International journal of systematic and evolutionary microbiology最新文献

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).

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).

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).

A novel, strictly anaerobic, Gram-positive, rod-shaped bacterium, designated strain LBM23126^T, was isolated from the pit clay of strong aroma-type liquor-making, exhibiting high temperature tolerance and lacking motility. LBM23126^T had a genome size of 2,416,380 bp and a G+C content of 52.5 mol%. The major fatty acid was C_16 : 0 (16.46%). The polar lipids of strain LBM23126^T were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three glycolipids, nine phospholipids, two aminolipids, two aminophospholipids and six unidentified lipids. LBM23126^T thrived in a pH range from 6.0 to 8.5 (optimum, pH 7.0-8.0), a temperature from 30 °C to 40 °C (optimum, 35-40 °C) and a salt tolerance of 0-2 % (w/v) sodium chloride (optimum, 0%). Notably, this bacterium was unable to utilize common sugars like glucose, maltose and sucrose, making it unique within the family Oscillospiraceae. LBM23126^T can use pyruvate as the carbon source to produce acetic acid as the primary metabolic product. LBM23126^T grew well with yeast extract, beef extract and tryptone. Comparing the 16S rRNA gene sequence identities of LBM23126^T with other Oscillospiraceae members, LBM23126^T showed the closest relationship with Intestinimonas butyriciproducens SRB-521-5-I^T (91.94%) and followed by Intestinimonas massiliensis GD2^T (91.22%). The average nucleotide identity (ANIb) based on blastn values for strain LBM23126^T with I. butyriciproducens SRB-521-5-I^T and I. massiliensis GD2^T were 74.05 and 74.07 %, respectively. The average amino acid identity (AAI) values for strain LBM23126^T with I. butyriciproducens SRB-521-5-I^T and I. massiliensis GD2^T were 53.63 and 53.31 %, respectively, while the percentage of conserved proteins (POCP) was 35 and 34 %, respectively. The AAI and POCP values were all lower than the thresholds required for classifying a new genus. Based on morphology, physiology, biochemistry, genotypic characteristics and phylogenetic analysis, strain LBM23126^T represents a novel species of a novel genus of the family Oscillospiraceae, for which the name Acidaminobacterium chupaoyuni gen. nov., sp. nov. is proposed. The type strain is LBM23126^T (=GDMCC 1.4723^T=JCM 37290^T).

A Gram-stain-negative, aerobic, motile-by-gliding bacterium, designated strain RHTr2^T, was isolated from the marine sponge Rhabdastrella globostellata collected in waters surrounding the Penghu Islands, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RHTr2^T displayed the highest 16S rRNA gene sequence similarities to Aquimarina versatilis CBA3207^T (94.2%), Aquimarina acroporae D1M17^T (93.7%) and Aquimarina intermedia LMG 23204^T (93.2%). Strain RHTr2^T grew with 1-5% (w/v) NaCl (optimum, 2-3%), at 17-37 °C (optimum, 30 °C) and at pH 6.0-8.0 (optimum, pH 6.0-7.0). Strain RHTr2^T was able to degrade starch, Tweens (20, 40 and 80) and gelatin; flexirubin-type pigments were produced. Strain RHTr2^T contained menaquinone 6 as the major respiratory quinone, and iso-C_15 : 0 and iso-C_17 : 0 3-OH as major fatty acids (> 10%). The polar lipids of strain RHTr2^T were an unidentified aminophospholipid, three aminolipids, a phospholipid and an unidentified polar lipid. The DNA G+C content was 31.4 mol% based on genome sequence analysis. The average nucleotide identity and digital DNA-DNA hybridization values between strain RHTr2^T and the most closely related members of the Aquimarina genus were lower than the recommended thresholds for species delineation. Based on its phenotypic and genotypic characteristics and on the phylogenetic and phylogenomic evidence presented, strain RHTr2^T represents a novel species of the genus Aquimarina for which the name Aquimarina rhabdastrellae sp. nov. is proposed. The type strain is RHTr2^T (=JCM 37598^T=UCCCB 217^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.

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).