International journal of systematic and evolutionary microbiology最新文献

The genus Bartonella comprises over 40 species, most of which are haemoparasites of mammals. Herein, we describe Bartonella bennetti sp. nov., a novel member of the genus, isolated from field voles (Microtus agrestis) in Kielder Forest, UK. Polyphasic characterization of three strains (C271^T, D105 and J117) of the proposed species indicated that they were closely related to members of phylogenetic lineage 3 (L3) of the genus. The average nucleotide identity (ANI) between C271^T and other L3 species ranged between 88.8 and 90.6%, supporting the proposal of a new species. C271^T shared ANIs approaching 96% with other members of L3 that are yet to be validly published but exhibited marked genomic, ecological and biogeographical differences from them, further justifying the creation of a new taxon. All three B. bennetti sp. nov. strains were found to possess genes encoding three VirB/D4 type IV secretion systems and associated effector proteins and to harbour a chromosomally integrated F-type conjugative plasmid, which forms an Hfr-like configuration not previously observed in the Bartonella genus. This integration could facilitate large-scale chromosomal gene transfer during conjugation, with potential consequences for adaptation, recombination and niche differentiation. The phylogenetic structure of L3, coupled with the ecological partitioning of its members, suggests that covert host specificity, not generalism, is the dominant mode of diversification. The absence of the Trw system, which facilitates host switching in lineage 4 (L4), may constrain ecological breadth in L3, thought to be undergoing a parallel adaptive radiation with L4. The discovery of B. bennetti sp. nov. underscores the importance of combining genomic, ecological and evolutionary evidence when delimiting species boundaries in Bartonella and raises new hypotheses about the role of Hfr-mediated recombination in the evolutionary dynamics of host-adapted pathogens. The type strain of B. bennetti sp. nov. is C271^T (CSUR B1113^T, NCTC 15117^T).

An actinobacterial strain, designated TRA05-7^T, was isolated from a saline lake sediment in the Ngari Prefecture, Xizang Autonomous Region, China. The cells were Gram-stain-positive, aerobic and short-rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TRA05-7^T was most closely related to members of the genus Homoserinimonas, with the highest sequence similarity to Homoserinimonas hongtaonis 194^T (98.48%). However, whole-genome phylogenetic analysis revealed a closer relationship with Homoserinimonas sedimenticola SYSU T00001^T, with the two strains forming a distinct cluster. The average nucleotide identity and digital DNA-DNA hybridization values between strain TRA05-7^T and H. sedimenticola were 77.3 and 20.7%, respectively. The genomic DNA G+C content was 65.7 mol%. Growth occurred at 4-40 °C (optimum 28 °C), pH 7-11 (optimum pH 7) and with 0-8% (w/v) NaCl (optimum 1%). The major menaquinones were MK-12, MK-11 and MK-13. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified lipid. The major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and anteiso-C_15:0. UV-Vis and HPLC analysis indicated that strain TRA05-7^T had the ability to produce carotenoids. Based on phylogenetic, genomic, phenotypic and chemotaxonomic analyses, strain TRA05-7^T represents a novel species of the genus Homoserinimonas, for which the name Homoserinimonas flava sp. nov. is proposed. The type strain is TRA05-7^T (=MCCC 1K10024^T=KCTC 59574^T).

A core genome-based phylogenomic analysis of representative strains of the species Limosilactobacillus reuteri identified eight lineages that differ from the six previously described L. reuteri subspecies. Four of them are represented by isolates obtained from intestinal digesta or faeces of rodents and primates, including strains LR77^T and LR80 (lineage X), mlc3^T and LR92 (lineage VIII), LR51^T and LR88 (lineage VII) and LR66^T and LR52 (lineage IX). Analyses of pairwise average nucleotide identity and digital DNA-DNA hybridization values further support their genetic divergence from existing L. reuteri subspecies. These findings suggest the classification of these four lineages as one novel species of Limosilactobacillus and three new subspecies of L. reuteri. Therefore, we propose the novel species Limosilactobacillus secundus sp. nov. (type strain LR77^T=DSM 113335^T=LMG 32469^T) and the novel subspecies L. reuteri subsp. pararodentium subsp. nov. (type strain mlc3^T=DSM 113337^T=LMG 32470^T), L. reuteri subsp. peregrinus subsp. nov. (type strain LR51^T=DSM 113336^T=LMG 32467^T) and L. reuteri subsp. simiae subsp. nov. (type strain LR66^T=DSM 113334^T=LMG 32468^T). This expanded taxonomic framework enhances our understanding of the genetic diversity of L. reuteri and further supports its adaptations to diverse vertebrate hosts.

Active hydrothermal chimneys were sampled from the newly discovered La Scala Vent Field, located on the Woodlark Ridge in the Pacific Ocean. Enrichment cultures yielded hyperthermophilic methanogens, from which several strains were isolated. Phylogenetic analysis based on the 16S rRNA gene and genome sequences revealed that strain 28A^T belongs to the genus Methanocaldococcus, within the family Methanocaldococcaceae and the order Methanococcales. Strain 28A^T shared 95.4-99.1% 16S rRNA gene sequence similarity with other species of Methanocaldococcus and was most closely related to Methanocaldococcus bathoardescens. Cells of strain 28A^T were coccoid in shape, with diameters ranging from 1.0 to 3.0 µm. The strain grew at temperatures between 50 and 85 °C (optimum: 75-80 °C), at pH values between 5.3 and 7.0 (optimum: pH 6.5) and in sodium chloride (NaCl) concentrations ranging from 5 to 50 g l⁻¹ (optimum: 20 g l⁻¹). Genome analysis revealed the presence of a 3.9 kbp plasmid. Based on 16S rRNA and genome phylogenetic analysis, average nucleotide identity and digital DNA-DNA hybridization values, we propose that strain 28A^T represents a novel species, for which the name Methanocaldococcus abyssi sp. nov. is proposed. The type strain is 28Aᵀ (=DSM 120179ᵀ=JCM 39640ᵀ).

Strains CF4.4^T and KK5.5^T, previously isolated from samples of biocrust and permafrost, respectively, collected from Northern Greenland, were characterized using a polyphasic approach. Both strains were Gram-stain-positive, non-motile and non-endospore-forming cocci, and showed growth between 4 and 25 °C and 0-20% (w/v) NaCl. Strain CF4.4^T showed growth at pH 6-11 [optimal growth at pH 9-10 and 5% (w/v) NaCl]. Its 16S rRNA gene sequence showed similarities over 99% with Nesterenkonia jeogali JG-241^T, Nesterenkonia lutea YIM 70081^T and Nesterenkonia sandarakina YIM 70009^T. Based on digital DNA-DNA hybridization, the closest type strain to strain CF4.4^T was Nesterenkonia aurantiaca DSM 27373^T (31.8% similarity). The major respiratory menaquinones of strain CF4.4^T were MK-7, MK-8, MK-9 and MK-10, and its major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and iso-C_16:0. Its cells contained diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. Strain KK5.5^T showed growth at pH 6-10, with optimal growth at pH 8-9 and 0-2.5% (w/v) NaCl. Phylogenetic analysis based on its 16S rRNA gene sequence showed that it was most closely related to Arthrobacter halodurans JSM 078085^T (99.1%), Arthrobacter ginkgonis SYP-A7299^T (97.7%) and Zafaria cholistanensis NCCP-1664^T (97.6%). The genome of strain KK5.5^T showed the most similarity to A. halodurans DSM 21081^T (22.6%) based on digital DNA-DNA hybridization. The major respiratory menaquinones of strain KK5.5^T were MK-9(H₂) and MK-10(H₂), with small amounts of MK-11(H₂). Its major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0 and iso-C_15:0, and its cells contained diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and an unidentified phospholipid. Based on the results presented in this study, we conclude that both strains represent novel species, for which we propose the names Nesterenkonia maliinae sp. nov. (type strain CF4.4^T=DSM 120326^T=LMG 34127^T) and Arthrobacter arnarulunnguaqae sp. nov. (type strain KK5.5^T=DSM 120323^T=LMG 34129^T).

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).

 A novel, strictly anaerobic, thermotolerant/halotolerant, heterotrophic bacterial strain, SD5^T, was isolated from a brine lake near Esperance, Western Australia. The strain was a non-motile, non-spore-forming, Gram-stain-positive rod. The DNA G+C content was 53.1 mol%, and the length of the closed genome was 3.14 Mbp, with 2,978 protein-encoding genes. 16S rRNA gene sequence identity indicates that the strain is most closely related to Fusibacter fontis KhalAKB1^T (89.50% identity). SD5^T was phylogenomically distinct from its closest neighbors in the family Acidaminobacteraceae, with percentage of conserved proteins values ranging from 38.74% to 42.66%. The strain grew between 4 and 42 °C (optimum 37 °C), at pH values between 6.5 and 9.0 (optimum 7.0) and with 1-10% (w/v) sodium chloride (optimum 5%). The strain exhibited an aggregated growth phenotype associated with biofilm formation under stress, with cell chains reaching nearly 100 µm in length. The predominant fatty acids were iso-C_15:1  ω7c (11.8%), iso-C_15:0 (9.3%) and C_16:0 (9.3%). Based on phylogenomic and chemotaxonomic analyses, SD5^T represents a novel species in a new genus, for which the name Halotolerantifilum yawarlongkerapense gen. nov., sp. nov., is proposed. The type strain is SD5^T (=DSM 117693^T=ATCC TSD-463^T). From this work, we also propose the reassignment of several currently unranked genera within the class Clostridia to families within the order Peptostreptococcales and propose the novel family Guggenheimellaceae fam. nov. based on our sequencing results.

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.