International journal of systematic and evolutionary microbiology最新文献

{"title":"Emended descriptions of <i>Streptomyces javensis</i> and <i>Streptomyces rhizosphaericus</i> based on reclassifications of <i>Streptomyces yogyakartensis</i>, <i>Streptomyces cangkringensis,</i> and <i>Streptomyces indonesiensis</i>.","authors":"Hisayuki Komaki","doi":"10.1099/ijsem.0.006881","DOIUrl":"https://doi.org/10.1099/ijsem.0.006881","url":null,"abstract":"<p><p>Although some <i>Streptomyces</i> species share identical 16S rRNA gene sequences, their taxonomic relationships have not been adequately re-examined. Type strains of <i>Streptomyces javensis</i>, <i>Streptomyces yogyakartensis</i> and <i>Streptomyces violaceusniger</i> share the same 16S rRNA gene sequence. This study aimed to determine whether <i>S. javensis</i>, <i>S. yogyakartensis</i> and <i>S. violaceusniger</i> represent the same taxon using molecular and genome-based methods. Digital DNA-DNA hybridization revealed a relatedness of 89.4% between <i>S. javensis</i> JCM 11446^T and <i>S. yogyakartensis</i> JCM 11448^T, whereas the values for <i>S. violaceusniger</i> NBRC 13459^T to <i>S. javensis</i> JCM 11446^T and <i>S. yogyakartensis</i> JCM 11448^T were 53.7% and 55.1%, respectively. The type strains of <i>S. javensis</i> and <i>S. yogyakartensis</i> formed an independent clade in the phylogenomic tree, displaying similar phenotypes and sharing the same type I polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. Accordingly, <i>S. yogyakartensis</i> was reclassified as a later heterotypic synonym of <i>S. javensis</i>. Furthermore, the phylogenomic tree suggested that <i>Streptomyces rhizosphaericus</i> JCM 11447^T, <i>Streptomyces cangkringensis</i> DSM 41769^T and <i>Streptomyces indonesiensis</i> DSM 41759^T may be synonymous. DNA-DNA relatedness among them ranged 97.1-98.4%. Additionally, these type strains showed similar phenotypes, and most of their type I PKS and NRPS gene clusters were conserved. Based on these results, <i>S. cangkringensis</i> and <i>S. indonesiensis</i> were reclassified as heterotypic synonyms of <i>S. rhizosphaericus</i>. Descriptions of <i>S. javensis</i> and <i>S. rhizosphaericus</i> were emended according to the reclassifications.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816613","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>Nitrincola salilacus</i> sp. nov., isolated from Niya Fish Salt Lake Sediment in Xinjiang, Northwest China.","authors":"Qingyu Wang, Yi Xiao, Danning Gao, Longyi Su, Yongliang Yan, Yuhua Zhan, Zhengfu Zhou, Xiubin Ke","doi":"10.1099/ijsem.0.006894","DOIUrl":"https://doi.org/10.1099/ijsem.0.006894","url":null,"abstract":"<p><p>A Gram-stain-negative, aerobic, rod-shaped, oxidase- and catalase-positive and non-motile bacterium, named MINF-07-Sa-05^T, was isolated from sediment samples collected from Niya Fish Salt Lake in Xinjiang, northwest China. Phylogenetic tree based on 16S rRNA gene sequences showed that strain MINF-07-Sa-05^T consistently fell within the genus <i>Nitrincola</i> and formed a clade together with <i>Nitrincola alkalilacustris</i> ZV-19^T (98.97%) and <i>Nitrincola lacisaponensis</i> 4CA^T (96.16%). Genomic average nucleotide identity values for strain MINF-07-Sa-05^T with the type strains within the genus <i>Nitrincola</i> ranged from 69.8 to 87.8%, while the <i>in silico</i> DNA-DNA hybridization values for strain MINF-07-Sa-05^T with these strains ranged from 20.4 to 33.7%. The genome sequence size of the strain was 4.81 Mb, with a DNA G+C content of 52.6 mol%. Its growth occurred at 4-40 °C, at pH 6.0-10.0, and tolerated up to 9% (w/v) NaCl. The major fatty acids contained summed feature 8 (C_18:1 <i> ω</i>7<i>c</i>/C_18:1 <i> ω</i>6<i>c</i>; 59.8%), summed feature 3 (C_16:1 <i> ω</i>7<i>c</i>/C_16:1 <i> ω</i>6<i>c</i>; 20.4%) and C_16:0 (13.8%). The primary respiratory quinone was ubiquinone-8. The main polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Genomic analyses showed a high abundance of genes involved in the nitrogen, sulphur cycle and antibiotic resistance. According to the genotypic, phylogenetic and chemotaxonomic data, strain MINF-07-Sa-05^T represents a novel species within the genus <i>Nitrincola</i>, for which the name <i>Nitrincola salilacus</i> sp. nov. is proposed. The type strain is MINF-07-Sa-05^T (=GDMCC 1.4420^T=JCM 37233^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954114","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>Phaeobacter cretensis</i> sp. nov. and <i>Phaeobacter bryozoorum</i> sp. nov., isolated from seawater from off the coast of Crete and from Roskilde Fjord in Denmark.","authors":"Peter Bing Svendsen, Mille Rask Sander, Cecille Jasmin Elizabeth Hobbs, Philip Staffeldt, Jette Melchiorsen, Sarah Kirstein, Yuyan Liu, Paul Kempen, Mikkel Bentzon-Tilia, Lone Gram, Line Roager","doi":"10.1099/ijsem.0.006902","DOIUrl":"https://doi.org/10.1099/ijsem.0.006902","url":null,"abstract":"<p><p>Two Gram-negative, motile, rod-shaped bacteria, designated as C3_T13_0^T and A36a-5a^T, were isolated from marine environments collected off the coast of Crete, Greece, and from a biofilm in Jyllinge Harbor in Roskilde Fjord, Denmark, respectively. 16S rRNA gene phylogeny revealed that the two strains belong to the genus <i>Phaeobacter</i>. The major cellular fatty acids (>5%) were C_18 : 1 <i> ω</i>7<i>c</i> for strain A36a-5a^T and C_18 : 1 <i> ω</i>7<i>c</i>, C_18 : 2 <i> ω</i>7,13 and C_16 : 0 for strain C3_T13_0^T. The major respiratory quinone was ubiquinone-10, and the predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, and phosphatidylethanolamine for both strains. C3_T13_0^T and A36a-5a^T both produce the antimicrobial compound tropodithietic acid. The C3_T13_0^T strain grows at temperatures between 8 and 37 °C with an optimum of 25 °C, whereas A36a-5a^T grows between 5 and 37 °C with an optimum of 30 °C. The salinity range for growth was 2-9 % NaCl (w/v) for C3_T13_0^T with an optimum of 3-4% and 0-10% NaCl (w/v) for A36a-5a^T with an optimum of 2-6%. The genomes of the two strains shared an average nucleotide identity (ANI) of 84% and had lower than 87% ANI when compared with genomes of <i>Phaeobacter</i> spp. type strains. The genome of C3_T13_0^T was 4,432,895 bp with a G+C content of 55.96 mol%, and the genome of A36a-5a^T was 4,050,005 bp with a G+C content of 61.37 mol%. Based on the phylogenetic and phenotypic analyses presented here, the two isolates C3_T13_0^T (=DSM 118664^T=LMG 33738^T) and A36a-5a^T (=DSM 118663^T=LMG 33737^T) are considered to represent two novel species belonging to the genus <i>Phaeobacter</i>, for which the names <i>Phaeobacter cretensis</i> sp. nov. and <i>Phaeobacter bryozoorum</i> sp. nov. are proposed, respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954167","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>Curtobacterium phyllosphaerae</i> sp. nov. and <i>Curtobacterium guangdongense</i> sp. nov., isolated from the citrus phyllosphere.","authors":"Songzhen Yang, Jiali Li, Xiang Rong, Qingying Chen, Xueying Lu, Jun Zhang, Ming-Rong Deng, Honghui Zhu, Guang-Da Feng","doi":"10.1099/ijsem.0.006870","DOIUrl":"https://doi.org/10.1099/ijsem.0.006870","url":null,"abstract":"<p><p>Two yellow-pigmented, Gram-stain-positive and aerobic bacterial strains, designated RRHDQ10^T and RRHDQ66^T, were isolated from citrus leaves collected from a well-known production area located in Renhua County of Guangdong Province, P. R. China. The 16S rRNA gene comparison showed that strain RRHDQ10^T shared the highest similarity to <i>Curtobacterium ammoniigenes</i> NBRC 101786^T (98.32%) and <i>Curtobacterium albidum</i> DSM 20512^T (98.32%), and strain RRHDQ66^T shared that to <i>Curtobacterium flaccumfaciens</i> JCM 9670^T (99.86%) and <i>Curtobacterium allii</i> 20TX0166^T (99.86%). Phylogenetic analyses based on the 16S rRNA gene and genome sequences showed that they belonged to the genus <i>Curtobacterium</i>, among which strain RRHDQ10^T was most closely related to <i>C. ammoniigenes</i> NBRC 101786^T, and strain RRHDQ66^T showed a close relationship with <i>C. flaccumfaciens</i> JCM 9670^T and <i>Curtobacterium herbarum</i> NBRC 103064^T. The genome-derived average nucleotide identity between the two strains and their closely related type strains was below 82.06% and 85.55%, respectively, and the corresponding digital DNA-DNA hybridization values were below 22.3% and 26.2%, respectively. Anteiso-C_15:0 and iso-C_16: 0 were their major fatty acids. Moreover, summed feature 8 (C_18:1 <i> ω</i>7<i>c</i> and/or C_18:1 <i> ω6</i>c) and anteiso-C_17 : 0 served as major components in strains RRHDQ10^T and RRHDQ66^T, respectively. They took menaquinone-9 (MK-9) as the predominant respiratory quinone and ornithine as the principal cell-wall diamino acid. Their major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unidentified glycolipids. The genomic DNA G+C contents of strains RRHDQ10^T and RRHDQ66^T were 71.2 and 70.5 mol%, respectively. Based on phenotypic, genotypic and chemotaxonomic analyses, they should be considered as two novel species of the genus <i>Curtobacterium</i>, for which the names <i>Curtobacterium phyllosphaerae</i> sp. nov. and <i>Curtobacterium guangdongense</i> sp. nov. are proposed, with RRHDQ10^T (=GDMCC 1.2671^T=JCM 34831^T) and RRHDQ66^T (=GDMCC 1.2666^T= JCM 34827^T) as the type strains, respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144764878","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>Spathaspora cesarfonsecae</i> sp. nov., a xylose-fermenting yeast isolated from gut of passalid beetles and rotting wood in the Amazonian rainforest biome.","authors":"Karen Costa, Mariana R Lopes, Katharina O Barros, Gisele F L Souza, Ana Raquel O Santos, Lauren M D Souza, Luiz H Rosa, Maxwel A Abegg, Paula B Morais, Marc-André Lachance, Carlos A Rosa","doi":"10.1099/ijsem.0.006871","DOIUrl":"https://doi.org/10.1099/ijsem.0.006871","url":null,"abstract":"<p><p>Two yeast isolates of a novel d-xylose-fermenting species were obtained from rotting wood and gut of a passalid beetle collected in the Brazilian Amazonian Rainforest biome. Sequence analysis of the internal transcribed spacer-5.8S region and the D1/D2 domains of the LSU rRNA gene showed that the isolates represent a novel species of the genus <i>Spathaspora</i>, phylogenetically related to <i>Spathaspora passalidarum</i>. The yeast produced asci with a single malformed elongated ascospore with curved ends. The name <i>Spathaspora cesarfonsecae</i> sp. nov. is proposed to accommodate the novel species. The holotype of <i>Sp. cesarfonsecae</i> is CBS 14235 (MycoBank MB859328). Notably, <i>Sp. cesarfonsecae</i> demonstrated the ability to produce ethanol and xylitol from d-xylose, a biotechnologically valuable trait.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799070","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>Clostridium caseinilyticum</i> sp. nov., a close relative of <i>Clostridium tepidum</i> and <i>Clostridium sporogenes</i>, isolated from spoiled cheese and silage.","authors":"Noam Shani, Miriam Zago, Hélène Berthoud, Daniel Marzohl, Emilie Michellod, Katia Gindro, Giorgio Giraffa, Emmanuelle Arias-Roth","doi":"10.1099/ijsem.0.006875","DOIUrl":"10.1099/ijsem.0.006875","url":null,"abstract":"<p><p>Several <i>Clostridium</i> species are responsible for significant losses in the food industry. Here, a novel obligately anaerobic, spore-forming, motile bacterium, designated <i>Clostridium caseinilyticum</i> sp. nov., was isolated from hard and extra-hard cheeses with a defect consisting of a degradation of the cheese matrix. The type strain, FAM 1755^T, was obtained from Swiss Emmentaler cheese in 1983, and additional strains CREA 4990 and FAM 27665 were isolated from Italian Grana Padano in 2022 and from Swiss silage in 2012, respectively. The rod-shaped, Gram-positive cells of FAM 1755^T measured 3-4.5 µm in length and 0.7-0.9 µm in width. Phylogenetic analyses of whole-genome and 16S rRNA gene sequences placed the new taxon close to <i>Clostridium tepidum</i> DSM 104389^T and to members of the <i>Clostridium botulinum</i> Group I, such as <i>Clostridium sporogenes</i> DSM 795^T. Average nucleotide identity (ANI) values with related species were below the 95% prokaryotic species threshold, with the highest similarity to <i>C. tepidum</i> DSM 104389^T (91.4% ANI). The new species grew at a slightly lower temperature range (20-40 °C) than <i>C. tepidum</i> and <i>C. sporogenes</i> and was more halotolerant [0-5% (w/v) NaCl] than <i>C. tepidum</i>. Although genetically closer to <i>C. tepidum</i>, its growth preferences were more similar to those of <i>C. sporogenes</i>. It was catalase-, oxidase- and urease-negative, fermented glucose, and hydrolyzed gelatin but not aesculin. The polar lipid profile of FAM 1755^T included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, accompanied by an unidentified aminophospholipid, several unidentified aminolipids, phospholipids and lipids. Major cellular fatty acids were C_18 : 1 CIS 9, C_16 : 0, C_14 : 0, and C_18 : 1 DMA. The genomic DNA G+C content was 27.4 mol%. Unlike <i>C. tepidum</i>, the new species consistently hydrolyzed milk proteins, a feature implicated in cheese spoilage. Consequently, we propose the name <i>C. caseinilyticum</i> sp. nov., with the type strain FAM 1755^T (=DSM 117478^T=LMG 33232^T=CCOS 2102^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794397","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":"Phylogenomic and comparative analyses on protein sequences from <i>Halobacteria</i> to identify taxon-specific molecular markers which demarcate different <i>Halobacteriaceae</i> and <i>Haloarculaceae</i> genera.","authors":"Radhey S Gupta, Bashudev Rudra, Josh Tony, Sarah Bello","doi":"10.1099/ijsem.0.006879","DOIUrl":"10.1099/ijsem.0.006879","url":null,"abstract":"<p><p>Members of the class <i>Halobacteria</i>, due to their widespread distribution in different high-salt environments and potential biotechnological applications, are being discovered at a rapid pace. In recent years, the classification of <i>Halobacteria</i> has undergone major changes, and this class is now divided into 10 families consisting of >77 genera. However, different <i>Halobacteria</i> taxa are presently distinguished based mainly on their branching in phylogenomic trees. No specific characteristics are known which are unique to members of different taxa. To advance our understanding of <i>Halobacteria</i> taxa in this regard, we report here comprehensive phylogenomic and comparative analyses on species from two <i>Halobacteria</i> families, viz. <i>Haloarculaceae</i> and <i>Halobacteriaceae</i>. A phylogenomic tree for 385 <i>Halobacteria</i> species constructed in this work supported the current taxonomy. However, the main objective of this study was to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences which are uniquely found in the species from the above two families, or those which are specific to their different genera. Our work has identified 105 CSIs in diverse proteins, some of which are specific to <i>Halobacteriaceae</i>, whereas others are exclusively shared characteristics of different <i>Haloarculaceae</i> and <i>Halobacteriaceae</i> genera. Based upon the described CSIs, all genera from these two families containing two or more named species (viz. <i>Halapricum</i>, <i>Halarchaeum</i>, <i>Haloarcula</i>, <i>Halobacterium</i>, <i>Halocatena</i>, <i>Haloglomus</i>, <i>Halomarina</i>, <i>Halomicrobium</i>, <i>Halorarius</i>, <i>Halorhabdus</i>, <i>Halorientalis</i>, <i>Halosegnis</i>, <i>Halosimplex</i>, <i>Halovenus</i> and <i>Natronomonas</i>) can be robustly distinguished from all other <i>Halobacteria</i> genera. The identified CSIs, which are also present in uncharacterized strains of these taxa, provide more definitive means for the demarcation of these <i>Halobacteria</i> taxa and for the identification of new species/strains related to these genera. Because of the predicted functional importance of these CSIs, these taxon-specific molecular markers also provide novel tools for genetic, biochemical and functional studies on these groups of <i>Halobacteria</i>.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144873150","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>Campylobacter canis</i> sp. nov., isolated from the oral cavity of dogs.","authors":"Tatiana Camacho-Suntaxi, Jose Gonzalez-Morales, Javier Ojeda, Luis Collado","doi":"10.1099/ijsem.0.006860","DOIUrl":"https://doi.org/10.1099/ijsem.0.006860","url":null,"abstract":"<p><p>Some species of the genus <i>Campylobacter</i> have been responsible for several medically important diseases worldwide. Studies of their natural reservoirs have been mainly performed by analysing animal faecal samples. However, other types of samples, such as oral specimens, have been studied very little. In a recent survey of the oral mucosa of domestic dogs without signs of oral or gastrointestinal disease, 14 isolates suspected of belonging to a new <i>Campylobacter</i> species were recovered. A polyphasic study was performed using diverse techniques to assess cell morphology, growth characteristics and genomic content to clarify the taxonomic position of the novel isolates. Phenotypic characterization revealed that the strains isolated from the oral cavity of dogs are microaerophilic, Gram-negative, straight bacilli with a polar flagellum and are positive for catalase and oxidase, but negative for urease. Phylogenetic trees based on 16S rRNA and <i>hsp60</i> genes grouped them in a distinct clade from the previously described <i>Campylobacter</i> species, with members of the <i>Campylobacter concisus</i> group being the most closely related species (95-98% of 16S rRNA gene sequence similarity). This finding was confirmed through in silico analyses, including digital DNA-DNA hybridization and average nucleotide identity with values <19.6 and <72.6, respectively, with members of the <i>C. concisus</i> group and other valid published <i>Campylobacter</i> species. The type strain MOP7^T draft genome consists of ∼2.1 Mb, and the DNA G+C content is 37.6 mol%. The genetic results and the phenotypic differentiation revealed that the new strains from the oral cavity of dogs correspond to a new species of the genus <i>Campylobacter</i> for which we propose the name <i>Campylobacter canis</i> sp. nov., with MOP7^T (=LMG 33635^T; =CCUG 77916^T) as the type strain.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144794387","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>Pseudomonas boreopolis</i> Gray and Thornton 1928 (Approved Lists 1980) as <i>Xanthomonas boreopolis</i> comb. nov. and <i>Pseudomonas carboxydohydrogena</i> (ex Sanjieva and Zavarzin 1971) Meyer <i>et al.</i> 1980 as <i>Afipia carboxydohydrogena</i> comb. nov. based on comparative genomic analysis.","authors":"Mehdi Fatahi-Bafghi","doi":"10.1099/ijsem.0.006865","DOIUrl":"https://doi.org/10.1099/ijsem.0.006865","url":null,"abstract":"<p><p>In the present study, we conducted the whole-genome sequence analysis of <i>Pseudomonas boreopolis</i> JCM 13306^T and <i>Pseudomonas carboxydohydrogena</i> DSM 1083^T from the genus <i>Pseudomonas</i> for assigning taxonomic placement. Sequence analysis of the 16S rRNA gene revealed that <i>P. boreopolis</i> JCM 13306^T had the highest sequence similarity to <i>Xanthomonas</i> species, with sequence similarities ranging from 97.24% to 97.92% nucleotide identity. Likewise, sequence analysis of the 16S rRNA gene exhibited <i>P. carboxydohydrogena</i> DSM 1083^T with 99.36%, 99.00% and 98.93% similarity to <i>Afipia felis</i> ATCC 53690^T, <i>Afipia carboxidovorans</i> ATCC 49405^T and <i>Afipia clevelandensis</i> ATCC 49720^T, respectively. <i>P. boreopolis</i> JCM 13306^T and <i>P. carboxydohydrogena</i> DSM 1083^T have indicated a distinct position in the phylogenetic (based on concatenated sequences of 81 core proteins and 16S rRNA gene) and phylogenomic trees from some type strains of the <i>Pseudomonadaceae</i> family; however, <i>P. boreopolis</i> JCM 13306^T and <i>P. carboxydohydrogena</i> DSM 1083^T were strongly clustered with species of the <i>Xanthomonas</i> (family <i>Lysobacteraceae</i>) and <i>Afipia</i> (family <i>Nitrobacteraceae</i>), respectively. Besides, the amino acid identity values between <i>P. boreopolis</i> JCM 13306^T and the members of the <i>Pseudomonadaceae</i> family were 53.95-57.98%, as well as between <i>P. carboxydohydrogena</i> DSM 1083^T and this family which were 50.43-51.41%. These values were below the cut-off level for genus demarcation (60-85%). The scores of digital DNA-DNA hybridization (70%), average nucleotide identity by blast (95-96%) and average nucleotide identity using MUMmer (96%) between <i>P. boreopolis</i> JCM 13306^T and <i>P. carboxydohydrogena</i> DSM 1083^T, with the members of the <i>Pseudomonadaceae</i> family, were below the threshold value for bacterial species delineation. Therefore, based on genomic and phylogenomic analysis, we propose reclassifying <i>P. boreopolis</i> JCM 13306^T and <i>P. carboxydohydrogena</i> DSM 1083^T as <i>Xanthomonas boreopolis</i> comb. nov. in the <i>Lysobacteraceae</i> family and <i>Afipia carboxydohydrogena</i> comb. nov. in the <i>Nitrobacteraceae</i> family, respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12367434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144954100","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>Ovoidimarina sediminis</i> gen. nov., sp. nov., a novel member of the <i>Roseobacteraceae</i> isolated from tidal flat sediment.","authors":"Akila Kathiresan, Jaincy N Jayan, Hee-Su Kim, Hyung-Seop Kim, Cong Li, Ke Dong, Sathiyaraj Srinivasan, Sang-Seob Lee","doi":"10.1099/ijsem.0.006857","DOIUrl":"10.1099/ijsem.0.006857","url":null,"abstract":"<p><p>A strictly aerobic, Gram-stain-negative, ovoid-shaped and non-motile bacterium, designated as strain MJ-SS7^T, was isolated from tidal mudflat sediment collected at a macro-tidal clam farm in Gochang, Republic of Korea. Strain MJ-SS7^T exhibited oxidase- and catalase-positive activities. Growth occurred at 20-37 °C (optimum: 30 °C), pH 6-8 (optimum: pH 7) and in the presence of 0-9% (w/v) NaCl (optimum: 3%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that MJ-SS7^T belonged to the family <i>Roseobacteraceae</i>. Its closest relatives, based on sequence similarity, were <i>Rhodophyticola porphyridii</i> KACC 18805^T (95.9%), <i>Kangsaoukella pontilimi</i> KCTC 72224^T (95.8%) and <i>Actibacterium pelagium</i> JN33^T (95.5%). The major fatty acids included summed feature 8 (C_18:1 <i> ω7c</i>/C_18:1 <i> ω6c</i>), C_16:0, C_16:0 2OH and C_18:0. The major polar lipids consisted of phosphatidylglycerol, five unidentified phospholipids, four unidentified aminolipids, two unidentified aminophospholipids and four unidentified lipids. The major respiratory quinone was ubiquinone-10. The genome size was 5.20 Mb, with a DNA G+C content of 63.4 mol%, encoding 5,031 protein-coding genes, 3 rRNA genes and 46 tRNA genes. Comparative genomic analyses confirmed its novelty, with average nucleotide identity (<73%) and average amino acid identity (<70%) values below the species delineation thresholds. Based on polyphasic taxonomic data, strain MJ-SS7^T represents a novel species of a new genus within the family <i>Roseobacteraceae</i>, for which the name <i>Ovoidimarina sediminis</i> gen. nov., sp. nov. is proposed. The type strain is MJ-SS7^T (=KEMB 21436^T=KCTC 8329^T=JCM 36750^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775375","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}