International journal of systematic and evolutionary microbiology最新文献

Four novel strains, designated p1-h21^T/p2-l61 and p3-h83^T/p4-l81, characterized as Gram-stain-negative, oxidase-positive, catalase-positive, obligately aerobic, non-motile and rod-shaped, isolated from blowhole swab samples of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis), collected from Hubei Province, China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two species. Strains p1-h21^T and p2-l61 were most closely related to Paracoccus endophyticus SYSUP0003^T (97.18% similarity) and Paracoccus aurantiacus TK008^T (97.03% similarity), whereas strains p3-h83^T and p4-l81 exhibited 96.89% similarity to Paracoccus kondratievae GB^T, and 96.53% similarity to Phaeovulum vinaykumarii DSM 18714^T. The DNA G+C contents of type strains p1-h21^T and p3-h83^T are 65.7 mol% and 66.9 mol%, respectively. These strains had summed feature 8 (comprising C_18 : 1  ω6c and/or C_18 : 1  ω7c) as major cellular fatty acids, ubiquinone 10 as the sole respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine as major polar lipids, which are typical for members of the genus Paracoccus. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the four novel strains and their reference strains (ANI <75.3%, dDDH <20.5%) are lower than the species delineation thresholds, along with distinct phenotypic and biochemical characteristics, distinguishing them from their closest relatives and other recognized Paracoccus species. Therefore, strains p1-h21^T/p2-l61 and p3-h83^T/p4-l81 represent two novel species in the genus Paracoccus, for which the names Paracoccus jiaweipingae sp. nov. and Paracoccus zhouxuedongae sp. nov. are proposed, with p1-h21^T (=GDMCC 1.4971^T=JCM 37697^T) and p3-h83^T (=GDMCC 1.4972^T=JCM 37698^T) as type strains.

An anaerobic, salt-tolerant, rod-shaped bacterium, strain JL216-2^T, was isolated from the shell of the hydrothermal gastropod Alviniconcha marisindica in the Tianxiu hydrothermal field on the Carlsberg Ridge, Indian Ocean. Cells of strain JL216-2^T were motile and 0.5×3-6 µm in size. Strain JL216-2^T grew at 10-32 °C (optimal 28 °C), pH 6.0-9.0 (optimal pH 7.0) and 0.5-12.0% (w/v) sodium chloride(NaCl, optimal 2.5%). Strain JL216-2^T exhibited metabolic versatility, being capable of heterotrophic growth on complex organic compounds. It also performed autotrophic growth by utilizing carbon dioxide (CO₂) fixation or sodium bicarbonate (NaHCO₃) as the sole carbon source, driven by hydrogen oxidation coupled with Fe(III) reduction. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to Helicovermis profundi S502^T (90.43% sequence similarity). The genome size of strain JL216-2^T was 4.91 Mb, with a G+C content of 39.54 mol%. Phylogenomic analysis and overall genome relatedness indices values indicated a close relatedness of strain JL216-2^T to H. profundi S502^T and Fusibacter spp. The combined genotypic and phenotypic data showed that strain JL216-2^T represents a novel genus within the order Eubacteriales. The type strain is JL216-2^T (=MCCC M30262^T=KACC 23553^T).

A Gram-negative bacillus isolated from human clinical cases in Aotearoa | New Zealand (NZ) and Australia was identified as a new species within the genus Yersinia based on genetic and phenotypic characteristics. This species demonstrated distinct biochemical differences in comparison to those typically reported for Yersinia enterocolitica (biotypes 1A, 1B, 2, 3, 4 and 5), including the ability to utilise raffinose and melibiose. Whole-genome sequencing data identified a total of 11 strains as a novel multi locus sequence type 598 (using the seven-gene McNally scheme). A closed genome for this species was obtained using Oxford Nanopore long-read sequencing, polished with high-accuracy Illumina short-read sequence data. Analysis of the 16S rRNA showed the closest similarity (98.36%) to Yersinia hibernica and Yersinia artesiana. Average nucleotide identity (ANI) values were below the threshold of ≤95% ANI when compared to the type strains of other Yersinia species, with Y. enterocolitica subsp. enterocolitica (94.1%) identified as the closest relative, thereby providing evidence that these strains should be considered as a novel species. The type strain is NZRM 4767^T =DSM 120367^T.

A novel Gram-stain-negative, rod-shaped, non-spore-forming, non-flagellated, strictly aerobic strain, designated as R2331^T, was isolated from coastal seawater of Yantai, P.R. China (127.59° E, 37.46° N). The organism grew optimally at 28-32 °C, at pH 7.0 and in the presence of 3.0% (w/v) NaCl. Strain R2331^T contained ubiquinone-10 as the predominant respiratory quinone and C_18 : 1  ω7c and/or C_18 : 1  ω6c as the major fatty acids. The predominant polar lipids of strain R2331^T were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and two unidentified aminolipids. The DNA G+C content of strain R2331^T was 59.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Yoonia ponticola KCTC 42133^T with 96.3% sequence similarity. Calculated ANI values, dDDH values and AAI values between strain R2331^T and the phylogenetically related species were in the range 71.4-73.7 %, 18.0-19.4 % and 67.2-71.1 %, respectively. Strain R2331^T fell within the cluster of the genus Cognatiyoonia in the phylogenomic tree. Based on polyphasic analyses, strain R2331^T represents a novel species of the genus Cognatiyoonia, for which the name Cognatiyoonia denitrificans sp. nov. is proposed. The type strain is R2331^T (=KCTC 8319^T=MCCC 1K04209^T).

A novel chlorophototrophic bacterium, strain BV2-C^T, was isolated from a microbial mat (~40 °C) at Rupite hot springs, Bulgaria. Cells were rod-shaped, Gram-negative, with numerous fimbriae/pili, but non-motile. Optimal growth occurred under micro-oxic conditions in the light (20-50 µmol photons m^-2 s^-1) at 45 °C (range 35-50 °C) and pH 7.2 (range pH 5.5-9.0). Bacteriochlorophyll c, bacteriochlorophyll a _P, echinenone and γ-carotene were the major pigments in cells capable of producing chlorosomes and type-1 homodimeric reaction centres. Dense liquid culture appeared greenish-brown, with cells forming small clumps and aggregates. Strain BV2-C^T grows photoheterotrophically using organic compounds as carbon source (i.e. a mixture of 20 proteinogenic amino acids or peptone) and thioglycolate as reduced sulphur source. Strain BV2-C^T obligately required branched-chain amino acids (l-isoleucine, l-leucine and l-valine) and l-lysine for growth. It is closely related to Chloracidobacterium thermophilum and 'Candidatus Chloracidobacterium aggregatum' with 16S rRNA gene sequence identities of 96.97 and 97.78%, respectively. The genome of strain BV2-C^T comprises two circular chromosomes of 2,659,040 and 1,000,103 bp (total genome, 3.65 Mb) and G+C content of 59.9 mol%. Phenotypic, phylogenetic and genomic analyses demonstrated that Chloracidobacterium validum strain BV2-C^T (=DSM 113832^T=JCM 39534^T) represents a novel species of the genus 'Candidatus Chloracidobacterium', which we hereby propose as Chloracidobacterium gen. nov. with Chloracidobacterium validum sp. nov. as the type species. Based on phylogenomic analyses, we also propose a new family, Chloroacidobacteriaceae fam. nov., and a new order, Chloracidobacteriales ord. nov., within the class Blastocatellia. We further propose the name 'Ca. C. aggregatum' for pro-valid publication with the genome sequence of strain E as nomenclatural type.

Mucin-degrading bacteria are recognized as potential players in weakening of the colonic mucus barrier and increased susceptibility to pathogens in the human gut due to their use of mucus as a nutrient source, sometimes in the context of a fibre-deficient diet. Using intact porcine gastric mucin glycoprotein as the main nutrient source, we isolated a Gram-positive, non-motile, rod-shaped, obligately anaerobic bacterium (UGRO018_0423^T) from faecal samples of a healthy adult. The strain grows with cells arranged in chains. Based on 16S rRNA gene sequence, the strain UGRO018_0423^T shared the highest similarity (96.94% and 96.75%) with Eubacterium hominis New-5^T and Amedibacillus hominis NSJ-176^T, respectively. Phylogenomic analyses based on 120 concatenated phylogenetically informative protein markers (full-length protein and protein domain sequences) and examination of the placement within the Genome Taxonomy Database (GTDB) reference tree revealed that the strain UGRO018_0423^T is not affiliated with the genera Eubacterium or Amedibacillus sensu stricto, and placed UGRO018_0423^T within the family Erysipelotrichaceae. This also indicated the problematic taxonomic status of both E. hominis and A. hominis that were placed within the same genus as UGRO018_0423^T based on phylogenomic analyses. Genomic comparisons based on average nucleotide identity and digital DNA-DNA hybridization between UGRO018_0423^T and E. hominis New-5^T and A. hominis NSJ-176^T indicated that the strain UGRO018_0423^T represents a novel species. These results combined with further chemotaxonomic and phenotypic characterization indicated that strain UGRO018_0423^T (=DSM 116809^T=ATCC TSD-466^T) represents a novel species within a novel genus in the family Erysipelotrichaceae, for which the name Hoskinsella mucinilytica gen. nov., sp. nov. is proposed. In addition, based on genomic comparisons and phylogenomic analysis, A. hominis is reclassified as a later heterotypic synonym of E. hominis, and both species are transferred into the genus Hoskinsella gen. nov. with reclassification of E. hominis as Hoskinsella hominis comb. nov. and A. hominis as Hoskinsella hominifaecis nom. nov.

The high carbon to nitrogen ratio in oil-contaminated environments limits the efficiency of bioremediation. Therefore, isolating nitrogen-fixing bacteria from oil-contaminated environments will provide functional strain resources for improving bioremediation efficiency. A novel Gram-stain-negative, spiral-shaped and nitrogen-fixing bacterium, designated strain DQ9^T, was isolated from the oil sludge of Daqing Oilfield, Daqing City, Heilongjiang Province, China. Cells grew at 18-45 °C (optimum of 40 °C), at pH of 6.5-9.0 (optimum of 7.0) and with 0-2.0% (w/v) NaCl (optimum of 0%). The respiratory quinone was ubiquinone 8 (Q-8). The major cellular fatty acids were summed feature 8 (C_18:1  ω7c and/or C_18:1  ω6c) (46.8%), summed feature 3 (C_16:1 ω7c and/or C_16:1  ω6c) (14.6%) and C_16:0 (17.4%). The polar lipids consisted of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), an unidentified aminophospholipid (UAPL), an unidentified aminolipid (UAL) and two unidentified lipids (UL1-2). Strain DQ9^T exhibited the highest 16S rRNA gene sequence similarities with Novispirillum itersonii subsp. itersonii LMG 4337^T (94.10%), N. itersonii subsp. nipponicum LMG 7370^T (94.10%), Marispirillum indicum B142^T (94.04%) and Caenispirillum bisanense K92^T (93.44%). The genomic DNA G+C content was 69.8 mol%. Comparing strain DQ9^T with closely related type strains, the digital DNA-DNA hybridization values were 18.5-22.0%, the average nucleotide identity values based on blast+ were 67.88-73.76%, the average amino acid identity values were 58-62% and the percentage of conserved proteins values were 45.53-58.80%. In the phylogenetic trees based on 16S rRNA genes and whole-genome sequences, strain DQ9^T formed an independent branch within the family Rhodospirillaceae. Based on the results of phylogenetics, morphology, physiology and chemotaxonomy, strain DQ9^T represents a novel species of a novel genus in the family Rhodospirillaceae, for which the name Cauispirillum nitrogeniifigens gen. nov., sp. nov. is proposed. The type strain is DQ9^T (=KCTC 8951^T=CGMCC 1.65428^T).

A novel fructophilic lactic acid bacterium, designated strain 1H7-5^T, was isolated from fresh honey in Japan. The strain exhibited poor glucose assimilation under anaerobic conditions and required external electron acceptors for glucose metabolism, indicating a fructophilic lifestyle. Cells were non-motile, rod-shaped, catalase-negative and facultatively anaerobic. Strain 1H7-5^T grew at 20-37 °C and at pH 5.0-7.5. Comparative 16S rRNA gene sequence analysis and phylogeny based on core genome sequences revealed that strain 1H7-5^T is affiliated within the genus Apilactobacillus, showing the highest similarity to Apilactobacillus apinorum. Average nucleotide identity and digital DNA-DNA hybridization values between strain 1H7-5^T and type strains of Apilactobacillus species were below the thresholds for species demarcation. The major cellular fatty acids were C_16:0, C_18:1  ω9c and C_19:0 cyclo ω8c, and the genomic DNA G+C content was 34.5 mol%. Based on phenotypic, chemotaxonomic and genomic evidence, strain 1H7-5^T represents a novel species within the genus Apilactobacillus, for which the name Apilactobacillus pseudapinorum sp. nov. is proposed. The type strain is 1H7-5^T (=JCM 37175^T=DSM 118410^T).

A bacterial strain, designated as P4^T, was isolated from an oil-contaminated soil sample. The cells were Gram-stain-positive, short rod-shaped and motile with a single lateral flagellum. Growth of the strain was observed at 20-40 °C (optimum at 30 °C), at pH 6.0-11.0 (optimum at pH 7.0) and with 0-5.0 % (w/v) NaCl (optimum at 1.0%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P4^T was closely related to the members of genus Cellulomonas, with the highest sequence similarity to Cellulomonas hominis DSM 9581^T (99.5%), followed by Cellulomonas endometrii Marseille-Q7820^T (99.1%), Cellulomonas pakistanensis NBRC 110800^T (99.0%) and Cellulomonas denverensis NBRC 110783^T (98.1%). The draft genome sequence of strain P4^T was 3.98 Mb in length, with a DNA G+C content of 75.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain P4^T and the closely related type strains were in the range of 78.6-84.4 % and 21.9-28.2 %, respectively. The predominant cellular fatty acids of strain P4^T included anteiso-C_15 :0, C_16:0, C_14:0, iso-C_15:0 and anteiso-C_17:0. The main polar lipid was composed of diphosphatidylglycerol, glycophospholipid, glycolipid and three phosphatidylinositol mannosides and the major menaquinone was MK-9(H4). Based on the polyphasic characterization, strain P4^T (=KCTC 49393^T=CCTCC AB 2019402^T) represents a novel species of the genus Cellulomonas, for which the name Cellulomonas olei sp. nov. is proposed.