International journal of systematic and evolutionary microbiology最新文献

A Gram-stain-negative, aerobic, oxidase- and catalase-positive, motile with a polar flagellum, rod-shaped bacterium designated as strain EMRT-3^T was isolated from sediment collected in a coal mine drainage treatment system in the Republic of Korea. Growth of strain EMRT-3^T was observed in Reasoner's 2A medium at 10-35 °C (optimum, 25-30 °C) and pH 4.5-8.0 (optimum, pH 6.5-7.5) and in the presence of 0-0.5% NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain EMRT-3^T belongs to the genus Asticcacaulis and was closely related to Asticcacaulis solisilvae CGM1-3EN^T, Asticcacaulis biprosthecium DSM 4723^T, Asticcacaulis benevestitus DSM 16100^T and Asticcacaulis taihuensis CGMCC 1.3431^T with 97.0, 96.3, 96.2 and 95.9% sequence similarities, respectively. A phylogenomic tree also showed that strain EMRT-3^T formed a distinct clade within genus Asticcacaulis and clustered with the four type species (CGM1-3EN^T, DSM 4723^T, DSM 16100^T and CGMCC 1.3431^T). The average nucleotide identity and digital DNA-DNA hybridization values between strain EMRT-3^T and closely related type strains were 72.8-75.6% and 20.0-20.7%, respectively. The genomic DNA G+C content of EMRT-3^T was 60.0 mol%. Genome annotation for strain EMRT-3^T indicated broad metabolic capacity, encompassing complete pathways for central carbohydrate and amino acid metabolism as well as the biosynthesis of essential cofactors and vitamins. Importantly, the detection of genes associated with copper, nickel/cobalt and iron homeostasis, along with acid tolerance, highlights its adaptation to metal-rich and acidic environments. The major fatty acids of EMRT-3^T were C_12:0, C_16:0, C_12:0 3-OH, C_15:0 2-OH, C_16:0 2-OH, C_16:1 2-OH, summed feature 3 (C_16:1  ω7c and/or C_16:1  ω6c) and summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c). The major polar lipids were phosphatidylglycerol, aminophospholipids and glycolipids. Based on the polyphasic taxonomic evidence, strain EMRT-3^T represents a novel species within the genus Asticcacaulis, for which the name Asticcacaulis carbonis sp. nov. is proposed. The type strain is EMRT-3^T (=KACC 22206^T=JCM 34539^T=FBCC-B5258^T).

Mangrove sediments are recognized as hotspots for methane emissions and harbour diverse methanogenic archaea. In this study, we describe two novel methanogens, strains T3^T and Mfa9^T, isolated from mangrove sediment samples in the Futian Mangrove Nature Reserve in Shenzhen, People's Republic of China. Cells of strains T3^T and Mfa9^T are irregularly coccoid in shape, with diameters of 0.7-1.4 µm and 0.6-1.7 µm, respectively. Both strains utilize methanol, methylamine, dimethylamine, trimethylamine, dimethyl sulphide and acetate as the sole carbon source for growth and methanogenesis, but not H₂/CO₂, formate, choline, betaine or pyruvate. Strain T3^T grew at 15-42 °C (optimum 37 °C), pH 6.0-8.0 (optimum 6.5) and 0-0.72 M NaCl (optimum 0.10 M NaCl). Strain Mfa9^T grew at 20-33 °C (optimum 25 °C), pH 5.5-7.5 (optimum 7.0) and 0-0.72 M NaCl (optimum 0.51 M NaCl). The genomic G+C contents of strains T3^T and Mfa9^T are 43.3 mol% and 46.2 mol%, respectively. Phylogenetic analyses revealed that both strains are classified within the genus Methanosarcina. Strain T3^T was mostly related to Methanosarcina siciliae T4/M^T, with 16S rRNA gene similarity of 99.7%, an average nucleotide identity of 88.8% and a digital DNA-DNA hybridization of 35.7%. By contrast, strain Mfa9^T shared 98.8% 16S rRNA gene similarity with Methanosarcina semesiae MD1^T. As M. semesiae MD1^T is unavailable and lacks genomic data, comparative analyses with its closer relative Methanosarcina sp. MTP4 (99.8% 16S rRNA gene identity), together with genomic and phenotypic differences from M. semesiae, support the designation of strain Mfa9^T as a novel species. In conclusion, two novel species of the genus Methanosarcina, Methanosarcina mangrovi sp. nov. and Methanosarcina sediminis sp. nov., are proposed. The type strain of M. mangrovi sp. nov. is T3^T (=CCAM 2189^T=JCM 39553^T), and the type strain of M. sediminis sp. nov. is Mfa9^T (=CCAM 2190^T=JCM 39554^T).

Four strains of a Gram-stain-positive, coccoid, catalase-positive, non-motile bacterium were recovered from nasal lavage samples collected from children in Wisconsin during the Spring of 2008. These strains, designated RSM42^T, RSM292, RSM386 and RSM407, were subjected to a comprehensive biochemical and polyphasic taxonomic investigation. Despite the novel bacterium sharing 99.6% 16S rRNA gene sequence identity with Rothia mucilaginosa 5762/67^T, BLAST+ average nucleotide identity, MUMmer3 average nucleotide identity and digital DNA-DNA hybridization values of 91.3%, 91.9% and 43.1%, respectively, were below the cut-off values routinely used for species demarcation. Consistent with these findings, phylogenetic and pangenomic comparisons indicated that RSM42^T, RSM292, RSM386 and RSM407 form a separate lineage within the genus Rothia. Strain RSM42^T is further distinguished from R. mucilaginosa 5762/67^T by its unique ability among Rothia species to use fructose-6-phosphate as a sole carbon source. RSM42^T also exhibits an enzyme activity profile consistent with R. mucilaginosa, as it is positive for valine arylamidase and negative for C4 esterase, β-glucosidase, pyrazinamidase and trypsin, a combination not observed in other Rothia species. The major fatty acids were anteiso-C_15:0 (44.2%) and iso-C_16:0 (14.4%), and the moderate fatty acids were anteiso-C_13:0 (2.3%), iso-C_14:0 (6.0%), C_14:0 (2.3%), iso-C_15:0 (5.9%), C_15:0 (1.9%), C_16:0 (9.3%) and anteiso-C_17:0 (9.5%). The major polar lipids were aminoglycolipid and diphosphatidylglycerol. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, these isolates represent a novel species within the genus Rothia, closely related to R. mucilaginosa, for which the name Rothia similimucilaginosa sp. nov. is proposed. The type strain is RSM42^T (=ATCC TSD-447^T=DSM 118581^T).

Bartonella species are host-associated Pseudomonadota causing various human diseases and a broad range of clinical manifestations. These bacteria are primarily maintained in animal reservoirs and transmitted to humans through direct contact or via haematophagous vectors. In this study, six novel Bartonella species - Bartonella numerosa sp. nov. strain CB178^T (=CSUR B1106^T=JCM 36790^T), Bartonella vaga sp. nov. strain CB169^T (=CSUR B1103^T=JCM 36788^T), Bartonella occidentalis sp. nov. strain CB175^T (=CSUR B1104^T=JCM 36789^T), Bartonella rhinolophi sp. nov. strain CB74^T (=CSUR B1102^T=JCM 36787^T), Bartonella eidoli sp. nov. strain CB189^T (=CSUR B1105^T=JCM 36791^T) and Bartonella propinqua sp. nov. strain CB54^T (=CSUR B1101^T=JCM 36786^T) - were isolated from Eidolon helvum, Rhinolophus fumigatus and Epomophorus gambianus bats in Senegal. Phylogenetic analyses of these species reveal their widespread distribution across Africa. Notably, B. vaga, isolated from E. helvum, clusters with rodent-associated Bartonella strains. This highlights the importance of studying both hosts, which may serve as reservoirs for Bartonella species and potentially contribute to the emergence of zoonotic diseases. All strains are Gram-negative, aerobic, rod-shaped and non-spore-forming. The predominant cellular fatty acids of strains CB169^T, CB175^T, CB74^T and CB54^T were C_18 : 1  ω7c, C_18 : 0 and C_16 : 0, except for strains CB178^T and CB189^T, in which C_18 : 1  ω7c, C_16 : 0 and C_18 : 0 were dominant.

The genus Dysgonomonas, established in 2000 and currently comprising nine isolated species, belongs to the order Bacteroidales. Despite its increasing ecological and clinical relevance, the genus remains taxonomically ambiguous, and criteria for genus-level classification have not been systematically assessed. In this study, we re-evaluated the taxonomy of Dysgonomonas using core genome phylogeny, average amino acid identity and percentage of conserved proteins. These genome-based metrics and physiological data revealed that the genus Dysgonomonas comprises at least three distinct genus-level lineages, and (i) Dysgonomonas sensu stricto represented by Dysgonomonas gadei, (ii) Indolivaga gen. nov. represented by Dysgonomonas capnocytophagoides and (iii) Pseudodysgonomonas gen. nov. represented by Dysgonomonas massiliensis are proposed. In addition, two strains MK137_Hg11^T and MK137_Hg34^T, facultative anaerobic bacteria, were isolated from the gut of the subterranean termite Reticulitermes speratus. On the basis of the collected data, we propose that strain MK137_Hg11^T represents a novel species within Dysgonomonas, while strain MK137_Hg34^T represents a novel species belonging to a fourth, previously unrecognized genus within the family Dysgonomonadaceae. We therefore propose the names Dysgonomonas reticulitermitis sp. nov. (type strain MK137_Hg11^T=JCM 35194^T=DSM 118089^T) and Viscerimonas tarda gen. nov., sp. nov. (type strain MK137_Hg34^T=JCM 35195^T=DSM 118090^T).

Strain G2-8^T was isolated from a soil sample collected from the saline area of Baodi District in Tianjin City. The isolate was a Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, and its colonies were round, raised, pale yellow, with a smooth surface, regular and clean edges. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain G2-8^T belonged to the genus Microbacterium and shared the highest sequence similarity with Microbacterium excoecariae CBS5P-1^T (98.5%), followed by Microbacterium amylolyticum N5^T (98.2%), Microbacterium gubbeenense DSM 15944^T (98.1%), Microbacterium indicum BBH6^T (97.5%), Microbacterium suaedae YZYP 306^T (97.5%) and Microbacterium karelineae TRM 80801^T (97.4%). Phylogenomic analysis showed that strain G2-8^T was related to members of the genus Microbacterium and represented an independent lineage. Growth occurred at 4-40 °C (optimum, 28 °C), up to 13.0% (w/v) NaCl (optimum, 0-2.0%) and pH 6.0-10.0 (optimum, pH 8.0). Its main fatty acids were anteiso-C_15 : 0 and anteiso-C_17 : 0. The major respiratory quinone of strain G2-8^T was MK-10, MK-11 and MK-12. The polar lipid profile of strain G2-8^T comprised diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. The genome of strain G2-8^T was 3.46 Mbp with a G+C content of 69.7 mol%. The average nucleotide identity (ANI) values between strain G2-8^T and other related species of the genus Microbacterium were found to be low (ANIm <84.8%, ANIb <77.2% and OrthoANIu <79.6%). Furthermore, the digital DNA-DNA hybridization and average amino acid identity values between strain G2-8^T and the closely related species ranged from 19.0 to 24.2% and from 65.9 to 79.6%, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain G2-8^T represents a novel species of the genus Microbacterium, for which the name Microbacterium salitolerans sp. nov. is proposed. The type strain is G2-8^T (=KCTC 49757^T=GDMCC 1.2353^T).

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.