Systematic and applied microbiology最新文献

{"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":"47 5","pages":"Article 126538"},"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":"47 5","pages":"Article 126527"},"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":"47 5","pages":"Article 126528"},"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":"47 4","pages":"Article 126525"},"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}

{"title":"Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names","authors":"William B. Whitman ,&nbsp;Stephanus N. Venter","doi":"10.1016/j.syapm.2024.126524","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126524","url":null,"abstract":"<div><p>Amendments were proposed to the International Code of Nomenclature of Prokaryotes (ICNP) in January [Arahal et al. (2024) Int. J Syst. Evol. Microbiol. 74: 006188] that would cause major changes in the treatment of <em>Candidatus</em> names. The amendments introduce Section 10 to name taxa whose names cannot be validly published under the ICNP because of the absence of type strains. This section creates a parallel ‘pro-nomenclature’ and formalizes alternative material which could serve as nomenclatural types. When conspecific isolates of taxa with <em>Candidatus</em> names are deposited in culture collections as type strains, the names can be validly published, and it is required that the same <em>Candidatus</em> name be used. While the amendments are promoted to provide stable names and rules of nomenclature for uncultivated taxa, the system is deeply flawed. It removes the permanent association between names and types, which will make the meaning of names imprecise and ambiguous. It creates ‘pro-nomenclature’, which is confusing and unnecessary. Since many taxa which cannot be validly named under the ICNP can already be named under the SeqCode, it duplicates and creates overlap with an established nomenclatural system without providing tangible benefits. As the SeqCode recognizes names formed under the ICNP, the ICNP should recognize names formed under the SeqCode as they have done for the <em>Cyanobacteria</em> named under the International Code of Nomenclature for algae, fungi and plants (ICN). For these reasons, we urge the members of the International Committee of Systematics of Prokaryotes (ICSP) to reject these amendments.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126524"},"PeriodicalIF":3.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141322670","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":"Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov.","authors":"PK Sreya ,&nbsp;Atham Hari Naga Papa Rao ,&nbsp;Gandham Suresh ,&nbsp;Chintalapati Sasikala ,&nbsp;Chintalapati Venkata Ramana","doi":"10.1016/j.syapm.2024.126523","DOIUrl":"10.1016/j.syapm.2024.126523","url":null,"abstract":"<div><p>Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the <em>Rhodopirellula</em> genus. The type strain was identified as JC737^T, which shared 99.1 % 16S rRNA gene sequence identity with <em>Rhodopirellula baltica</em> SH1^T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737^T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and <em>d</em>DDH values of the strain JC737^T were 75.8–76.1 % and 20.8–21.3 %, respectively, in comparison to other <em>Rhodopirellula</em> members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum <em>Planctomycetota</em>. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as <em>Rhodopirellula halodulae</em> sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126523"},"PeriodicalIF":3.4,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141389974","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":"Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov","authors":"M.A. Khomyakova ,&nbsp;A.Y. Merkel ,&nbsp;A.I. Slobodkin","doi":"10.1016/j.syapm.2024.126522","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126522","url":null,"abstract":"<div><p>One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextr^T) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20–37 ⁰C (optimum at 30 ⁰C). The pH range for growth was 6.5–10.0, with an optimum at pH 8.0–8.5. Strain M17dextr^T fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C_16:0 and C_18:0. The genome of strain M17dextr^T had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextr^T were members of the order <em>Sedimentisphaerales</em>, class <em>Phycisphaerae</em>. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with <em>Anaerohalosphaera lusitana</em>. According to phylogenomic analysis strain M17dextr^T together with many uncultured representatives of <em>Sedimentisphaerales</em> forms a separate family‐level lineage. We propose to assign strain M17dextr^T to a novel genus and species, <em>Anaerobaca lacustris</em> gen. nov., sp. nov.; the type strain is M17dextr^T (=VKM B-3571 ^T = DSM 113417 ^T = JCM 39238 ^T = KCTC 25381 ^T = UQM 41474 ^T). This genus is placed in a novel family, <em>Anaerobacaceae</em> fam. nov. within the order <em>Sedimentisphaerales.</em></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126522"},"PeriodicalIF":3.4,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141290007","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":"Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria","authors":"Dimitry Y. Sorokin ,&nbsp;Alexander Y. Merkel ,&nbsp;Tatyana V. Kolganova ,&nbsp;Nicole J. Bale ,&nbsp;Jaap S. Sinninghe Damsté","doi":"10.1016/j.syapm.2024.126519","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126519","url":null,"abstract":"<div><p>The genus <em>Natronospira</em> is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, <em>N. proteinivora</em>, the isolates are extremely salt-tolerant obligate alkaliphiles. However, <em>N. proteinivora</em> was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus <em>Natronospira</em> as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (<em>Natronospiraceae</em>) and order (<em>Natronospirales</em>) within the class <em>Gammaproteobacteria.</em> On the basis of distinct phenotypic and genomic properties, strain AB-CW1^T (JCM 335396 = UQM 41579) is proposed to be classified as <em>Natronospira elongata</em> sp. nov., and AB-CW4^T (JCM 335397 = UQM 41580) as <em>Natronospira bacteriovora</em> sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126519"},"PeriodicalIF":3.4,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S072320202400033X/pdfft?md5=9ad22332e74e292a8c610f955924194f&pid=1-s2.0-S072320202400033X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140951036","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":"Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov.","authors":"Izzet Burcin Saticioglu ,&nbsp;Hilal Ay ,&nbsp;Soner Altun ,&nbsp;Nihed Ajmi ,&nbsp;Enes Said Gunduz ,&nbsp;Huban Gocmen ,&nbsp;Muhammed Duman","doi":"10.1016/j.syapm.2024.126518","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126518","url":null,"abstract":"<div><p>Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus <em>Flavobacterium</em> based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 ^T and <em>Flavobacterium bizetiae</em>, 99.0 % for strain F-65 ^T and <em>Flavobacterium branchiarum</em>, 98.7 % for strain F-126 ^T and <em>Flavobacterium tructae</em>, 98.2 % for strain F-323 ^T and <em>Flavobacterium cupreum</em> while 99.7 % identity level was detected for strain F-70 ^T and <em>Flavobacterium geliluteum</em>. In addition, strains F-33, Fl-77, and F-70 ^T shared 100 % identical 16S rRNA genes, while strains F-323 ^T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus <em>Flavobacterium</em>. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 ^T, F-65 ^T, F-70 ^T, F126^T and F-323 ^T represent five novel species within the genus <em>Flavobacterium</em> for which <em>Flavobacterium piscisymbiosum</em> sp. nov. F-30 ^T (=JCM 34194 ^T = KCTC 82254 ^T), <em>Flavobacterium pisciphilum</em> sp. nov. F-65 ^T (=JCM 34197 ^T = KCTC 82257 ^T), <em>Flavobacterium flavipigmentatum</em> sp. nov. F-70 ^T (Fl-33 = Fl-77 = JCM 34198 ^T = KCTC 82258 ^T), <em>Flavobacterium lipolyticum</em> sp. nov. F-126 ^T (JCM 34199 ^T = KCTC 82259 ^T) and <em>Flavobacterium cupriresistens</em> sp. nov. F-323 ^T (Fl-318 = JCM 34200 ^T = KCTC 82260 ^T), are proposed.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126518"},"PeriodicalIF":3.4,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140951035","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":"Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus","authors":"Undine Behrendt ,&nbsp;Valentin Burghard ,&nbsp;Sonja Wende ,&nbsp;Kristina Ulrich ,&nbsp;Jacqueline Wolf ,&nbsp;Meina Neumann-Schaal ,&nbsp;Andreas Ulrich","doi":"10.1016/j.syapm.2024.126516","DOIUrl":"10.1016/j.syapm.2024.126516","url":null,"abstract":"<div><p>The tolerance of ash trees against the pathogen <em>Hymenoscyphus fraxineus</em> seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species <em>Achromobacter aestuarii</em>. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name <em>Schauerella fraxinea</em> gen. nov., sp. nov. is proposed, with the type strain B3P038^T (=LMG 33092 ^T = DSM 115926 ^T). Additionally, a reclassification of the species <em>Achromobacter aestuarii</em> as <em>Schauerella aestuarii</em> comb. nov. is proposed.</p><p>In a co-cultivation assay, the strains were able to inhibit the growth of a <em>H. fraxineus</em> strain. Accordingly, a functional analysis of the genome of <em>S. fraxinea</em> B3P038^T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 4","pages":"Article 126516"},"PeriodicalIF":3.4,"publicationDate":"2024-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000304/pdfft?md5=863b75ac7145c8f11e191c95b97b3c66&pid=1-s2.0-S0723202024000304-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141037842","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}