C_16 : 0 and C_14 : 0. Phenotypic, phylogenetic and chemotaxonomic properties indicate that strain DL9XJH-110^T represents a novel species in a new genus, for which the name Thermorhabdus hydrogeniformans gen. nov., sp. nov. is proposed. The type strain is DL9XJH-110^T (=CCAM 2419^T=JCM 39573^T).

Two strains, B21^T and C4-1^T, were obtained from soil near Sinpung Station, the Republic of Korea. The two aerobic, Gram-negative, rod-shaped bacterial strains were designated B21^T and C4-1^T. Phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that the strains B21^T and C4-1^T belonged to the genera Gordonia and Nocardioides, respectively. The draft genome of strain B21ᵀ consists of 4.99 Mb with a G+C content of 68.3 mol%, while that of strain C4-1ᵀ is 4.80 Mb with a 72.8 mol% G+C content. The cells of strain B21^T were non-motile and grew at a temperature of 15-50 °C (optimum, 40 °C), in the presence of 0-11.0% (w/v) sodium chloride (NaCl) (optimum, 0.0%) and at pH 5.0-12.0 (optimum, 8.0). The cells of strain C4-1^T were non-motile and grew at a temperature of 15-30 °C (optimum, 30 °C), in the presence of 0-8.0% (w/v) NaCl (optimum, 0%) and at pH 5.0-10.0 (optimum, 8.0). The novel strains B21^T and C4-1^T exhibited average nucleotide identity values of 73.9-87.2% and 75.0-81.4% and digital DNA-DNA hybridization values of 19.9-32.8% and 20.0-24.0%, with reference strains in the genera Gordonia and Nocardioides, respectively. We thus propose the names Gordonia aurantiaca (type strain B21^T=KACC 23739^T=TBRC 19009^T) and Nocardioides secundeburneus (type strain C4-1^T=KACC 23738^T=TBRC 19008^T).

In the present study, genome-based metrics, phylogenetic and pangenomic analyses were used to investigate the relationship between three closely related species within the genus Virgibacillus (Virgibacillus salexigens, Virgibacillus kapii and Virgibacillus massiliensis). While 16S rRNA gene comparison revealed high similarity, overall genomic relatedness indices, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), exceeded the species delineation thresholds (ANI: 95-96 %, dDDH: 70%), indicating an even closer genetic relationship. Additionally, the phylogenomic analysis, along with pan-genome analysis, further supported the close relationship, placing the three species in a well-supported branch with a significant proportion of 3,809 shared core genes. Based on the combined evidence from genomic and phenotypic comparison, we propose reclassifying V. kapii Daroonpunt et al. 2016 and V. massiliensis Khelaifia et al. 2023 as later heterotypic synonyms of V. salexigens (Garabito et al. 1997) Heyrman et al. 2003. This study underscores the effectiveness of genome-based methods for accurate and reliable bacterial classification.

Four Gram-stain-positive bacterial strains, designated as YY-01^T, YY-02^T, YY-03^T and YY-04, were isolated from pit mud (YY-01^T, YY-02^T and YY-04) and daqu (YY-03^T) samples collected at a winery in Shandong Province, China. Phylogenetic and genomic analyses, along with bioassays and antibiotic susceptibility testing, revealed that the four strains, YY-01^T, YY-02^T, YY-03^T and YY-04, represent three novel species within the genus Microbacterium. Phylogenetic reconstruction based on 16S rRNA gene sequences revealed the closest relatives as follows: strain YY-01^T shares closest affinity with Microbacterium pseudoresistens CC-005209^T (97.1% similarity), strains YY-02^T and YY-04 cluster with Microbacterium esteraromaticum DSM 8609^T (98.3-98.4% similarity) and strain YY-03^T aligns with Microbacterium mitrae M4-8^T (97.6% similarity). Genome phylogeny further resolved strain YY-01^T as a sister lineage to Microbacterium laevaniformans DSM 20140^T, while strains YY-02^T, YY-03^T and YY-04 exhibited phylogenetic relationships congruent with the 16S rRNA topology. Genomic relatedness analysis demonstrated that strains YY-02^T and YY-04 share an OrthoANIu value of 99.9% and a digital DNA-DNA hybridization (dDDH) value of 100%, confirming their classification as conspecific. In contrast, OrthoANIu and dDDH values between strains YY-01^T, YY-02^T and YY-03^T and other Microbacterium species were ≤82.1 and 28.3%, respectively, supporting their distinct species status. Chemotaxonomic analysis revealed distinct profiles for each strain. Strain YY-01^T was characterized by MK-13 menaquinones; major fatty acids anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0; and the polar lipids diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). Strain YY-02^T contained predominant menaquinones MK-11 and MK-13 and major fatty acids anteiso-C_17 : 0, anteiso-C_15 : 0 and iso-C_16 : 0, along with DPG and PG. Strain YY-03^T possessed major menaquinones MK-11 and MK-13; major fatty acids anteiso-C_15 : 0, iso-C_15 : 0 and iso-C_16 : 0; and polar lipids DPG and PG. Integrative genomic, phenotypic and phylogenetic evidence supports the proposal of three novel species: Microbacterium luticellae sp. nov. (type strain YY-01^T=GDMCC 1.5102^T=KCTC 59478^T), Microbacterium alcoholitolerans sp. nov. (type strain YY-02^T=GDMCC 1.5103^T=KCTC 59479^T) and Microbacterium daqui sp. nov. (type strain YY-03^T=GDMCC 1.5104^T=KCTC 59480^T).

A comparison of 16S rRNA gene sequences between Peribacillus frigoritolerans DSM 8801 ^T and Peribacillus castrilensis N3^T revealed 99.9% sequence similarity, suggesting their close relatedness and the possibility of these strains belonging to the same species. The genus Peribacillus includes 21 species with validly published names. The type species P. frigoritolerans DSM 8801^T (=ATCC 25097^T=CCUG 43489^T=CIP 67.20^T=JCM 11681^T) was isolated from arid soil in Morocco, while P. castrilensis N3^T (=CECT 30509^T=LMG 32505^T) was isolated from the faeces of a river otter in Castril (Granada, southern Spain). The present study used whole-genome data to clarify the taxonomic assignment of these two closely related Peribacillus species. P. frigoritolerans DSM 8801^T and P. castrilensis N3^T share similar chemotaxonomic and phenotypic characteristics. Their main cellular fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0. Overall genomic relatedness indices analyses indicated that P. frigoritolerans DSM 8801^T and P. castrilensis N3^T shared average nucleotide identity and digital DNA-DNA hybridization values >95% and >70%, which are the currently accepted thresholds for species-level delineation. Additionally, these taxa formed a tight cluster within the genus Peribacillus in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree. Based on the combined evidence and the earliest valid publication, priority is given to P. frigoritolerans (Delaporte and Sasson 1967) Montecillo and Bae 2022. Peribacillus castrilensis Rodríguez et al. 2023 is proposed to be a later heterotypic synonym of P. frigoritolerans (Delaporte and Sasson 1967) Montecillo and Bae 2022.