International journal of systematic and evolutionary microbiology最新文献

{"title":"<i>Rhizobium aouanii</i> sp. nov., efficient nodulating rhizobia isolated from <i>Acacia saligna</i> roots in Tunisia.","authors":"Jihed Hsouna, Takwa Gritli, Houda Ilahi, Jia-Cheng Han, Walid Ellouze, Xiao Xia Zhang, Maroua Mansouri, Praveen Rahi, Mustapha Missbah El Idrissi, Mouad Lamrabet, Pierre Emmanuel Courty, Daniel Wipf, Abdelkader Bekki, James T Tambong, Bacem Mnasri","doi":"10.1099/ijsem.0.006515","DOIUrl":"10.1099/ijsem.0.006515","url":null,"abstract":"<p><p>Three bacterial strains, 1AS14I^T, 1AS12I and 6AS6, isolated from root nodules of <i>Acacia saligna</i>, were characterized using a polyphasic approach. Phylogenetic analysis based on <i>rrs</i> sequences placed all three strains within the <i>Rhizobium leguminosarum</i> complex. Further phylogeny, based on 1 756 bp sequences of four concatenated housekeeping genes (<i>recA</i>, <i>atpD</i>, <i>glnII</i> and <i>gyrB</i>), revealed their distinction from known rhizobia species of the <i>R. leguminosarum</i> complex (Rlc), forming a distinct clade. The closest related species, identified as <i>Rhizobium laguerreae</i>, with a sequence identity of 96.4% based on concatenated <i>recA</i>-<i>atpD</i>-<i>glnII</i>-<i>gyrB</i> sequences. The type strain, 1AS14I^T, showed average nucleotide identity (ANI) values of 94.9, 94.3 and 94.1% and DNA-DNA hybridization values of 56.1, 57.4 and 60.0% with the type strains of closest known species: <i>R. laguerreae</i>, <i>Rhizobium acaciae</i> and <i>'Rhizobium indicum',</i> respectively. Phylogenomic analyses using 81 up-to-date bacteria core genes and the Type (Strain) Genome Server pipeline further supported the uniqueness of strains 1AS14I^T, 1AS12I and 6AS6. The relatedness of the novel strains to NCBI unclassified <i>Rhizobium</i> sp. (396 genomes) and metagenome-derived genomes showed ANI values from 76.7 to 94.8% with a species-level cut-off of 96%, suggesting that strains 1AS14I, 1AS12I and 6AS6 are a distinct lineage. Additionally, differentiation of strains 1AS14I^T, 1AS12I and 6AS6 from their closest phylogenetic neighbours was achieved using phenotypic, physiological and fatty acid content analyses. Based on the genomic, phenotypic and biochemical data, we propose the establishment of a novel rhizobial species, <i>Rhizobium aouanii</i> sp. nov., with strain 1AS14I^T designated as the type strain (=DSM 113914^T=LMG 33206^T). This study contributes to the understanding of microbial diversity in nitrogen-fixing symbioses, specifically within <i>Acacia saligna</i> ecosystems in Tunisia.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11376454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132719","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":"Reclassification of <i>Butyrivibrio crossotus</i> Moore <i>et al</i>. 1976 (Approved Lists 1980) into a novel genus as <i>Eshraghiella crossota</i> gen. nov., comb. nov.","authors":"Mehdi Fatahi-Bafghi","doi":"10.1099/ijsem.0.006509","DOIUrl":"10.1099/ijsem.0.006509","url":null,"abstract":"<p><p>The reclassification of <i>Butyrivibrio crossotus</i> Moore <i>et al</i>. 1976 (Approved Lists 1980) as <i>Eshraghiella crossota</i> gen. nov., comb. nov. is proposed within the family <i>Lachnospiraceae</i>. This reclassification is based on differences revealed through the analysis of 16S rRNA, <i>groEL</i>, <i>recA</i>, and <i>rpoB</i> genes, as well as genome sequences, distinguishing it from other <i>Butyrivibrio</i> species. Comparative analysis showed that <i>B. crossotus</i> exhibited digital DNA-DNA hybridization (dDDH) values of 19.40-27.20% and average nucleotide identities based on blast (ANIb) values of 67.06-67.64% with other <i>Butyrivibrio</i> species. These values are significantly below the species delineation thresholds (dDDH, 70%; ANIb, 95-96%), justifying the proposed reclassification. Additionally, the results of the average amino acid identity (AAI) analysis indicated that this species shares 59.22-60.17% AAI with the other species of the genus <i>Butyrivibrio</i>, which is below the AAI threshold (65%) for a genus boundary. In addition, biochemical and morphological characteristics also support the proposal that this species is different from other species of the genus <i>Butyrivibrio</i>. The type strain is ATCC 29175^T (DSM 2876^T=T9-40A^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142119796","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":"Proposal of <i>Paenimyroides marinum</i> (Song <i>et al</i>. 2013) comb. nov. to replace the illegitimate name <i>Paenimyroides aquimaris</i> (García-López <i>et al</i>. 2020) Zhang <i>et al</i>. 2023.","authors":"Meng-Syun Li","doi":"10.1099/ijsem.0.006522","DOIUrl":"10.1099/ijsem.0.006522","url":null,"abstract":"<p><p>In this article, the author addresses the issue of nomenclatural illegitimacy of <i>Paenimyroides aquimaris</i> (García-López <i>et al</i>. 2020) Zhang <i>et al</i>. 2023. This name was formed without re-establishment of the earlier legitimate epithet <i>marinum</i> and should be considered to be illegitimate according to Rule 41a. As required by Rule 54, the author proposes <i>Paenimyroides marinum</i> (Song <i>et al</i>. 2013) as a new combination to replace the illegitimate name <i>Paenimyroides aquimaris</i>.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153992","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>Virgibacillus tibetensis</i> sp. nov., isolated from salt lake on the Tibetan plateau of China.","authors":"Dongyang Li, Dorji Phurbu, Xuan Zhang, Zi-Xuan Liu, Rui Wang, Yan-Yan Zheng, Yu-Guang Zhou, Ya-Jing Yu, Lu Xue, Ai-Hua Li","doi":"10.1099/ijsem.0.006525","DOIUrl":"10.1099/ijsem.0.006525","url":null,"abstract":"<p><p>One bacterial strain, designated as C22-A2^T, was isolated from Lake LungmuCo in Tibet. Cells of strain C22-A2^T were long rod-shaped, Gram-stain-negative, non-spore-forming, with positive catalase and oxidase activity. Optimal growth occurred at 20-25 °C, pH 8.0 and with 3.0-7.0% (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene and whole genome sequences revealed that strain C22-A2^T belonged to the genus <i>Virgibacillus</i>, showing the highest 16S rRNA gene similarity to <i>Virgibacillus halodenitrificans</i> DSM 10037^T (97.6%). The average nucleotide identity values between strain C22-A2^T and the type strains of related species in the genus <i>Virgibacillus</i> were less than 74.4% and the digital DNA-DNA hybridization values were less than 20.2%, both below the species delineation thresholds of 95 and 70% respectively. The genome analysis revealed that strain C22-A2^T harboured genes responsible for osmotic and oxidative stress, enabling it to adapt to its surrounding environment. In terms of biochemical and physiological characteristics, strain C22-A2^T shared similar characteristics with the genus <i>Virgibacillus,</i> including the predominant cellular fatty acid anteiso-C_15 : 0, the major respiratory quinone MK-7, as well as the polar lipids phosphatidylglycerol and diphosphatidylglycerol. Based on the comprehensive analysis of phylogenetic, phylogenomic, morphological, physiological and biochemical characteristics, strain C22-A2^T is proposed to represent a novel species of the genus <i>Virgibacillus</i>, named as <i>Virgibacillus tibetensis</i> sp. nov. (=CGMCC 1.19202^T=KCTC 43426^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287293","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>Aequorivita flava</i> sp. nov., isolated from deep-sea sediments.","authors":"Xiangwei Chen, Jinmei Xia, Xiaoteng Fu, Qiliang Lai, Jianning Wang, Yaping Du, Xiupian Liu, Guangyu Li, Xixiang Tang, Zongze Shao","doi":"10.1099/ijsem.0.006513","DOIUrl":"10.1099/ijsem.0.006513","url":null,"abstract":"<p><p>Three Gram-stain-negative, aerobic, non-motile, chemoheterotrophic, short-rod-shaped bacteria, designated CDY1-MB1^T, CDY2-MB3, and BDY3-MB2, were isolated from three marine sediment samples collected in the eastern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus <i>Aequorivita</i> and close to the type strain of <i>Aequorivita vitellina</i> F4716^T (with similarities of 98.0-98.1%). Strain CDY1-MB1^T can grow at 15-37 °C (optimum 30 °C) and in media with pH 6-9 (optimum, pH 7), and tolerate up to 10% (w/v) NaCl. The predominant cellular fatty acids of strain CDY1-MB1^T were iso-C_15 : 0 (20.7%) and iso-C_17 : 0 3-OH (12.8%); the sole respiratory quinone was menaquinone 6; the major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. The digital DNA-DNA hybridization/average nucleotide identity values between strains CDY1-MB1^T, CDY2-MB3, and BDY3-MB2 and <i>A. vitellina</i> F4716^T were 24.7%/81.6-81.7%, thereby indicating that strain CDY1-MB1^T should represent a novel species of the genus <i>Aequorivita</i>. The genomic DNA G+C contents were 37.6 % in all three strains. Genomic analysis showed the presence of genes related to nitrogen and sulphur cycling, as well as metal reduction. The genetic traits of these strains indicate their possible roles in nutrient cycling and detoxification processes, potentially shaping the deep-sea ecosystem's health and resilience. Based upon the consensus of phenotypic and genotypic analyses, strain CDY1-MB1^T should be classified as a novel species of the genus <i>Aequorivita</i>, for which the name <i>Aequorivita flava</i> sp. nov. is proposed. The type strain is CDY1-MB1^T (=MCCC 1A16935^T=KCTC 102223^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125616","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>Spencermartinsiella nicolii</i> sp. nov., a potential opportunistic pathogenic yeast species isolated from rotting wood in Brazil.","authors":"Katharina O Barros, Aline D Valério, Thiago M Batista, Ana Raquel O Santos, Gisele F L Souza, Flávia B M Alvarenga, Mariana R Lopes, Camila G Morais, Cristina Alves, Aristóteles Goes-Neto, Marcos J S Vital, Ana Paula T Uetanabaro, Daniela L Souza, Feng-Yan Bai, Glória R Franco, Marc-André Lachance, Carlos A Rosa, Susana Johann","doi":"10.1099/ijsem.0.006520","DOIUrl":"https://doi.org/10.1099/ijsem.0.006520","url":null,"abstract":"<p><p>Nineteen isolates representing a candidate for a novel yeast species belonging to the genus <i>Spencermartinsiella</i> were recovered from rotting wood samples collected at different sites in Atlantic Rainforest and Amazonian Forest ecosystems in Brazil. Similarity search of the nucleotide sequence of the intergenic spacer (ITS)-5.8S and large subunit D1/D2 regions of the ribosomal gene cluster showed that this novel yeast is closely related to <i>Spencermartinsiella cellulosicola</i>. The isolates differ by four nucleotide substitutions in the D1/D2 domain and six substitutions and 31 indels in the ITS region from the holotype of <i>S. cellulosicola</i>. Phylogenomic analysis based on 1474 single-copy orthologues for a set of <i>Spencermartinsiella</i> species whose whole genome sequences are available confirmed that the novel species is phylogenetically close to <i>S. cellulosicola</i>. The low average nucleotide identity value of 83% observed between <i>S. cellulosicola</i> and the candidate species confirms that they are distinct. The novel species produced asci with hemispherical ascospores. The name <i>Spencermartinsiella nicolii</i> sp. nov. is proposed. The holotype is CBS 14238^T. The MycoBank number is MB855027. Interestingly, the D1/D2 sequence of the <i>S. nicolii</i> was identical to that of an uncultured strain of <i>Spencermartinsiella</i> causing systemic infection in a male adult crocodile (<i>Crocodylus niloticus</i>). The characterization of some virulence factors and antifungal susceptibility of <i>S. nicolii</i> isolates suggest that this yeast may be an opportunistic pathogen for animals, including humans; the isolates grow at 37 °C.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140082","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>Polaribacter ponticola</i> sp. nov., isolated from seawater, reclassification of <i>Polaribacter undariae</i> as a later heterotypic synonym of <i>Polaribacter sejongensis</i>, and emended description of <i>Polaribacter sejongensis</i> Kim <i>et al</i>. 2013.","authors":"Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon","doi":"10.1099/ijsem.0.006526","DOIUrl":"10.1099/ijsem.0.006526","url":null,"abstract":"<p><p>A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5^T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C_15 : 0, summed feature 3 (C_16 : 1 <i> ω</i>7<i>c</i> and/or C_16 : 1 <i> ω</i>6<i>c</i>), iso-C_15 : 0 3-OH, and C_15 : 1 <i> ω</i>6<i>c</i> were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5^T formed a distinct lineage within the genus <i>Polaribacter</i>. The genome of strain MSW5^T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5^T exhibited the highest similarity to <i>Polaribacter atrinae</i> WP25^T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5^T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5^T is proposed to represent a novel species, with the name <i>Polaribacter ponticola</i> sp. nov. The type strain is MSW5^T (=KACC 22340^T=NBRC 116025^T). In addition, whole genome sequence comparisons and phenotypic features suggested that <i>Polaribacter sejongensis</i> and <i>Polaribacter undariae</i> belong to the same species, with <i>P. undariae</i> proposed as a later heterotypic synonym of <i>P. sejongensis</i>. An emended description of <i>Polaribacter sejongensis</i> is also proposed.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11392042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287277","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>Microbulbifer spongiae</i> sp. nov., isolated from marine sponge <i>Diacarnus erythraeanus</i>.","authors":"Nabila Ishaq, Mimi Zhang, Luyao Gao, Micha Ilan, Zhiyong Li","doi":"10.1099/ijsem.0.006521","DOIUrl":"https://doi.org/10.1099/ijsem.0.006521","url":null,"abstract":"<p><p>A novel bacterium, designated as MI-G^T, was isolated from marine sponge <i>Diacarnu</i>s <i>erythraeanus</i>. Cells of strain MI-G^T are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-G^T is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-G^T shows 98.35, 97.32 and 97.25% similarity to those of <i>Microbulbifer variabilis</i> Ni-2088^T, <i>Microbulbifer maritimus</i> TF-17^T and <i>Microbulbifer echini</i> AM134^T, respectively. Phylogenetic analysis also exhibits that strain MI-G^T falls within a clade comprising members of the genus <i>Microbulbifer</i> (class <i>Gammaproteobacteria</i>). The genome size of strain MI-G^T is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-G^T and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-G^T and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-G^T are composed of summed feature 8 (C_{18 : 1} <i>ω</i>7<i>c</i> or C_{18 : 1} <i>ω</i>6<i>c</i>), iso-C_{11 : 0} 3-OH, iso-C_{15 : 0}, C_{16 : 0}, and summed feature 9 (C_{17 : 1} iso <i>ω</i>9<i>c</i> or C_{16 : 0} 10-methyl). The polar lipids of MI-G^T mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-G^T is considered to represent a novel species of genus <i>Microbulbifer</i>, for which the name <i>Microbulbifer spongiae</i> sp. nov. is proposed. The type strain is MI-G^T (=MCCC 1K07826^T=KCTC 8081^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142346740","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>Paralimibaculum aggregatum</i> gen. nov. sp. nov. and <i>Biformimicrobium ophioploci</i> gen. nov. sp. nov., two novel heterotrophs from brittle star <i>Ophioplocus japonicus</i>.","authors":"Keisuke Kawano, Tatsuya Awano, Arata Yoshinaga, Junji Sugiyama, Shigeki Sawayama, Satoshi Nakagawa","doi":"10.1099/ijsem.0.006530","DOIUrl":"https://doi.org/10.1099/ijsem.0.006530","url":null,"abstract":"<p><p>Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23^T and NKW57^T, were isolated from a brittle star <i>Ophioplocus japonicus</i> collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23^T represented a member of the family <i>Paracoccaceae</i>, with <i>Limibaculum halophilum</i> CAU 1123^T as its closest relative (94.4% sequence identity). NKW57^T was identified as representing a member of the family <i>Microbulbiferaceae,</i> with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23^T formed a novel lineage, branching deeply prior to the divergence of the genera <i>Limibaculum</i> and <i>Thermohalobaculum,</i> with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57^T similarly formed a distinct lineage separate from the species of the genus <i>Microbulbifer</i>. The major respiratory quinones of NKW23^T and NKW57^T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23^T and NKW57^T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: <i>Paralimibaculum aggregatum</i> gen. nov., sp. nov., with strain NKW23^T (=JCM 36220^T=KCTC 8062^T) as the type strain, and <i>Biformimicrobium ophioploci</i> gen. nov., sp. nov., with strain NKW57^T (=JCM 36221^T=KCTC 8063^T) as the type strain.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11426391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142346742","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":"Actinomycetota <i>Amycolatopsis nalaikhensis</i> sp. nov. and <i>Amycolatopsis carbonis</i> sp. nov., two novel actinobacteria with antimicrobial activity isolated from a coal mining site in Mongolia.","authors":"Bilguun Oyuntsetseg, Seung Bum Kim","doi":"10.1099/ijsem.0.006511","DOIUrl":"10.1099/ijsem.0.006511","url":null,"abstract":"<p><p>Two-novel filamentous actinobacteria designated strains 2-2^T and 2-15^T were isolated from soil of a coal mining site in Mongolia, and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that each of the strains formed a distinct clade within the genus <i>Amycolatopsis</i>. The 16S rRNA gene sequence similarity analysis showed that both strains were mostly related to <i>Amycolatopsis rhabdoformis</i> NCIMB 14900^T with 99.0 and 99.4% sequence similarity, respectively. The genome-based comparison indicated that strain 2-2^T shared the highest digital DNA-DNA hybridization value of 35.6% and average nucleotide identity value of 86.9% with <i>Amycolatopsis pretoriensis</i> DSM 44654^T, and strain 2-15^T shared the corresponding values of 36.5 and 87.9% with <i>A. rhabdoformis</i> NCIMB 14900^T, all of which being well below the thresholds for species delineation. The chemotaxonomic properties of both strains were typical of the genus <i>Amycolatopsis</i>. <i>In silico</i> prediction of chemotaxonomic markers was also carried out, and the results were consistent with the chemotaxonomic profiles of the genus. Genome mining for secondary metabolite production in strains 2-2^T and 2-15^T revealed the presence of 29 and 24 biosynthetic gene clusters involved in the production of polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides, lanthipeptide, terpenes, siderophore, and a number of other unknown type compounds. Both strains showed broad antifungal activity against several filamentous fungi and also antibacterial activity against methicillin-resistant <i>Staphylococcus aureus</i> and <i>Acinetobacter baumannii</i>. The phenotypic, biochemical, and chemotaxonomic properties indicated that both strains could be clearly distinguished from other species of <i>Amycolatopsis</i>, and thus the names <i>Amycolatopsis nalaikhensis</i> sp. nov. (type strain, 2-2^T=KCTC 29695^T=JCM 30462^T) and <i>Amycolatopsis carbonis</i> (type strain, 2-15^T=KCTC 39525^T=JCM 30563^T) are proposed accordingly.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287294","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}