Systematic and applied microbiology最新文献

{"title":"The symbiovar mediterranense of Sinorhizobium meliloti nodulates Phaseolus vulgaris across Lanzarote (Canary Islands): A revision of this symbiovar supports a proposal to delimit symbiovars boundaries in Sinorhizobium and to define four new symbiovars","authors":"José David Flores-Félix ,&nbsp;Fernando Sánchez-Juanes ,&nbsp;Laura Pulido-Suárez ,&nbsp;Encarna Velázquez ,&nbsp;Milagros León-Barrios","doi":"10.1016/j.syapm.2024.126517","DOIUrl":"10.1016/j.syapm.2024.126517","url":null,"abstract":"<div><p>The symbiovar mediterranense of <em>Sinorhizobium meliloti</em> was initially found in <em>Phaseolus vulgaris</em> nodules in Tunisia and in an eastern location of Lanzarote (Canary Islands). Here we show that the symbiovar mediterranense of <em>S. meliloti</em> also nodulates <em>P. vulgaris</em> in two western locations of this Island. The analyses of the symbiotic <em>nodA</em> and <em>nodC</em> genes reveal the complexity of the symbiovar mediterranense which encompasses strains belonging to several phylogenetic lineages and clusters. The comparison of the <em>nodA</em> and <em>nodC</em> phylogenies showed that the <em>nodC</em> was the most resolutive phylogenetic marker for the delineation of <em>Sinorhizobium</em> symbiovars. Considering that the similarity of this gene within several symbiovars, particularly mediterranense, is around 95 %, the cut-off value for their differentiation should be lower. Considering that a <em>nodC</em> gene cut-off similarity value of around 92 % is accepted for the genus <em>Bradyrhizobium</em> and that the symbiovar concept is identical in all rhizobial genera, we propose to apply this value for symbiovars delineation within all these genera. Therefore, using this cut-off value for the <em>nodC</em> gene analysis of <em>Sinorhizobium</em> symbiovars, we propose to merge the symbiovars aegeanense and fredii into the single symbiovar fredii and to define four novel symbiovars with the names asiaense, culleni, sudanense and tunisiaense.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126517"},"PeriodicalIF":3.4,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141044758","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}

{"title":"Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota","authors":"Hiroki Kawamoto ,&nbsp;Miho Watanabe ,&nbsp;Hanako Mochimaru ,&nbsp;Nozomi Nakahara ,&nbsp;Xiang-Ying Meng ,&nbsp;Sachiko Sakamoto ,&nbsp;Kana Morinaga ,&nbsp;Taiki Katayama ,&nbsp;Hideyoshi Yoshioka ,&nbsp;Nobuhiko Nomura ,&nbsp;Hideyuki Tamaki","doi":"10.1016/j.syapm.2024.126515","DOIUrl":"10.1016/j.syapm.2024.126515","url":null,"abstract":"<div><p>A novel anaerobic, thermophilic bacterium of the class <em>Atribacteria</em>, strain M15^T, was isolated from a high-temperature gas reservoir, Japan. Cells of strain M15^T were gram-negative, short oval-shaped, and lacked flagella. Growth occurred at 45–75 °C (optimum 70–75 °C) and pH 6.5–8.5 (optimum pH 7.5–8.0) and was fast under optimal conditions (doubling time 11.4 h). Yeast extract was required for growth. Fermentative growth with glucose, arabinose, xylose, and cellobiose was observed. The major fermentative end products of glucose were acetate and hydrogen. The major cellular fatty acids were C_16:0, <em>iso</em>-C_15:0, and C_18:0. The genomic G + C content was 46.0 mol%. Fluorescence and electron microscopy observations revealed the intracellular localization of genomic DNA surrounded by a membrane in the cells of strain M15^T as reported in a sole validly described species of the class <em>Atribacteria</em> in the phylum <em>Atribacterota</em>, <em>Atribacter laminatus</em> strain RT761^T, suggesting that the unique morphological traits are widely shared in this class. Phylogenetic analyses indicated that strain M15^T belongs to a distinct family-level lineage in the class <em>Atribacteria</em> and shows low similarities to <em>Atribacter laminatus</em> strain RT761^T (16S rRNA gene sequence identity of 90.1 %, average nucleotide identity [ANI] of 66.1 %, average amino acid identity [AAI] of 55.8 %). Phenotypic traits of strain M15^T (thermophilic, fast-growing, relatively high G + C content, etc.) were clearly distinct from <em>A. laminatus.</em> Based on these phenotypic and genomic properties, we propose a novel genus and species, <em>Atrimonas thermophila</em> gen. nov., sp. nov. for strain M15^T (=JCM39389^T, =KCTC25731^T) representing a novel family <em>Atrimonadaceae</em> fam., nov. in the class <em>Atribacteria</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126515"},"PeriodicalIF":3.4,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000298/pdfft?md5=b9c8c8f687794ac5baf697b6a8ac5b64&pid=1-s2.0-S0723202024000298-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141039484","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}

{"title":"Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae","authors":"Emily St. John,&nbsp;Anna-Louise Reysenbach","doi":"10.1016/j.syapm.2024.126507","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126507","url":null,"abstract":"<div><p>Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse <em>Thermoproteota.</em> Despite their prevalence in high-temperature submarine communities, <em>Thermoproteota</em> are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the <em>Aeropyrum–Thermodiscus–Caldisphaera</em>. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the <em>Aeropyrum–Thermodiscus–Caldisphaera.</em> At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. <em>Tiamatella incendiivivens, Hestiella acidicharens</em> and <em>Calypsonella navitae.</em> A fourth genus was also identified related to <em>Thermodiscus maritimus,</em> for which no available sequenced genome exists. We propose the novel species <em>Thermodiscus eudorianus</em> to describe our high-quality <em>Thermodiscus</em> MAG<em>,</em> which represents the type genome for the genus. All three novel genera and <em>T. eudorianus</em> are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some <em>Tiamatella, Calypsonella</em> and <em>T. eudorianus</em> may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, <em>Hestiella,</em> may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family <em>Acidilobaceae</em> be amended to include <em>Caldisphaera, Aeropyrum, Thermodiscus</em> and <em>Stetteria</em> and the novel genera described here.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126507"},"PeriodicalIF":3.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140822835","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}

{"title":"Natronosalvus hydrolyticus sp. nov., a beta-1,3-glucan utilizing natronoarchaeon from hypersaline soda lakes","authors":"Dimitry Y. Sorokin ,&nbsp;Alexander G. Elcheninov ,&nbsp;Nicole J. Bale ,&nbsp;Jaap Sininghe Damsté ,&nbsp;Ilya V. Kublanov","doi":"10.1016/j.syapm.2024.126514","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126514","url":null,"abstract":"<div><p>Use of curldlan, an insoluble β-1,3-glucan, as an enrichment substrate under aerobic conditions resulted in the selection from hypersaline soda lakes of a single natronarchaeon, strain AArc-curdl1. This organism is an obligately aerobic saccharolytic, possessing a poorly explored (in Archaea) potential to utilize beta-1–3 glucans, being only a second example of a haloarchaeon with this ability known in pure culture. The main phenotypic property of the isolate is the ability to grow with insoluble β-1,3-backboned glucans, i.e. curdlan and pachyman. Furthermore, the strain utilized starch family α-glucans, beta-fructan inulin and a limited spectrum of sugars. The major ether-bound membrane polar phospholipids included PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. According to phylogenomic analysis, AArc-curdl1 represents a separate species in the recently described genus <em>Natronosalvus</em> within the family <em>Natrialbaceae.</em> The closest related species is <em>Natronosalvus amylolyticus</em> (ANI, AAI and DDH values of 90.2, 91.6 and 44 %, respectively). On the basis of its unique physiological properties and phylogenomic distance, strain AArc-curdl1^T is classified as a novel species <em>Natronosalvus hydrolyticus</em> sp. nov. (=JCM 34865 = UQM 41566).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126514"},"PeriodicalIF":3.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140905657","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}

{"title":"Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode","authors":"Juan F. Gago ,&nbsp;Tomeu Viver ,&nbsp;Mercedes Urdiain ,&nbsp;Elaine Ferreira ,&nbsp;Pedro Robledo ,&nbsp;Ramon Rossello-Mora","doi":"10.1016/j.syapm.2024.126506","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126506","url":null,"abstract":"<div><p>Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed <em>Pseudomonadota</em> to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus <em>Costitxia debesea</em> gen. nov., sp. nov., affiliated with the novel family <em>Costitxiaceae</em> fam. nov<em>.</em>, order <em>Costitxiales</em> ord. nov. and class <em>Costitxiia</em> class. nov.; and the new new species and genus <em>Lloretia debesea</em> gen. nov. sp. nov. affiliated with the novel family <em>Lloretiaceae</em> fam. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126506"},"PeriodicalIF":3.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000201/pdfft?md5=1a25fb9ae3fca24ad4164b29088d3762&pid=1-s2.0-S0723202024000201-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140606939","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}

{"title":"SeqCode facilitates naming of South African rhizobia left in limbo","authors":"Melandré van Lill ,&nbsp;Stephanus N. Venter ,&nbsp;Esther K. Muema ,&nbsp;Marike Palmer ,&nbsp;Wai Y. Chan ,&nbsp;Chrizelle W. Beukes ,&nbsp;Emma T. Steenkamp","doi":"10.1016/j.syapm.2024.126504","DOIUrl":"10.1016/j.syapm.2024.126504","url":null,"abstract":"<div><p>South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa’s current national regulations. Here, we describe seven new <em>Mesorhizobium</em> species obtained from root nodules of <em>Vachellia karroo</em>, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126504"},"PeriodicalIF":3.4,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000183/pdfft?md5=885b47be2491e2918543c1a10b18b6fa&pid=1-s2.0-S0723202024000183-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140403534","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}

{"title":"A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees","authors":"Juliana Botero ,&nbsp;Charlotte Peeters ,&nbsp;Evelien De Canck ,&nbsp;David Laureys ,&nbsp;Anneleen D. Wieme ,&nbsp;Ilse Cleenwerck ,&nbsp;Eliza Depoorter ,&nbsp;Jessy Praet ,&nbsp;Denis Michez ,&nbsp;Guy Smagghe ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2024.126505","DOIUrl":"10.1016/j.syapm.2024.126505","url":null,"abstract":"<div><p>The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of <em>Fructobacillus</em> in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with <em>Fructobacillus</em> bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 <em>Fructobacillus</em> isolates from bumble bees demonstrated that they represented four species, i.e. <em>Fructobacillus cardui</em>, <em>Fructobacillus fructosus, Fructobacillus tropaeoli</em>, and the novel species <em>Fructobacillus evanidus</em> sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct <em>Fructobacillus</em> species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with <em>F. evanidus</em> and <em>F. tropaeoli</em> genomes featuring a higher number of complete metabolic pathways. While <em>Fructobacillus</em> genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple <em>Fructobacillus</em> species from several bumble bee gut samples in the present study also argued against a specific partnership between <em>Fructobacillus</em> species and their bumble bee hosts.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126505"},"PeriodicalIF":3.4,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140279708","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}

{"title":"Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil","authors":"Ze-Shen Liu ,&nbsp;Xiao-Kang Wang ,&nbsp;Ke-Huan Wang ,&nbsp;Mei-Ling Yang ,&nbsp;De-Feng Li ,&nbsp;Shuang-Jiang Liu","doi":"10.1016/j.syapm.2024.126503","DOIUrl":"10.1016/j.syapm.2024.126503","url":null,"abstract":"<div><p>A taxonomic investigation was conducted on four bacterial strains isolated from soil contaminated with polycyclic aromatic hydrocarbons and heavy metals. Phylogenetic analysis revealed that these strains belonged to the family <em>Chitinophagaceae</em>. Examination of the 16S rRNA genes indicated that their sequence identities were below 97.6 % compared to any known and validly nominated bacterial species. The genomes of the four strains ranged from 4.12 to 8.76 Mb, with overall G + C molar contents varying from 41.28 % to 50.39 %. Predominant cellular fatty acids included <em>iso</em>-C_15:0, <em>iso</em>-C_15:1 G, and <em>iso</em>-C_17:0 3-OH. The average nucleotide identity ranged from 66.90 % to 74.63 %, and digital DNA-DNA hybridization was 12.5–12.8 %. Based on the genomic and phenotypic features of the new strains, four novel species and two new genera were proposed within the family Chitinophagaceae. The ecological distributions were investigated by data-mining of NCBI databases, and results showed that additional strains or species of the newly proposed taxa were widely distributed in various environments, including polluted soil and waters. Functional analysis demonstrated that strains H1-2-19X^T, JS81^T, and JY13-12^T exhibited resistance to arsenite (III) and chromate (VI). The proposed names for the four novel species are <em>Paraflavitalea pollutisoli</em> (type strain H1-2-19X^T = JCM 36460^T = CGMCC 1.61321^T), <em>Terrimonas pollutisoli</em> (type strain H1YJ31^T = JCM 36215^T = CGMCC 1.61343^T), <em>Pollutibacter soli</em> (type strain JS81^T = JCM 36462^T = CGMCC 1.61338^T), and <em>Polluticoccus soli</em> (type strain JY13-12^T = JCM 36463^T = CGMCC 1.61341^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126503"},"PeriodicalIF":3.4,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127464","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}

{"title":"Stomatohabitans albus gen. nov., sp. nov., an oral living facultative anaerobic actinobacteria isolated form Steller sea lion, and proposal of Stomatohabitantaceae fam. nov. and Stomatohabitantales ord. nov","authors":"Zi-Wen Yang ,&nbsp;Wen-Li Liu ,&nbsp;Peng Zhang ,&nbsp;Dan-Yuan Guo ,&nbsp;Hong-Chuan Wang ,&nbsp;Jia-Ling Li ,&nbsp;Pan-Deng Wang ,&nbsp;Gui-Xin Dong ,&nbsp;Guo-Xing Nie ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2024.126501","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126501","url":null,"abstract":"<div><p>Two novel actinobacteria, designated as SYSU M7M538^T and SYSU M7M531, were isolated from oral of <em>Eumetopias jubatus</em> in Zhuhai Chimelong Ocean Kingdom, China. The cells of these microorganisms stained Gram-positive and were rod shaped. These strains were facultative anaerobic, and catalase-positive. Optimal growth occurred at 37 °C and pH 7.0 over 7 days of cultivation. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol and phosphocholine as the major polar lipids. The main menaquinone was MK-9(H₄). The major fatty acids were C_16:0, C_17:1 <em>_w</em>₈<em>_c</em>, C_17:0, C_18:1 <em>_w</em>₉<em>_c</em> and C_18:0. Analyses of genome sequences revealed that the genome size of SYSU M7M538^T was 2.1 Mbp with G + C content of 52.5 %, while the genome size of SYSU M7M531 was 2.3 Mbp with G + C content of 52.7 %. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains and other recognized <em>Nitriliruptoria</em> species were less than 64.9 % and 89.0 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains SYSU M7M538^T and SYSU M7M531 formed a well-separated phylogenetic branch distinct from other orders of <em>Nitriliruptoria</em>. Based on the data presented here, these two strains are considered to represent a novel species of a novel genus, for which the name <em>Stomatohabitans albus</em> gen. nov., sp. nov., with the type strain SYSU M7M538^T (=KCTC 59113^T = GDMCC 1.4286^T), are proposed. We also propose that these organisms represent a novel family named <em>Stomatohabitantaceae</em> fam. nov. of a novel order <em>Stomatohabitantales</em> ord. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126501"},"PeriodicalIF":3.4,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140066881","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}

{"title":"Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds","authors":"Kohli Pragya ,&nbsp;Pannikurungottu Sreya ,&nbsp;Lakshmanan Vighnesh ,&nbsp;Dhurka Mahima ,&nbsp;Mallick Sushmita ,&nbsp;Chintalapati Sasikala ,&nbsp;Chintalapati Venkata Ramana","doi":"10.1016/j.syapm.2024.126502","DOIUrl":"10.1016/j.syapm.2024.126502","url":null,"abstract":"<div><p>Six metagenome-assembled genomes (JB008^Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order <em>Spirochaetales</em> were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008^Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2–93.4 %, respectively with uncultivated <em>Spirochaetaceae</em> family members, and &lt; 90 % identity with <em>Marispirochaeta aestuari</em> JC444^T. While, the bin JB015 showed 99.1 % identity with <em>Pleomorphochaeta naphthae</em> SEBR 4209^T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008^Ts confirmed that these members belong to the family <em>Spirochaetaceae</em> and bins JB015, JB002, JB003, and JB004 belong to the genus <em>Pleomorphochaeta</em> within the family <em>Sphaerochaetaceae</em>. The AAI values of the binned genomes JB007 and JB008^Ts compared to other members of the <em>Spirochaetaceae</em> family were between 53.9- 56.8 % and 53.8–57.1 %, respectively. Furthermore, the comparison of ANI, <em>d</em>DDH, and POCP metrics of the binned genomes JB007 and JB008^Ts, both among themselves and with the members of <em>Spirochaetaceae,</em> was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008^Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name <em>Thalassospirochaeta sargassi</em> gen. nov. sp. nov., in the family <em>Spirochaetaceae</em> while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other <em>Pleomorphochaeta</em> members.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126502"},"PeriodicalIF":3.4,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140044344","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}