International journal of systematic and evolutionary microbiology最新文献

{"title":"A whole-genome study suggests a taxonomic rearrangement of <i>Saccharopolyspora subtropica</i> as a later heterotypic synonym of <i>Saccharopolyspora thermophila</i> and <i>Saccharopolyspora spinosporotrichia</i> as a later heterotypic synonym of <i>Saccharopolyspora erythraea</i>.","authors":"Guendouz Dif, Nadjette Djemouai, Atika Meklat, Abdelghani Zitouni","doi":"10.1099/ijsem.0.006731","DOIUrl":"10.1099/ijsem.0.006731","url":null,"abstract":"<p><p>The genus <i>Saccharopolyspora</i> consists of Gram-positive bacteria that are found in nature. The <i>Saccharopolyspora</i> genus, belonging to the family <i>Pseudonocardiaceae</i> and order <i>Pseudonocardiales</i>, has shown considerable phylogenetic and taxonomic overlaps. Therefore, a phylogenetic, phylogenomic and comparative genomic investigation was conducted to elucidate the taxonomic position of four <i>Saccharopolyspora</i> taxa. Analysis of the 16S rRNA genes showed that the sequence similarity between the tested species ranged from 95.59 to 100%, with <i>Saccharopolyspora hirsuta</i> VKM Ac-666^T as the type species. Moreover, the analysis of digital DNA-DNA hybridization revealed that <i>Saccharopolyspora subtropica</i> CGMCC 4.7206ᵀ and <i>Saccharopolyspora thermophila</i> JCM 10664ᵀ were 97.97% and <i>Saccharopolyspora erythraea</i> DSM 40517ᵀ and <i>Saccharopolyspora spinosporotrichia</i> JCM 10303ᵀ reached 99.9%. In addition, the average nucleotide identity values for all the combinations exceed 99%, indicating little genomic variation for these strains. Our genomic data strongly indicate the close genetic affinity between <i>S. subtropica</i> Wu <i>et al.</i> 2016 and <i>S. thermophila</i> Liu <i>et al.</i> 2001 and <i>S. spinosporotrichia</i> Zhou <i>et al.</i> 1998 and <i>S. erythraea</i> corrig. (Waksman 1923) Labeda 1987, which support their reclassification.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Psychrobacter saeujeotis</i> sp. nov., a novel halophilic bacterium isolated from salted shrimp jeotgal.","authors":"Eiseul Kim, Yinhua Cai, Seung-Min Yang, Woojung Lee, Hae-Yeong Kim","doi":"10.1099/ijsem.0.006734","DOIUrl":"10.1099/ijsem.0.006734","url":null,"abstract":"<p><p>A novel bacterial species, designated FBL11^T, was isolated from salted shrimp jeotgal, a traditional Korean fermented food sampled in the Republic of Korea. This strain showed the highest 16S rRNA gene sequence similarity to <i>Psychrobacter halodurans</i> strain F2608^T (NR_181578.1) at 98.3%. The genome size of strain FBL11^T was 3,294,493 bp with a G+C content of 42.5 mol%. Computation of relatedness indicates that strain FBL11^T shares the highest relatedness of 78.5% with <i>Psychrobacter fulvigenes</i> strain KC-40^T (NZ_CAJGZP01) and 25.2% with <i>Psychrobacter piechaudii</i> strain CIP110854^T (NZ_FUGE01), with values clearly below the cut-offs for species distinction. Polyphasic characterization using biochemical tests and matrix-assisted laser desorption/ionization time-of-flight MS analysis confirmed these findings. Strain FBL11^T grew at 10-30 °C (optimum, 20-30 °C) with 0-15% NaCl (w/v; optimum, 3-6%). Analysis of biosynthetic gene clusters responsible for secondary metabolite production revealed that strain FBL11^T generates unique products such as beta-lactone and redox-cofactors within this genus. Based on the genomic and phenotypic data obtained, we propose that strain FBL11^T represents a novel species, for which we propose the name <i>Psychrobacter saeujeotis</i> sp. nov. (type strain FBL11^T=KACC 23745^T=KCTC 8655^T=JCM 37231^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: <i>Sulfitobacter sediminis</i> gen. nov.,sp. nov., a novel halophilic bacterium isolated from tidal flat sediment.","authors":"Jaincy N Jayan, Ke Dong, Sathiyaraj Srinivasan, Sang-Seob Lee","doi":"10.1099/ijsem.0.006740","DOIUrl":"10.1099/ijsem.0.006740","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Dentiradicibacter hellwigii</i> gen. nov., sp. nov., isolated from a secondary infected root canal in the human oral cavity.","authors":"Sibylle Bartsch, Annette Wittmer, Ann-Kathrin Weber, Meina Neumann-Schaal, Jacqueline Wolf, Sabine Gronow, Jake David Turnbull, Christian Tennert, Georg Häcker, Fabian Cieplik, Ali Al-Ahmad","doi":"10.1099/ijsem.0.006690","DOIUrl":"10.1099/ijsem.0.006690","url":null,"abstract":"<p><p>A motile, rod-shaped and anaerobic strain WK13^T was isolated from a secondary root canal infection of a human tooth. WK13^T cells were Gram-stain-negative, catalase-positive and oxidase-negative. The major fatty acids (≥ 5.0%) were C_16 : 0, C_18 : 0, C_16 : 1 <i> ω</i>7c, C_18 : 1 <i> ω</i>9c and C_18 : 2 <i> ω</i>6,9c. The DNA G+C content was 57.94 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol, phosphatidylcholine and lysophosphatidylcholine. There were no respiratory quinones detectable. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WK13^T belongs to the class <i>Betaproteobacteria</i>. WK13^T showed a 93.6% and 93.5% 16S rRNA gene sequence similarity to the most closely related cultured species, <i>Propionivibrio pelophilus</i> strain DSM 12018^T and <i>Propionivibrio dicarboxylicus</i> strain DSM 5885^T, respectively. On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class <i>Betaproteobacteri</i>a, for which we propose the name <i>Dentiradicibacter hellwigii</i> gen. nov., sp. nov. The type strain is WK13^T (=DSM 112713^T=NCTC 14938^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Microbacterium candidum</i> sp. nov. and <i>Microbacterium capsulatum</i> sp. nov., isolated from waste landfill.","authors":"Wen Wen, Yuanyuan Zhao, Bing Xie, Jie Lv","doi":"10.1099/ijsem.0.006715","DOIUrl":"10.1099/ijsem.0.006715","url":null,"abstract":"<p><p>Two Gram-stain-positive, oxidase-negative, non-motile and rod-shaped strains (ASV49^T and ASV81^T) were isolated from a waste landfill in Shanghai, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains are associated with members of the genus <i>Microbacterium</i>. Strains ASV49^T and ASV81^T were most closely related to <i>Microbacterium rhizosphaerae</i> JCM 31396^T and <i>Microbacterium bovistercoris</i> CCTCC AA 2018025^T with 98.5 and 98.0% 16S rRNA gene sequence similarities, respectively. The genomic DNA G+C contents of strains ASV49^T and ASV81^T were 69.5 and 70.5 mol %, respectively. Strains ASV49^T and ASV81^T exhibited the highest average nucleotide identity values of 81.7 and 85.3% against their closest relatives <i>Microbacterium xylanilyticum</i> JCM 13591^T and <i>M. rhizosphaerae</i> JCM 31396^T, respectively. Corresponding digital DNA-DNA hybridization values were 25.1 and 30.9%, respectively. Strains ASV49^T and ASV81^T grew optimally at pH 7.0 and 28 °C on Reasoner's 2A. Strain ASV81^T produced capsules, but ASV49^T did not. Both isolates shared the following chemotaxonomic characteristics in common: the major fatty acids of anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0; the respiratory quinones of MK-11, MK-12, MK-13 and MK-10; the polar lipids of diphosphatidylglycerol and phosphatidylglycerol; and the cell wall amino acids of ornithine, alanine, glycine and glutamic acid. Based on the genomic, phenotypic and chemical characteristics, strains ASV49^T and ASV81^T represent two novel species of the genus <i>Microbacterium</i>, for which the names <i>Microbacterium candidum</i> sp. nov. and <i>Microbacterium capsulatum</i> sp. nov. are proposed. The type strains are ASV49^T (=GDMCC 1.4109^T=JCM 36480^T) and ASV81^T (=GDMCC 1.4110^T=JCM 36481^T), respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reclassification of <i>Bifidobacterium faecale</i> Choi <i>et al.</i> 2014 as a later heterotypic synonym of <i>Bifidobacterium adolescentis</i> Reuter 1963.","authors":"Shinnosuke Okuhama, Hidenori Takahashi, Yasunori Nakayama, Akihito Endo","doi":"10.1099/ijsem.0.006706","DOIUrl":"10.1099/ijsem.0.006706","url":null,"abstract":"<p><p><i>Bifidobacterium faecale</i> CU 3-7^T (=JCM 19861^T=KACC 17904^T) was identified as a novel species primarily through phylogenetic analyses of the 16S rRNA gene, heat shock protein 60 (<i>hsp60</i>) and <i>dnaJ1</i> sequences, and <i>in vitro</i> DNA-DNA hybridization (DDH) compared to <i>Bifidobacterium adolescentis</i>. However, genome-based taxonomic approaches have not been studied yet. This study reassessed the taxonomic relationship between <i>B. faecale</i> and <i>B. adolescentis</i> using overall genome-associated indices. The type strains of the two species possessed heterogeneous copies of the 16S rRNA gene within their genomes, with similarities below the species threshold of 98.7-99.0%. Therefore, we were unable to assess the 16S rRNA gene similarity-based taxonomic relationships. This indicated that the 16S rRNA gene is not an appropriate marker for studying the taxonomy of <i>B. adolescentis</i>-associated taxa. The type strains exhibited an ortho average nucleotide identity uncorrected value of 97.7% and a digital DDH value of 80.7%, indicating that they should be assigned to a single taxon. A genome-based re-assessment indicated that <i>B. faecale</i> should be reclassified as a later heterotypic synonym of <i>B. adolescentis</i>.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Novosphingobium rhizovicinum</i> sp. nov. and <i>Novosphingobium kalidii</i> sp. nov., two novel species isolated from rhizosphere soil and a root of halophyte <i>Kalidium cuspidatum</i>.","authors":"Rui-Qi Sun, Wen-Xia Dong, Jia-Hui Zeng, Hua-Mei Wei, Lian Xu, Ji-Quan Sun","doi":"10.1099/ijsem.0.006710","DOIUrl":"10.1099/ijsem.0.006710","url":null,"abstract":"<p><p>Two bacteria, designated strain M1R2S20^T and RD2P27^T, were isolated from rhizosphere soil and a root of <i>Kalidium cuspidatum</i> in Baotou, Inner Mongolia, China. Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strains M1R2S20^T and RD2P27^T were tightly clustered and both shared the highest 16S rRNA gene similarities (98.6 and 98.5 %) to <i>Novosphingobium fluoreni</i> ACCC 19180^T and less than 97.8% similarities with all other current type strains. Values of the digital DNA-DNA hybridization (dDDH), the average nucleotide identity based on the blast method (ANIb) and the average amino acid identity (AAI) of the two strains and their closely related species were 32.2, 79.0, and 84.5%, which were lower than the threshold values (70% for dDDH, 95% for ANIb and 95% for AAI). The major fatty acids of strains M1R2S20^T and RD2P27^T were C_18 : 1 <i> ω7</i>c and summed feature 3 (C_16 : 1 <i> ω6</i>c and/or C_16 : 1 <i> ω7</i>c). The only quinone was ubiquinone-10. Spermidine was the predominant polyamine. The genomic DNA G+C contents for strain M1R2S20^T and RD2P27^T were 62.4 and 62.7%. The phenotypic, chemotaxonomic and phylogenetic results supported that strains M1R2S20^T and RD2P27^T could be identified as two novel species within the genus <i>Novosphingobium</i>, for which the name <i>Novosphingobium rhizovicinum</i> sp. nov. and <i>Novosphingobium kalidii</i> sp. nov. are proposed. The type strains are <i>N. rhizovicinum</i> M1R2S20^T (=CGMCC 1.62060^T=KCTC 8106^T) and <i>N. kalidii</i> RD2P27^T (=CGMCC 1.62131^T=KCTC 8107^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143597003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Buchananella felis</i> sp. nov. isolated from feline pyothorax.","authors":"Simon Feyer, Stephanie Fuss, Natascha Gross, Sandra Zumwald, Isabelle Brodard, Sonja Kittl","doi":"10.1099/ijsem.0.006723","DOIUrl":"10.1099/ijsem.0.006723","url":null,"abstract":"<p><p>We here describe a novel, Gram-stain positive, catalase positive and oxidase negative bacterium isolated from pyothorax samples of cats. The four described strains 14KM1171, 17KM0085, 22MD1345 and 22MD1512^T have a genome size of 2.35-2.40 Mb and a DNA G+C content of 68.3-68.4 mol%. They are genetically most closely related to <i>Buchananella hordeovulneris</i> with a 16S rRNA similarity of 96.9%, digital DNA-DNA hybridization value of 15% and an average nucleotide identity of 73.5%, all clearly below the species threshold. The major cellular fatty acids (C_16:0, C_15:0 anteiso and C_14:0) are the same as in <i>B. hordeovulneris</i> supporting classification in that genus. We therefore propose that our isolates represent a novel species with the name <i>Buchananella felis</i> sp. nov. with type strain 22MD1512^T (=CCOS 2118^T=DSM 117562^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Anaeromyces corallioides,</i> sp. nov., a new anaerobic gut fungus from the faeces of cattle.","authors":"Carrie J Pratt, Emma E England, Julia M Vinzelj, Noha H Youssef, Mostafa S Elshahed","doi":"10.1099/ijsem.0.006719","DOIUrl":"10.1099/ijsem.0.006719","url":null,"abstract":"<p><p>We report on the isolation and characterization of three isolates of anaerobic gut fungi from a cattle faecal sample obtained in Stillwater, OK, USA. The isolates produced polycentric thalli with nucleated rhizomycelia, lobed appressorium-like structures, intercalary sporangia and constricted sausage-like hyphae. These morphological features are characteristic of members of the genus <i>Anaeromyces</i>. No zoospore production was observed during the isolation process or thereafter. The strains seemed to have propagated solely through their nucleated hyphae post initial enrichment. Phylogenetic analysis of the D1/D2 region of the large ribosomal subunit (D1/D2 LSU) rRNA, the ribosomal intergenic spacer region 1 (ITS1), RNA polymerase II large subunit (RPB1) and comparative average amino acid identity using transcriptomic datasets further confirmed the position of the type strain as a distinct member of the genus <i>Anaeromyces</i>, family <i>Anaeromycetaceae</i> and phylum <i>Neocallimastigomycota</i>. We propose to accommodate these isolates into a new species (<i>Anaeromyces corallioides</i>) within the genus <i>Anaeromyces</i>. The type strain is EE.1.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143648498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Cladosporium</i> diversity within seeds of <i>Allium wallichii</i> and description of a novel species, <i>Cladosporium allii-wallichii</i>.","authors":"Xing-Wen Dai, Ya-Lan Zhao, He-Xin Cui, Yi Cao, Ze-Fen Yu","doi":"10.1099/ijsem.0.006730","DOIUrl":"10.1099/ijsem.0.006730","url":null,"abstract":"<p><p><i>Allium wallichii</i> is a perennial herbaceous plant with high genetic diversity, which is mainly distributed in the southwest of Yunnan. During our investigation of the diversity of seed endophytic fungi of <i>A. wallichii</i>, 157 strains of fungi were isolated; among them, 50 strains were identified as <i>Cladosporium</i> spp. based on internal transcribed spacer (ITS) sequences. Then, two additional loci, <i>tef1-α</i> and <i>act</i>, were sequenced for all strains of <i>Cladosporium</i>. Based on combined ITS, <i>tef1-α</i> and <i>act</i> sequence analyses, these strains were further identified to species level, including 15 known species and a new, so far undescribed, species. Based on combined morphological characteristics and phylogenetic analyses, one new species is introduced under the name <i>Cladosporium allii-wallichii</i>. Detailed descriptions, illustrations and phylogenetic analyses of the new species are provided in this study.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}