International journal of systematic and evolutionary microbiology最新文献

The prokaryotic generic names Brachymonas Hiraishi et al. 1995 and Bosea Das et al. 1996 are illegitimate because they are later homonyms of the genus names Brachymonas Grassé 1952 (Protozoa, Polymastigidae) and Bosea He and Qian 1979 (a fossil dinoflagellate) [Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes (ICNP)]. We therefore propose the replacement names Allobrachymonas gen. nov., Allobrachymonas chironomi comb. nov., Allobrachymonas denitrificans comb. nov., Allobrachymonas wangyanguii comb. nov., Allobosea gen. nov., Allobosea beijingensis comb. nov., Allobosea caraganae comb. nov., Allobosea eneae comb. nov., Allobosea lathyri comb. nov., Allobosea lupini comb. nov., Allobosea massiliensis comb. nov., Allobosea minatitlanensis comb. nov., Allobosea psychrotolerans comb. nov., Allobosea robiniae comb. nov., Allobosea rubneri comb. nov., Allobosea spartocytisi comb. nov., Allobosea thiooxidans comb. nov., Allobosea vaviloviae comb. nov., Allobosea vestrisii comb. nov. and Alloboseaceae fam. nov.

A novel UV-resistant, red-pigmented, Gram-stain-positive, aerobic, non-motile, coccoid bacterial strain, designated SM5_A1^T, was isolated from lake sediment collected from Schirmacher Oasis, Queen Maud Land, Antarctica. The phylogenetic analysis, based on the 16S rRNA gene sequence, showed that the strain SM5_A1^T was closely related to Deinococcus saxicola DSM 15974^T (98.39%), Deinococcus frigens DSM 12807^T (97.69%) and Deinococcus marmoris DSM 12784^T (97.06%). The overall genome-related indices revealed D. marmoris DSM 12784^T as the phylogenetically nearest relative with an average nucleotide identity of 89.69%, an average amino acid identity of 92.14% and a digital DNA-DNA hybridization of 38.3%. The DNA G+C content of the isolate was 64.05 mol%, while the predominant respiratory quinone was menaquinone 8 (MK-8). The major cellular fatty acids were summed feature 3 (C_16:1  ω7c/C_16:1  ω6c), C_15:1  ω6c, C_16:0, summed feature 9 (C_17:1 iso ω9c) and C_15:0 iso. The prominently detected polar lipids were aminolipids, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphoglycolipids and phosphatidylglyceroylalkylamine. Based on the phenotypic, phylogenetic and chemotaxonomic data, the strain SM5_A1^T represents a novel species in the genus Deinococcus for which the name Deinococcus pantiae is proposed. The type strain is SM5_A1^T (MCC 5347^T=JCM 36669^T=KCTC 43670^T).

The novel strains CHS3-5^T and M-2^T were isolated from seawater collected near Suaeda japonica colonies on Seongmodo Island, Republic of Korea. Strain CHS3-5^T was Gram-stain-negative, motile with flagella, rod-shaped, strictly aerobic and formed circular, convex, ivory-coloured colonies, while strain M-2^T was Gram-stain-negative, motile by gliding, rod-shaped, strictly aerobic and formed circular, raised, dark yellow colonies. Based on 16S rRNA and draft genome analyses, strains CHS3-5^T and M-2^T were identified as members of the Oceanimonas and Arenibacter genera, respectively. Strain CHS3-5^T grew at temperatures of 10-40 °C, pH 4.0-10.0 and in the presence of 2.0-11.0% NaCl, with optimal growth at 30 °C, pH 7.0 and 3.0% NaCl. Strain M-2^T grew at temperatures of 15-40 °C, pH 6.0-9.0 and in the presence of 2.0-4.0% NaCl, with optimal growth at 30 °C, pH 7.0 and 3.0% NaCl. Both novel strains showed low genomic relatedness to their respective type species. The average nucleotide identity and digital DNA-DNA hybridization values were 84.5-85.7% and 26.5-34.7% for strain CHS3-5^T and 76.6-85.9% and 18.6-30.3% for strain M-2^T, respectively, supporting their classification as novel species. We propose the names Oceanimonas aquatica sp. nov. (type strain CHS3-5^T=KACC 23248^T=TBRC 17651^T) and Arenibacter flavimaris sp. nov. (type strain M-2^T=KACC 23249^T=TBRC 17650^T) for these strains.

Two aerobic, Gram-stain-negative, motile, rod-shaped bacteria, designated as strains TEGAF015^T and KACHI17^T, were isolated from surface lake and river waters in Japan. Strains TEGAF015^T and KACHI17^T had cell dimensions of ~0.4-0.6×1.3-2.9 µm and 0.4-0.5×2.5-4.8 µm (width×length), respectively. Strain KACHI17^T was positive for casein hydrolysis, whereas strain TEGAF015^T was negative. Phylogenetic analyses based on the 16S rRNA gene (1,290 bp) and 120 ubiquitous single-copy protein-encoding genes (5,035 aa) revealed that TEGAF015^T and KACHI17^T formed clusters closely related to Sediminibacterium salmoneum NJ-44^T and Sediminibacterium goheungense HME7863^T, respectively. However, the average nucleotide identity by orthology, average amino acid identity and digital DNA-DNA hybridization values confirmed that the isolates represent distinct species from closest phylogenetic relatives. The major cellular fatty acids identified in both strains included iso-C_15:0, iso-C_15:1 G, anteiso-C_15:0 and iso-C_17:0 3-OH. Additionally, TEGAF015^T contained anteiso-C_15:1 A, iso-C_15:0 3-OH and iso-C_16:0 3-OH. Phosphatidylethanolamine was identified as the major polar lipid of strains TEGAF015^T and KACHI17^T, which also contained menaquinone-7 as the predominant respiratory quinone and had DNA G+C contents of 38.5 and 40.0 mol%, respectively. Genome sequencing of the two isolates revealed genome sizes of 3.06 and 3.14 Mbp, respectively. Furthermore, both isolates were capable of converting dissolved organic nitrogen into ammonium during growth. These results indicated that strains TEGAF015^T and KACHI17^T represent two distinct novel species within the genus Sediminibacterium. The proposed names are Sediminibacterium planctonicum sp. nov. (type strain TEGAF015^T=JCM 16661^T=NCIMB 15525^T) and Sediminibacterium longum sp. nov. (type strain KACHI17^T=JCM 36264^T=LMG 33984^T).

A Gram-stain-negative, strictly aerobic and motile rod, designated strain SyP6R^T, was isolated from the freshwater alga Synura petersenii in Nakdong River, Republic of Korea, representing a niche expansion of Methylobacterium to the algae. Colonies were pink-coloured, convex and circular on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SyP6R^T formed a distinct phyletic lineage within the genus Methylobacterium, showing the highest similarity to Methylobacterium platani PMB02^T (98.9%). Genomic G+C content was 69.6 mol%, and phylogenomic analysis supported its distinct phyletic lineage. The average nucleotide identity values (89.2-89.6%) and digital DNA-DNA hybridization values (36.3-38.2%) with the closely related taxa were clearly below the species delineation thresholds. Notably, strain SyP6R^T possesses biosynthetic genes for B vitamins, including thiamine, riboflavin, pantothenate and folate, highlighting its potential ecological role as a vitamin-supplying symbiont. Strain SyP6R^T was oxidase-positive and catalase-negative, growing optimally at 30 °C and pH 7.0 and 0.25% (w/v) NaCl. Strain SyP6R^T possessed ubiquinone-10 as the sole respiratory quinone and C_16:0, summed feature 5 (comprising C_18:0 ante and/or C_18:2 ω6,9c), C_18:0, summed feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c) as the major cellular fatty acids (>5%). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. Based on polyphasic evidence, strain SyP6R^T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium synurae sp. nov. is proposed. The type strain is SyP6R^T (=KACC 19923^T=JCM 33308^T).

Bifidobacteria are among the most dominant members of the human gut microbiota throughout life and are associated with host health. Multiple Bifidobacterium species have been isolated from human faeces, with species composition differing according to host age and between individuals. This species- and subspecies-level diversity reflects adaptation to host niches. Bifidobacterium catenulatum currently comprises two subspecies catenulatum and kashiwanohense, which appear to exhibit different ecological adaptations. Our previous study suggested undefined lineages closely related to B. catenulatum. In this study, we investigated these lineages through comparative genomic and phylogenetic analyses of 43 strains, including new isolates from human faeces.Phylogenetic reconstructions based on 16S rRNA gene sequences, multilocus sequence analysis, average nucleotide identity (ANI) and core-gene alignments consistently supported the delineation of two distinct taxa. The first group, consisting of 15 strains, exhibited ANI values of ≥96.41% among themselves but ≤94.79% compared with the known subspecies of B. catenulatum, confirming its classification as a novel species, which was recently validated as Bifidobacterium hominis. The second group, comprising four strains, showed ANI values ranging from 94.38 to 95.65% compared to the existing subspecies of B. catenulatum, indicating that they belong to the same species. However, phylogenetic analyses and distinct substrate utilization profiles supported their designation as a novel subspecies, B. catenulatum subsp. puerorum subsp. nov.Comparative genomic analyses revealed key differences in genes associated with gut adaptation. B. catenulatum subsp. puerorum harboured genes involved in human milk oligosaccharide (HMO) and urea metabolism, consistent with its isolation from infant faeces. In contrast, B. hominis exhibited strain-dependent variation in genes for HMO and xylooligosaccharide utilization. Phenotypic analyses supported these distinctions, including unique inulin utilization by B. catenulatum subsp. puerorum. Based on these findings, we characterized the two clades and propose the novel subspecies B. catenulatum subspecies puerorum, with type strain YIT 11099^T (=JCM 37523^T=DSM 118686^T).

During a survey for natural-rubber-degrading actinobacteria associated with soils from Hevea brasiliensis plantations in Thailand, two strains, ABSL1-1^T and ABSL49-1^T, were isolated using mineral salts medium with natural rubber as the sole carbon source. Polyphasic taxonomy placed both strains within the genus Gordonia. Strain ABSL1-1^T showed the highest 16S rRNA gene sequence similarity to Gordonia otitidis NBRC 100426^T (98.5%) and Gordonia soli NBRC 108243^T (98.3%), while ABSL49-1^T showed the highest similarity to Gordonia polyisoprenivorans DSM 44302^T (98.4%). The digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on blast values between ABSL1-1^T and closely related type strains were 20.1-20.9%, and 74.1-76.5%, respectively, while those for ABSL49-1^T and closely related type strains were 20.6-22.9%, and 74.3-79.1%, respectively. The cell-wall peptidoglycan of both strains contained meso-diaminopimelic acid and the whole-cell sugars comprised ribose, arabinose, galactose and glucose. Both strains contained MK-9(H₂) as the major menaquinone and phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside were detected as the polar lipids. The predominant fatty acids of ABSL1-1^T were C_16:0, and C_18:1  ω9c, while those for ABSL49-1^T were C_16:0, C_18:1  ω9c, summed feature 3 (C_16:1  ω7c/_C16:1  ω6c) and C_18:0 10-methyl. The G+C contents of the genomic DNA of strains ABSL1-1^T and ABSL49-1^T were 67.0 mol% and 66.0 mol%, respectively. Based on the results of a polyphasic taxonomic analysis, strains ABSL1-1ᵀ and ABSL49-1ᵀ represent the type strains of two novel species of the genus Gordonia, for which the names Gordonia heveisoli sp. nov. (type strain ABSL1-1ᵀ=TBRC 15892ᵀ=NBRC 116252ᵀ) and Gordonia gummivorans sp. nov. (type strain ABSL49-1ᵀ=TBRC 15624ᵀ=NBRC 115559ᵀ) are proposed.

The prokaryotic genus names Baileyella Wylensek et al. 2021, Lucifera Sánchez-Andrea et al. 2019, and Microvenator Wang et al. 2022 are illegitimate because they are later homonyms of Baileyella Özdikmen 2009 (a fossil member of the Gonyaulacaceae, Gonyaulacales, Dinophyceae), Lucifera Baker 2010 (Keroplaridae, Diptera) and Microvenator Ostrom 1970 (a fossil member of the Caetagnatidae, Saurichia, Reptilia), respectively [Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes (ICNP)]. We therefore propose the replacement names Allobaileyella gen. nov., Allobaileyella intestinalis comb. nov., Allolucifera gen. nov., Allolucifera butyrica comb. nov., Allomicrovenator gen. nov., Allomicrovenator marinus comb. nov. and Allomicrovenatoraceae fam. nov.