Systematic and applied microbiology最新文献

{"title":"Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N)","authors":"Katie Sipes ,&nbsp;Joy Buongiorno ,&nbsp;Andrew D. Steen ,&nbsp;Andrey A. Abramov ,&nbsp;Chukwufumnanya Abuah ,&nbsp;Samantha L. Peters ,&nbsp;Richard J. Gianonne ,&nbsp;Robert L. Hettich ,&nbsp;Julia Boike ,&nbsp;Sarahi L. Garcia ,&nbsp;Tatiana A. Vishnivetskaya ,&nbsp;Karen G. Lloyd","doi":"10.1016/j.syapm.2024.126544","DOIUrl":"10.1016/j.syapm.2024.126544","url":null,"abstract":"<div><p>Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018–2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas <em>in situ</em> temperature is more stable vertically, ranging from −5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2–4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were <em>Acidobacteriota</em>, <em>Actinomycetota</em>, and <em>Chloroflexota</em>. <em>Actinomycetota</em> and <em>Chloroflexota</em> increase with depth, while <em>Acidobacteriota</em> classes <em>Thermoanaerobaculia</em> Gp7-AA8, <em>Blastocatellia</em> UBA7656, and <em>Vicinamibacteria Vicinamibacterales</em> are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and <em>Actinomycetota</em> and <em>Chloroflexota</em> have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. <em>Acidobacteriota</em> dominate the top 6 cm with their classes segregating by depth, whereas <em>Actinomycetota</em> and <em>Chloroflexota</em> dominate below ∼6 cm. This suggests that <em>Acidobacteriota</em> classes adapt to lower VWC at the surface, while <em>Actinomycetota</em> and <em>Chloroflexota</em> persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the <em>Acidobacteriota</em>, <em>Onstottus arcticum, Onstottus frigus</em>, and <em>Gilichinskyi gelida</em> and in the <em>Actinobacteriota</em>, <em>Mayfieldus profundus</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274061","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":"Harmonious naming across nomenclature codes exemplified by the description of bacterial isolates from the mammalian gut","authors":"Thomas C.A. Hitch ,&nbsp;David Wylensek ,&nbsp;Kevin Bisdorf ,&nbsp;Eva M. Buhl ,&nbsp;Nicole Treichel ,&nbsp;Birte Abt ,&nbsp;Jörg Overmann ,&nbsp;Thomas Clavel","doi":"10.1016/j.syapm.2024.126543","DOIUrl":"10.1016/j.syapm.2024.126543","url":null,"abstract":"<div><p>A dual system for naming prokaryotes is currently in place based on the well-established International Code of Nomenclature of Prokaryotes (ICNP) and the newly created Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Whilst recent creation of the SeqCode opened an avenue to accelerate the naming of uncultured taxa, the existence of two codes increases the risk of species being assigned multiple validly published names. In this work we present a workflow that aims to limit conflicts by firstly naming novel cultured taxa under the SeqCode, and secondly under the ICNP, enhancing the traceability of the taxa across the two codes. To exemplify this workflow, we describe four novel taxa isolated from the intestine of pigs: <em>Intestinicryptomonas porci</em> gen. nov., sp. nov. (strain CLA-KB-P66^T, genome accession GCA_033971905.1^TS) within a novel family, <em>Intestinicryptomonaceae</em>; <em>Grylomicrobium aquisgranensis</em> gen. nov., sp. nov. (CLA-KB-P133^T, GCA_033971865.1^TS); <em>Absicoccus intestinalis</em> sp. nov. (CLA-KB-P134^T, GCA_033971885.1^TS); and <em>Mesosutterella porci</em> sp. nov. (oilRF-744- wt-GAM-9^T, GCF_022134585.1^TS).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142009495","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":"Atacama desert is a source of new Micromonospora strains: description of Micromonospora sicca sp. nov","authors":"Lorena Carro ,&nbsp;Patrycja Golińska ,&nbsp;Zaki Saati-Santamaría ,&nbsp;José M. Igual ,&nbsp;Hans-Peter Klenk ,&nbsp;Michael Goodfellow","doi":"10.1016/j.syapm.2024.126542","DOIUrl":"10.1016/j.syapm.2024.126542","url":null,"abstract":"<div><p>Several strains were isolated from subsurface soil of the Atacama Desert and were previously assigned to the <em>Micromonospora</em> genus. A polyphasic study was designed to determine the taxonomic affiliation of isolates 4G51^T, 4G53, and 4G57. All the strains showed chemotaxonomic properties in line with their classification in the genus <em>Micromonospora</em>, including <em>meso</em>-diaminopimelic acid in the cell wall peptidoglycan, MK-9(H₄) as major respiratory quinone, <em>iso</em>-C_15:0 and <em>iso</em>-C_16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The 16S rRNA gene sequences of strains 4G51^T, 4G53, and 4G57 showed the highest similarity (97.9 %) with the type strain of <em>Micromonospora costi</em> CS1-12^T, forming an independent branch in the phylogenetic gene tree. Their independent position was confirmed with genome phylogenies, being most closely related to the type strain of <em>Micromonospora kangleipakensis</em>. Digital DNA-DNA hybridization and average nucleotide identity analyses between the isolates and their closest phylogenomic neighbours confirmed that they should be assigned to a new species within the genus <em>Micromonospora</em> for which the name <em>Micromonospora sicca</em> sp. nov. (4G51^T=PCM 3031^T=LMG 30756^T) is proposed.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000560/pdfft?md5=882c4ab4f7ab19cc401a795d2201ae08&pid=1-s2.0-S0723202024000560-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907761","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":"Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera","authors":"Olga A. Podosokorskaya,&nbsp;Alexander G. Elcheninov,&nbsp;Alexandra A. Klyukina,&nbsp;Alexander Y. Merkel","doi":"10.1016/j.syapm.2024.126541","DOIUrl":"10.1016/j.syapm.2024.126541","url":null,"abstract":"<div><p>A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-co^T, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75–100 °C and within a pH range of 5.4–8.2 with the optimum at 92 °C and pH 6.4–6.7. Strain 4213-co^T was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-co^T was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-co^T formed a species-level phylogenetic lineage within <em>Ignisphaera</em> genus. Our phylogenomic analysis also supports the delineation of the <em>Ignisphaera</em> genus into a separate family <em>Ignisphaeraceae</em>, as recently published. Here we propose a novel species <em>Ignisphaera cupida</em>, sp. nov. with type strain 4213-co^T (=JCM 39446^T=VKM B-3715^T=UQM 41593^T). Ecogenomic analysis showed that representatives of the <em>Ignisphaera</em> are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of <em>Ignisphaeraceae</em> – a rather understudied archaeal group.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141846051","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":"Comparative genomics of the carmine cochineal symbiont Candidatus Dactylopiibacterium carminicum reveals possible protection to the host against viruses via CRISPR/Cas","authors":"Rafael Bustamante-Brito ,&nbsp;Arturo Vera-Ponce de León ,&nbsp;Mónica Rosenblueth ,&nbsp;Esperanza Martínez-Romero","doi":"10.1016/j.syapm.2024.126540","DOIUrl":"10.1016/j.syapm.2024.126540","url":null,"abstract":"<div><p>We present new genomes from the bacterial symbiont <em>Candidatus</em> Dactylopiibacterium carminicum obtained from non-domesticated carmine cochineals belonging to the scale insect <em>Dactylopius</em> (Hemiptera: Coccoidea: Dactylopiidae). As <em>Dactylopiibacterium</em> has not yet been cultured in the laboratory, metagenomes and metatranscriptomics have been key in revealing putative symbiont functions. <em>Dactylopiibacterium</em> is a nitrogen-fixing beta-proteobacterium that may be vertically transmitted and shows differential gene expression inside the cochineal depending on the tissue colonized. Here we found that all cochineal species tested had <em>Dactylopiibacterium carminicum</em> which has a highly conserved genome. All <em>Dactylopiibacterium</em> genomes analyzed had genes involved in nitrogen fixation and plant polymer degradation. <em>Dactylopiibacterium</em> genomes resemble those from free-living plant bacteria, some found as endophytes. Notably, we found here a new putative novel function where the bacteria may protect the insect from viruses, since all <em>Dactylopiibacterium</em> genomes contain CRISPRs with a spacer matching nucleopolyhedrovirus that affects insects.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141789101","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":"Phylogenetically diverse bacterial species produce histamine","authors":"Kristen A. Engevik ,&nbsp;Amber Hazzard ,&nbsp;Brenton Puckett ,&nbsp;Kathleen M. Hoch ,&nbsp;Sigmund J. Haidacher ,&nbsp;Anthony M. Haag ,&nbsp;Jennifer K. Spinler ,&nbsp;James Versalovic ,&nbsp;Melinda A. Engevik ,&nbsp;Thomas D. Horvath","doi":"10.1016/j.syapm.2024.126539","DOIUrl":"10.1016/j.syapm.2024.126539","url":null,"abstract":"<div><p>Histamine is an important biogenic amine known to impact a variety of patho-physiological processes ranging from allergic reactions, gut-mediated anti-inflammatory responses, and neurotransmitter activity. Histamine is found both endogenously within specialized host cells and exogenously in microbes. Exogenous histamine is produced through the decarboxylation of the amino acid L-histidine by bacterial-derived histidine decarboxylase enzymes. To investigate how widespread histamine production is across bacterial species, we examined 102,018 annotated genomes in the Integrated Microbial Genomes Database and identified 3,679 bacterial genomes (3.6 %) which possess the enzymatic machinery to generate histamine. These bacteria belonged to 10 phyla: Bacillota, Bacteroidota, Actinomycetota, Pseudomonadota, Lentisphaerota, Fusobacteriota, Armatimonadota, Cyanobacteriota, Thermodesulfobacteriota, and Verrucomicrobiota. The majority of the identified bacteria were terrestrial or aquatic in origin, although several bacteria originated in the human gut microbiota. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted metabolomics to confirm our genome discoveries correlated with L-histidine-to-histamine conversion in a chemically defined bacterial growth medium by a cohort of select environmental and human gut bacteria. We found that environmental microbes <em>Vibrio harveyi, Pseudomonas fluorescens</em> and <em>Streptomyces griseus</em> generated considerable levels of histamine (788 – 8,730 ng/mL). Interestingly, we found higher concentrations of histamine produced by gut-associated <em>Fusobacterium varium, Clostridium perfringens, Limosilactobacillus reuteri</em> and <em>Morganella morganii</em> (8,510––82,400 ng/mL)<em>.</em> This work expands our knowledge of histamine production by diverse microbes.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000535/pdfft?md5=73cbb46d8f8d02364e67433dffcaa85a&pid=1-s2.0-S0723202024000535-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727883","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":"Streptococcus suis subsp. hashimotonensis subsp. nov.: Lancefield group A antigen–positive organisms isolated from human clinical specimens and wild boar oral cavity samples","authors":"Yuki Hasegawa ,&nbsp;Toyokazu Akita ,&nbsp;Tomokazu Kuchibiro ,&nbsp;Tohru Miyoshi-Akiyama ,&nbsp;Junko Tomida ,&nbsp;Ryo Kutsuna ,&nbsp;Ryota Mori ,&nbsp;Miki Okuno ,&nbsp;Yoshitoshi Ogura ,&nbsp;Yoshiaki Kawamura","doi":"10.1016/j.syapm.2024.126538","DOIUrl":"10.1016/j.syapm.2024.126538","url":null,"abstract":"<div><p>Three <em>Streptococcus suis</em>-like strains positive for Lancefield antigen group A were isolated from human boar bite wounds and the oral cavities of boars in Hashimoto City, Wakayama Prefecture, Japan, and their taxonomic positions were investigated. Application of the VITEK2 system identified all three isolates as <em>S. suis</em> with &gt; 94 % probability. The isolates were assigned to <em>S. suis</em> based on the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis (Biotyper score of 2.382) but were differentiated according to the characteristic signal peaks (4709 <em>m</em>/<em>z</em> and 9420 <em>m</em>/<em>z</em>) that were not present for <em>S. suis</em>. Sequence analysis of the 16S rRNA and <em>sodA</em> genes determined that the isolates were similar to <em>S. suis</em>; however, these genes appeared on a phylogenetic sub-branch. Phylogenetic analysis of the whole chromosomal DNA showed that the isolate formed a cluster with <em>S. suis</em> but with clear divergence. The average nucleotide index using BLAST between the clinical isolate (PAGU 2482) and a closely related reference strain of <em>S. suis</em> was 94.75 %, which was not clearly conclusive; however, digital DNA-DNA hybridization showed a value of 61.2 %. Biochemical reactions, including those with acid phosphatase, α-chymotrypsin, and tagatose (acidification), distinguished our isolates from <em>S. suis</em>. Thus, based on phylogenetic, genomic, and phenotypic characteristics and MALDI-TOF-MS signal patterns, we propose that the isolate with Lancefield group A positive characteristics be designated as a novel subspecies, <em>Streptococcus suis</em> subsp. <em>hashimotonensis</em> subsp. nov., with the type strain PAGU 2482^T (GTC 18290^T = CCUG 77434^T).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141693208","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":"Classification of a novel Serratia species, isolated from a wound swab in North Rhine-Westphalia: Proposal of Serratia sarumanii sp. nov","authors":"Levin Joe Klages ,&nbsp;Olaf Kaup ,&nbsp;Tobias Busche ,&nbsp;Jörn Kalinowski ,&nbsp;Christian Rückert-Reed","doi":"10.1016/j.syapm.2024.126527","DOIUrl":"10.1016/j.syapm.2024.126527","url":null,"abstract":"<div><p>Novel, white-pigmented, Gram-negative bacterial strains (K-M0706^T, K-M0228, K-M0252, K-M0260) were isolated from clinical samples. With a similarity of up to 69.7 % to <em>Serratia nevei</em> S15^T and up to 63.8 % to <em>Serratia marcescens</em> ATCC 13880^T, as determined by digital DNA-DNA hybridization, the strains were assigned as novel species of the genus <em>Serratia</em>. The species can easily be differentiated from the red colored <em>Serratia marcescens sensu stricto</em> by its white phenotype. Discrimination between this strain and <em>Serratia nevei</em> is possible due to alpha-glucosidase activity and O/129-resistance, as shown for strain K-M0706^T. The major fatty acids were determined as myristate, palmitate, cis–9,10-methylenehexadecanoate, linoleate, and (all <em>cis</em>-9,10)-methyleneoctadecanoate. These phenotypical and genomic data support the assignment of a novel species within the genus <em>Serratia</em>, named <em>S. sarumanii</em> due to its pathogenicity and white phenotype, with strain K-M0706^T as the type strain.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000419/pdfft?md5=3f51c76e52e48cc8cdddd0e7bbb7ba1c&pid=1-s2.0-S0723202024000419-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499082","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":"Rosettibacter primus gen. nov., sp. nov., and Rosettibacter firmus sp. nov., facultatively anaerobic moderately thermophilic bacteria of the class Ignavibacteria from hot springs of North Ossetia","authors":"Olga A. Podosokorskaya,&nbsp;Nika F. Petrova,&nbsp;Ekaterina N. Tikhonova,&nbsp;Alexandra A. Klyukina,&nbsp;Alexander G. Elcheninov","doi":"10.1016/j.syapm.2024.126528","DOIUrl":"10.1016/j.syapm.2024.126528","url":null,"abstract":"<div><p>A novel facultatively anaerobic moderately thermophilic bacteria, strains 4137-Me^T and 4148-Me^T, were isolated from hot springs of Karmadon and Ursdon, respectively (North Ossetia, Russian Federation). Gram-negative, motile rods were present singly, in pairs, rosettes, and aggregates, or formed biofilms. Both strains grew optimally at 50–55 °C, pH 7.0 and did not require sodium chloride or yeast extract for growth. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, starch, xylan, lichenan, galactan, xyloglucan, mannan, xanthan gum, guar gum) as well as proteinaceous substrates (gelatin, peptone, beef and yeast extract). Growth under anaerobic conditions was observed in presence and absence of external electron acceptors. Sulfur, thiosulfate, arsenate, Fe-citrate, and ferrihydrite were reduced with acetate, starch, or yeast extract as electron donors. The respiratory quinone was MK-7. Major cellular fatty acids of both strains were <em>iso</em>-C_15:0, <em>anteiso</em>-C_17:0, C_15:0, <em>iso</em>-C_16:0 and additionally <em>iso</em>-C_17:0 for strain 4137-Me^T. The size of the genome and genomic DNA G + C content of strain 4137-Me^T were 3.24 Mb. and 29.9 %, respectively; for strain 4148-Me^T – 3.33 Mb and 30.7 %. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strains 4137-Me^T and 4148-Me^T represented a distinct lineage of the family <em>Melioribacteraceae</em> within the class <em>Ignavibacteria</em>. Based on phylogenetic analysis and phenotypic features, the novel isolates were assigned to a novel genus, for which the name <em>Rosettibacter</em> gen. nov. is proposed. Strain 4148-Me^T represents its type species <em>Rosettibacter primus</em> sp. nov., while strain 4137-Me^T represents a new species <em>Rosettibacter firmus</em> sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499083","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":"Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode","authors":"Daniel Tamarit ,&nbsp;Stephan Köstlbacher ,&nbsp;Kathryn E. Appler ,&nbsp;Kassiani Panagiotou ,&nbsp;Valerie De Anda ,&nbsp;Christian Rinke ,&nbsp;Brett J. Baker ,&nbsp;Thijs J.G. Ettema","doi":"10.1016/j.syapm.2024.126525","DOIUrl":"10.1016/j.syapm.2024.126525","url":null,"abstract":"<div><p><em>Asgardarchaeota</em>, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name <em>Asgardarchaeota</em> lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2^TS, proposed to serve as the nomenclatural type for the species <em>Asgardarchaeum abyssi</em>^TS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that <em>A. abyssi</em> AB3033_2^TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for <em>Asgardarchaeota</em> using established <em>Thermoproteota</em> lineages in the GTDB r207 reference tree, we establish a robust classification and propose <em>Asgardarchaeum</em> as the type genus for the family <em>Asgardarchaeaceae</em> (fam. nov)., the order <em>Asgardarchaeales</em> (ord. nov.), the class <em>Asgardarchaeia</em> (class. nov.), and the phylum <em>Asgardarchaeota</em> (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000390/pdfft?md5=1ae401ded59e8ae03224a402356a7cfa&pid=1-s2.0-S0723202024000390-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141400744","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}