International journal of systematic and evolutionary microbiology最新文献

The genus Clostridium encompasses phylogenetically diverse, obligately anaerobic, Gram-positive, spore-forming bacteria, yet taxonomic resolution for several members remains limited by the conservatism of the 16S rRNA gene. We reassessed four closely related species pairs: Clostridium baratii and Clostridium nitritogenes; Clostridium thermopalmarium and Clostridium colicanis; Clostridium botulinum and Clostridium combesii; and Clostridium estertheticum subsp. estertheticum and Clostridium estertheticum subsp. laramiense. A polyphasic framework was applied, integrating 16S rRNA and core-genome phylogenies, whole-genome relatedness metrics (digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity), phenotypic characterization and carbohydrate-active enzyme profiling. Concordant genomic and phenotypic evidence supported the synonymization of C. nitritogenes (Prévot 1940) Bernard et al. 2018 with C. baratii (Prévot 1938) Holdeman and Moore 1970, C. colicanis Greetham et al. 2003 with C. thermopalmarium Soh et al. 1991 and C. estertheticum subsp. laramiense (Kalchayanand et al. 1993) Spring et al. 2003 with C. estertheticum subsp. estertheticum (Collins et al. 1993) Spring et al. 2003. By contrast, despite high genomic relatedness, C. botulinum (van Ermengem 1896) Bergey et al. 1923 and C. combesii (Prévot and Laplanche 1947) Bernard et al. 2018 displayed reproducible phenotypic and functional distinctions consistent with subspecies status. We, therefore, propose C. botulinum subsp. combesii comb. nov., alongside C. botulinum subsp. botulinum comb. nov., thereby refining genome-based classification within the genus.

Three strains of Gram-negative, cold-adapted, aerobic bacteria were isolated on the coast of the Alasheyev Bight in the area of the Vecherniy region, the Thala Hills Oasis, Enderby Land, East Antarctica. Strains TMP9^T and TMP25 were isolated from temporary meltwater ponds, while strain G.S.17^T was obtained from a sample of green snow. Strains TMP9^T and TMP25 were motile rods, catalase-negative and oxidase-positive, while G.S.17^T was rod-shaped and exhibited motility, but was catalase- and oxidase-positive. TMP9^T and TMP25 grew at 4-25 °C, pH 5.5-9.0 and tolerated up to 4.5% NaCl. G.S.17^T grew at 4-28 °C, pH 5.0-8.5 and NaCl concentration up to 3.0%. The 16S rRNA gene sequence analysis placed all strains within the genus Pseudomonas: strains TMP9^T and TMP25 are closely related to Pseudomonas peli DSM 17833^Т (99.5% identity), and the strain G.S.17^T exhibits the highest similarity to Pseudomonas rossensis P2663^T (99.1% identity). Whole-genome comparisons using average nucleotide identity suggested that strains TMP9^T and TMP25 represent a novel species within the genus Pseudomonas, which is most closely related to Pseudomonas guineae LMG 24016^T (83.3%). Strain G.S.17^T also represents a novel species within the genus Pseudomonas and is most closely related to Pseudomonas caspiana FBF102^T (80.5%). The predominant cellular fatty acids of strains TMP9^T, TMP25 and G.S.17^T were cis-9-hexadecenoic, hexadecanoic and trans-9-octadecenoic acids. Physiological and biochemical tests, as well as genomic analysis results, clearly differentiated strains TMP9^T, TMP25 and G.S.17^T from type strains of closely related species. Thus, according to the data obtained, two novel species within the genus Pseudomonas are proposed: Pseudomonas vesperimontis sp. nov. (type strain TMP9^T=BIM B-1560^T=VKM B-3887^T) and Pseudomonas viridinivis sp. nov. (type strain G.S.17^T=BIM B-1635^T=VKM B-3888^T).

Two bacterial strains, designated E22-M8^T and B22-R8^T, were isolated from water sample collected from LungmuCo lake in Xizang of China. The 16S rRNA gene analysis revealed that strain E22-M8^T was most closely related to members of the genus Pseudidiomarina, exhibiting the highest sequence similarity of 97.38 and 97.39% to Pseudidiomarina halophila BH195^T and Pseudidiomarina terrestris 1APP75-27a^T, respectively. While strain B22-R8^T showed the highest similarity to species of the genera Terrihabitans and Flaviflagellibacter: 97.69, 96.80 and 96.66% to 'Terrihabitans rhizophilus' PJ23^T, Terrihabitans soli IZ6^T and Flaviflagellibacter deserti SYSU D60017^T. For strain E22-M8^T, the digital DNA-DNA hybridization (dDDH) values with its closest relatives P. halophila BH195^T and P. terrestris 1APP75-27a^T were 25.7 and 20.1%, respectively; the average nucleotide identity (ANI) values were 83.5 and 78%; and the average amino acid identity (AAI) values were 90.4 and 86.4%, all below the recognized species delineation thresholds. For strain B22-R8^T, the corresponding dDDH, ANI and AAI values with its closest relatives 'T. rhizophilus' PJ23^T, T. soli IZ6^T and F. deserti SYSU D60017^T also fell below the respective species thresholds. Biochemically and physiologically, both strains exhibited distinct traits that further supported their novelty. Based on comprehensive polyphasic analyses, strain E22-M8^T (=CGMCC 1.19205^T=KCTC 92346^T) is proposed as a novel species named Pseudidiomarina xizangensis sp. nov., and strain B22-R8^T (=CGMCC 1.19187^T=KCTC 92343^T) as a novel species designated Terrihabitans aquatilis sp. nov.

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).

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.

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.

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.

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.