The strains designed PP-18T, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced l-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18T, JC-4 and JC-7 were closely related to Weizmannia coagulans LMG 6326T (97.27–97.64%) and W. acidiproducens KCTC 13078T (96.46–96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained meso-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18T were iso-C15:0, anteiso-C17:0, iso-C16:0 and anteiso-C15:0. The ANIb and ANIm values among the genomes of strains PP-18T, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and W. coagulans LMG 6326T and W. acidiproducens KCTC 13078T were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7–23.6% when compared with W. coagulans LMG 6326T and W. acidiproducens DSM 23148T. The DNA G + C contents of strains PP-18T, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18T, JC-4 and JC-7 should be represented as a novel species within the genus Weizmannia for which the name Weizmannia acidilactici sp. nov. is proposed. The type strain is PP-18T (=KCTC 33974T = NBRC 113028T = TISTR 2515T).
{"title":"Weizmannia acidilactici sp. nov., a lactic acid producing bacterium isolated from soils","authors":"Vasana Tolieng , Naoto Tanaka , Yuh Shiwa , Sitanan Thitiprasert , Pawina Kanchanasin , Wongsakorn Phongsopitanun , Auttaporn Booncharoen , Nuttha Thongchul , Somboon Tanasupawat","doi":"10.1016/j.syapm.2022.126389","DOIUrl":"10.1016/j.syapm.2022.126389","url":null,"abstract":"<div><p>The strains designed PP-18<sup>T</sup>, JC-4 and JC-7 isolated from soils, were Gram-stain-positive rods, facultative anaerobe, endospore-forming bacteria. The strains produced <span>l</span>-lactic acid from glucose. They showed positive for catalase but negative for oxidase, nitrate reduction and arginine hydrolysis. Strains P-18<sup>T</sup>, JC-4 and JC-7 were closely related to <em>Weizmannia coagulans</em> LMG 6326<sup>T</sup> (97.27–97.64%) and <em>W. acidiproducens</em> KCTC 13078<sup>T</sup> (96.46–96.74%) based on 16S rRNA gene sequence similarity, respectively. They contained <em>meso</em>-diaminopimelic acid in cell wall peptidoglycan and had seven isoprene units (MK-7) as the predominant menaquinone. The major cellular fatty acids of strain PP-18<sup>T</sup> were <em>iso</em>-C<sub>15:0</sub>, anteiso-C<sub>17:0</sub>, iso-C<sub>16:0</sub> and anteiso-C<sub>15:0</sub>. The ANIb and ANIm values among the genomes of strains PP-18<sup>T</sup>, JC-4 and JC-7 are above 99.4% while their ANIb and ANIm values among them and <em>W. coagulans</em> LMG 6326<sup>T</sup> and <em>W. acidiproducens</em> KCTC 13078<sup>T</sup> were ranged from 76.61 to 79.59%. These 3 strains showed the digital DNA-DNA hybridization (dDDH) values of 20.7–23.6% when compared with <em>W. coagulans</em> LMG 6326<sup>T</sup> and W. <em>acidiproducens</em> DSM 23148<sup>T</sup>. The DNA G + C contents of strains PP-18<sup>T</sup>, JC-4 and JC-7 were 45.82%, 45.86% and 45.86%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipids. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis indicated that the strains PP-18<sup>T</sup>, JC-4 and JC-7 should be represented as a novel species within the genus <em>Weizmannia</em> for which the name <em>Weizmannia acidilactici</em> sp. nov. is proposed. The type strain is PP-18<sup>T</sup> (=KCTC 33974<sup>T</sup> = NBRC 113028<sup>T</sup> = TISTR 2515<sup>T</sup>).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10534111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.1016/j.syapm.2022.126376
Hui Fan , Jiang Li , Weidong Wu , Rui Chen , Min Yang , Yinggang Zhang , Lulu Cong , Lirong Dai , Yu Deng , Lei Cheng , Shichun Ma
A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 T, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25–50 °C and pH 5.5–8.0 in the presence of 0–25 g l−1 NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 T was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were iso-C15:0 and C14:0. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to vancomycin (10 mg l−1). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based phylogenetic analysis showed that strain JN-28 T shares ≤ 89.3 % sequence similarity with its closest relatives Sporanaerobacter acetigenes DSM 13106 T and other members in the order Tissierellales. Based on phenotypic and phylogenetic characteristics, Acidilutibacter cellobiosedens gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 T (=CCAM 418 T = JCM 39087 T). Further phylogenetic and phylogenomic analyses suggested strain JN-28 T represents a novel family within the order Tissierellales, for which Acidilutibacteraceae fam. nov. is proposed. In addition, the family Tissierellaceae was reclassified, Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. were formally proposed. Emended description of the family Tissierellaceae is also provided.
{"title":"Description of a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov.","authors":"Hui Fan , Jiang Li , Weidong Wu , Rui Chen , Min Yang , Yinggang Zhang , Lulu Cong , Lirong Dai , Yu Deng , Lei Cheng , Shichun Ma","doi":"10.1016/j.syapm.2022.126376","DOIUrl":"10.1016/j.syapm.2022.126376","url":null,"abstract":"<div><p><span>A Gram-stain positive, moderately thermophilic, acidotolerant and aerotolerant anaerobic bacterium, designated JN-28 </span><sup>T</sup>, was isolated from the pit mud of Chinese strong-flavor liquor. Growth was observed at 25–50 °C and pH 5.5–8.0 in the presence of 0–25 g l<sup>−1</sup> NaCl (optimally at 45 °C, pH 6.0, without NaCl). Strain JN-28 <sup>T</sup> was heterotrophic, requiring yeast extract for growth. The major cellular fatty acids were <em>iso</em>-C<sub>15:0</sub> and C<sub>14:0</sub><span><span>. The DNA G + C content of genomic DNA was 33.54 mol%. The strain was resistant to </span>vancomycin (10 mg l</span><sup>−1</sup><span><span>). Genome analysis revealed the presence of genes involved in the response to mild acid stress and oxidative stress, and resistance to vancomycin. 16S rRNA gene-based </span>phylogenetic analysis showed that strain JN-28 </span><sup>T</sup> shares ≤ 89.3 % sequence similarity with its closest relatives <em>Sporanaerobacter acetigenes</em> DSM 13106 <sup>T</sup> and other members in the order <em>Tissierellales</em>. Based on phenotypic and phylogenetic characteristics, <em>Acidilutibacter cellobiosedens</em><span> gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain JN-28 </span><sup>T</sup> (=CCAM 418 <sup>T</sup> = JCM 39087 <sup>T</sup><span>). Further phylogenetic and phylogenomic analyses suggested strain JN-28 </span><sup>T</sup> represents a novel family within the order <em>Tissierellales</em>, for which <em>Acidilutibacteraceae</em> fam. nov. is proposed. In addition, the family <em>Tissierellaceae</em> was reclassified, <em>Sporanaerobacteraceae</em> fam. nov. and <em>Tepidimicrobiaceae</em> fam. nov. were formally proposed. Emended description of the family <em>Tissierellaceae</em> is also provided.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10533130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.1016/j.syapm.2022.126371
Ramon Rosselló-Móra , Konstantinos T. Konstantinidis , Rudolf Amann
{"title":"How Systematic and Applied Microbiology will deal with two nomenclature codes (ICNP and SeqCode) for prokaryotes, and which classification standards are recommended for new taxa descriptions","authors":"Ramon Rosselló-Móra , Konstantinos T. Konstantinidis , Rudolf Amann","doi":"10.1016/j.syapm.2022.126371","DOIUrl":"10.1016/j.syapm.2022.126371","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10666076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.1016/j.syapm.2022.126385
Izzet Burcin Saticioglu , Hilal Ay , Soner Altun , Muhammed Duman
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
{"title":"Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey","authors":"Izzet Burcin Saticioglu , Hilal Ay , Soner Altun , Muhammed Duman","doi":"10.1016/j.syapm.2022.126385","DOIUrl":"10.1016/j.syapm.2022.126385","url":null,"abstract":"<div><p>Four strains, designated as C-2, C-17<sup>T</sup>, C-39<sup>T</sup><span> and Ch-15, were isolated from farmed rainbow trout<span> samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17</span></span><sup>T</sup> shared the highest identity level of 98.1 % with the type strain of <span><em>Chryseobacterium</em><em> piscium</em></span> LMG 23089<sup>T</sup> while strains C-2, C-39<sup>T</sup> and Ch-15 were closely related to <em>Chryseobacterium balustinum</em> DSM 16775<sup>T</sup> with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17<sup>T</sup>, C-39<sup>T</sup> and Ch-15 formed two novel species within the genus <em>Chryseobacterium</em>. Chemotaxonomic analyses showed that strains C-17<sup>T</sup> and C-39<sup>T</sup> have typical characteristics of the genus <em>Chryseobacterium</em><span><span><span> by having phosphatidylethanolamine in their polar </span>lipid profile<span>, MK-6 as only isoprenoid </span></span>quinone and the presence of </span><em>iso</em>-C<sub>15:0</sub><span><span><span> as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have </span>antimicrobial resistance genes, </span>prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17</span><sup>T</sup> and C-39<sup>T</sup> are representatives of two novel species within the genus <em>Chryseobacterium</em>, for which the names <em>Chryseobacterium turcicum</em> sp. nov. and <em>Chryseobacterium muglaense</em> sp. nov. with the type strains C-17<sup>T</sup> (=JCM 34190<sup>T</sup> = KCTC 82250<sup>T</sup>) and C-39<sup>T</sup> (=JCM 34191<sup>T</sup> = KCTC 822251<sup>T</sup>), respectively, are proposed.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10538003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4T and Agncl-10, and Agncl-8T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4T (=DSM 107976T = CECT 9711T) and Agncl-8T (=DSM 107980T = CECT 9715T) as the respective type strains.
{"title":"Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa","authors":"Imen Nouioui , Faten Ghodhbane-Gtari , Gabriele Pötter , Hans-Peter Klenk , Michael Goodfellow","doi":"10.1016/j.syapm.2022.126377","DOIUrl":"10.1016/j.syapm.2022.126377","url":null,"abstract":"<div><p>The status of four <em>Frankia</em> strains isolated from a root nodule of <em>Alnus glutinosa</em> was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus <em>Frankia.</em> All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain <em>meso</em>-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, <em>iso</em>-C<sub>16:0</sub> as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, <em>Alnus</em>-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of <em>Frankia alni</em> and <em>Frankia torreyi.</em> All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4<sup>T</sup> and Agncl-10, and Agncl-8<sup>T</sup> and Agncl-18, be recognised as <em>Frankia gtarii</em> sp. nov. and <em>Frankia tisai</em> sp. nov. respectively, with isolates Agncl-4<sup>T</sup> (=DSM 107976<sup>T</sup> = CECT 9711<sup>T</sup>) and Agncl-8<sup>T</sup> (=DSM 107980<sup>T</sup> = CECT 9715<sup>T</sup>) as the respective type strains.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10537992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.1016/j.syapm.2022.126390
Pavel Švec , Hans-Jürgen Busse , Karel Sedlář , Jana Musilová , Stanislava Králová , Eva Staňková , Ondrej Šedo , Daniel Krsek , Vendula Koublová , Lucie Krištofová , Ivo Sedláček
A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (Pygoscelis adeliae) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus Corynebacterium and showed that Corynebacterium glyciniphilum and Corynebacterium terpenotabidum were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA–DNA hybridisation values confirmed the separation of the four groups from each other and from the other Corynebacterium species. Chemotaxonomically, the four strains P5828T, P5850T, P6136T, P7210T representing the studied groups were characterised by C16:0 and C18:1ω9c as the major fatty acids, by the presence of meso-diaminopimelic acid in the peptidoglycan, the presence of corynemycolic acids and a quinone system with the predominant menaquinone MK-9(H2). The results of this study show that the strains studied represent four new species of the genus Corynebacterium, for which the names Corynebacterium antarcticum sp. nov. (type strain P5850T = CCM 8835T = LMG 30620T), Corynebacterium marambiense sp. nov. (type strain P5828T = CCM 8864T = LMG 31626T), Corynebacterium meridianum sp. nov. (type strain P6136T = CCM 8863T = LMG 31628T) and Corynebacterium pygosceleis sp. nov. (type strain P7210T = CCM 8836T = LMG 30621T) are proposed.
{"title":"Corynebacterium antarcticum sp. nov., Corynebacterium marambiense sp. nov., Corynebacterium meridianum sp. nov., and Corynebacterium pygosceleis sp. nov., isolated from Adélie penguins (Pygoscelis adeliae)","authors":"Pavel Švec , Hans-Jürgen Busse , Karel Sedlář , Jana Musilová , Stanislava Králová , Eva Staňková , Ondrej Šedo , Daniel Krsek , Vendula Koublová , Lucie Krištofová , Ivo Sedláček","doi":"10.1016/j.syapm.2022.126390","DOIUrl":"10.1016/j.syapm.2022.126390","url":null,"abstract":"<div><p><span>A taxonomic study was conducted on 16 bacterial strains isolated from wild Adélie penguins (</span><span><em>Pygoscelis adeliae</em></span><span>) from Seymour (Marambio) Island and James Ross Island. An initial screening by repetitive sequence-based PCR fingerprinting divided the strains studied into four coherent groups. Phylogenetic analysis based on 16S rRNA gene sequences assigned all groups to the genus </span><span><em>Corynebacterium</em></span> and showed that <em>Corynebacterium glyciniphilum</em> and <em>Corynebacterium terpenotabidum</em><span> were the closest species with 16S rRNA gene sequence similarities between 95.4 % and 96.5 %. Further examination of the strains studied with ribotyping<span>, MALDI-TOF mass spectrometry, comprehensive biotyping and calculation of average nucleotide identity and digital DNA–DNA hybridisation values confirmed the separation of the four groups from each other and from the other </span></span><em>Corynebacterium</em> species. Chemotaxonomically, the four strains P5828<sup>T</sup>, P5850<sup>T</sup>, P6136<sup>T</sup>, P7210<sup>T</sup> representing the studied groups were characterised by C<sub>16:0</sub> and C<sub>18:1</sub> <em>ω9c</em> as the major fatty acids, by the presence of <em>meso</em><span>-diaminopimelic acid in the peptidoglycan<span>, the presence of corynemycolic acids and a quinone<span> system with the predominant menaquinone MK-9(H</span></span></span><sub>2</sub>). The results of this study show that the strains studied represent four new species of the genus <em>Corynebacterium</em>, for which the names <span><em>Corynebacterium </em><em>antarcticum</em></span> sp. nov. (type strain P5850<sup>T</sup> = CCM 8835<sup>T</sup> = LMG 30620<sup>T</sup>), <em>Corynebacterium marambiense</em> sp. nov. (type strain P5828<sup>T</sup> = CCM 8864<sup>T</sup> = LMG 31626<sup>T</sup>), <em>Corynebacterium meridianum</em> sp. nov<strong>.</strong> (type strain P6136<sup>T</sup> = CCM 8863<sup>T</sup> = LMG 31628<sup>T</sup>) and <em>Corynebacterium pygosceleis</em> sp. nov. (type strain P7210<sup>T</sup> = CCM 8836<sup>T</sup> = LMG 30621<sup>T</sup>) are proposed.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10588493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-01DOI: 10.1016/j.syapm.2022.126388
Evgenii N. Frolov, Alexander V. Lebedinsky, Alexander G. Elcheninov, Ilya V. Kublanov
The family Thermodesulfobiaceae, comprising one genus Thermodesulfobium with two validly published species, is currently assigned to order Thermoanaerobacterales within the class Clostridia of the phylum Bacillota. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between Thermodesulfobium and other members of the phylum Bacillota. Subsequent studies of new Thermodesulfobium representatives supported deep phylogenetic branching of this lineage within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that Thermodesulfobium represents a distinct phylum-level lineage. Thus, we propose the transfer of the family Thermodesulfobiaceae to the new order Thermodesulfobiales within the new class Thermodesulfobiia and the new phylum Thermodesulfobiota.
{"title":"Taxonomic proposal for a deep branching bacterial phylogenetic lineage: transfer of the family Thermodesulfobiaceae to Thermodesulfobiales ord. nov., Thermodesulfobiia classis nov. and Thermodesulfobiota phyl. nov","authors":"Evgenii N. Frolov, Alexander V. Lebedinsky, Alexander G. Elcheninov, Ilya V. Kublanov","doi":"10.1016/j.syapm.2022.126388","DOIUrl":"10.1016/j.syapm.2022.126388","url":null,"abstract":"<div><p>The family <em>Thermodesulfobiaceae</em>, comprising one genus <em>Thermodesulfobium</em> with two validly published species, is currently assigned to order <em>Thermoanaerobacterales</em> within the class <span><em>Clostridia</em></span> of the phylum <em>Bacillota</em><span>. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between </span><em>Thermodesulfobium</em> and other members of the phylum <em>Bacillota</em>. Subsequent studies of new <em>Thermodesulfobium</em><span> representatives supported deep phylogenetic branching of this lineage<span> within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that </span></span><em>Thermodesulfobium</em> represents a distinct phylum-level lineage. Thus, we propose the transfer of the family <em>Thermodesulfobiaceae</em> to the new order <em>Thermodesulfobiales</em> within the new class <em>Thermodesulfobiia</em> and the new phylum <em>Thermodesulfobiota</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10533635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-01DOI: 10.1016/j.syapm.2022.126361
Meng-Meng Li , Ai-Ping Lv , Zi-Yu Zhao , Wen-Dong Xian , Zheng-Han Lian , Yu-Ting OuYang , Hong Ming , Sha Tan , Jian-Yu Jiao , En-Min Zhou , Lan Liu , Wen-Jun Li
Biological denitrification is a significant process in nitrogen biogeochemical cycle of terrestrial geothermal environments, and Thermus species have been shown to be crucial heterotrophic denitrifier in hydrothermal system. Five Gram-stain negative, aerobic and rod-shaped thermophilic bacterial strains were isolated from hot spring sediments in Tibet, China. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences indicated that these isolates should be assigned to the genus Thermus and were most closely related to Thermus caldifontis YIM 73026T, and Thermus brockianus YS38T. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the five strains and the type strains of the genus Thermus were lower than the threshold values (95% and 70%, respectively) recommended for bacterial species, which clearly distinguished the five isolates from other species of the genus Thermus and indicated that they represent independent species. Colonies are circular, convex, non-transparent. Cell growth occurred at 37–80 °C (optimum, 60–65 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0% (w/v) NaCl (optimum, 0–0.5%). Denitrification genes (narG, nirK, nirS, and norB genes) detected in their genomes indicated their potential function in nitrogen metabolism. The obtained results combined with those of morphological, physiological, and chemotaxonomic characteristics, including the menaquinones, polar lipids, and cellular fatty acids showed that the isolates are proposed as representing five novel species of the genus Thermus, which are proposed as Thermus hydrothermalis sp. nov. SYSU G00291T, Thermus neutrinimicus sp. nov. SYSU G00388T, Thermus thalpophilus sp. nov. SYSU G00506T, Thermus albus sp. nov. SYSU G00608T, Thermus altitudinis sp. nov. SYSU G00630T.
{"title":"Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments","authors":"Meng-Meng Li , Ai-Ping Lv , Zi-Yu Zhao , Wen-Dong Xian , Zheng-Han Lian , Yu-Ting OuYang , Hong Ming , Sha Tan , Jian-Yu Jiao , En-Min Zhou , Lan Liu , Wen-Jun Li","doi":"10.1016/j.syapm.2022.126361","DOIUrl":"10.1016/j.syapm.2022.126361","url":null,"abstract":"<div><p>Biological denitrification is a significant process in nitrogen biogeochemical cycle of terrestrial geothermal environments, and <em>Thermus</em> species have been shown to be crucial heterotrophic denitrifier in hydrothermal system. Five Gram-stain negative, aerobic and rod-shaped thermophilic bacterial strains were isolated from hot spring sediments in Tibet, China. Phylogenetic analysis based on 16S rRNA gene and whole genome sequences indicated that these isolates should be assigned to the genus <em>Thermus</em> and were most closely related to <em>Thermus caldifontis</em> YIM 73026<sup>T</sup>, and <em>Thermus brockianus</em> YS38<sup>T</sup>. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the five strains and the type strains of the genus <em>Thermus</em> were lower than the threshold values (95% and 70%, respectively) recommended for bacterial species, which clearly distinguished the five isolates from other species of the genus <em>Thermus</em> and indicated that they represent independent species. Colonies are circular, convex, non-transparent. Cell growth occurred at 37–80 °C (optimum, 60–65 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–2.0% (w/v) NaCl (optimum, 0–0.5%). Denitrification genes (<em>narG</em>, <em>nirK</em>, <em>nirS</em>, and <em>norB</em> genes) detected in their genomes indicated their potential function in nitrogen metabolism. The obtained results combined with those of morphological, physiological, and chemotaxonomic characteristics, including the menaquinones, polar lipids, and cellular fatty acids showed that the isolates are proposed as representing five novel species of the genus <em>Thermus</em>, which are proposed as <em>Thermus hydrothermalis</em> sp. nov. SYSU G00291<sup>T</sup>, <em>Thermus neutrinimicus</em> sp. nov. SYSU G00388<sup>T</sup>, <em>Thermus thalpophilus</em> sp. nov. SYSU G00506<sup>T</sup>, <em>Thermus albus</em> sp. nov. SYSU G00608<sup>T</sup>, <em>Thermus altitudinis</em> sp. nov. SYSU G00630<sup>T</sup>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33494865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-01DOI: 10.1016/j.syapm.2022.126352
Yang Liu, Juan Du, Tao Pei, Hanqin Du, Guang-Da Feng, Honghui Zhu
Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.
{"title":"Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions","authors":"Yang Liu, Juan Du, Tao Pei, Hanqin Du, Guang-Da Feng, Honghui Zhu","doi":"10.1016/j.syapm.2022.126352","DOIUrl":"10.1016/j.syapm.2022.126352","url":null,"abstract":"<div><p>Many genera closest to the family <span><em>Comamonadaceae</em></span><span> have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-</span><em>Comamonadaceae</em><span><span> (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S </span>rRNA gene<span> and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family </span></span><em>Comamonadaceae</em>, thereby proposing the CTC group as a novel family, <em>Sphaerotilaceae</em><span> fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed </span><em>Sphaerotilaceae</em><span>-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family </span><em>Sphaerotilaceae</em> and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40351313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-11-01DOI: 10.1016/j.syapm.2022.126354
Thomas C.A. Hitch , Kevin Bisdorf , Afrizal Afrizal , Thomas Riedel , Jörg Overmann , Till Strowig , Thomas Clavel
The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.
{"title":"A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter","authors":"Thomas C.A. Hitch , Kevin Bisdorf , Afrizal Afrizal , Thomas Riedel , Jörg Overmann , Till Strowig , Thomas Clavel","doi":"10.1016/j.syapm.2022.126354","DOIUrl":"10.1016/j.syapm.2022.126354","url":null,"abstract":"<div><p>The genus <em>Prevotella</em> comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of <em>Prevotella</em> into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus <em>Prevotella</em> into seven genera, including four novel genera for which the names <em>Segatella</em>, <em>Hoylesella</em>, <em>Leyella</em> and <em>Palleniella</em> are proposed. In addition to the reclassification of <em>Prevotella</em>, this work describes four novel species, <em>Hallella faecis</em>, <em>Xylanibacter rodentium</em>, <em>Xylanibacter muris</em>, and <em>Palleniella intestinalis</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2022-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202022000613/pdfft?md5=923fe0944099b7b5e2eb9b989f419c28&pid=1-s2.0-S0723202022000613-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40354241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}