Systematic and applied microbiology最新文献

{"title":"Mycoplasma bradburyae sp. nov. isolated from the trachea of sea birds","authors":"Ana S. Ramírez ,&nbsp;José B. Poveda ,&nbsp;Remco Dijkman ,&nbsp;Carlos Poveda ,&nbsp;Alejandro Suárez-Pérez ,&nbsp;Rubén S. Rosales ,&nbsp;Anneke Feberwee ,&nbsp;Michael P. Szostak ,&nbsp;Lorenzo Ressel ,&nbsp;Tomeu Viver ,&nbsp;Pascual Calabuig ,&nbsp;Salvatore Catania ,&nbsp;Federica Gobbo ,&nbsp;Dorina Timofte ,&nbsp;Joachim Spergser","doi":"10.1016/j.syapm.2023.126472","DOIUrl":"10.1016/j.syapm.2023.126472","url":null,"abstract":"<div><p><span>In the search for mollicutes in wild birds, six </span><span><em>Mycoplasma</em></span> strains were isolated from tracheal swabs taken from four different species of seabirds. Four strains originated from three Yellow-legged gulls (<em>Larus michahellis</em>) and a Cory’s shearwater (<span><em>Calonectris</em><em> borealis</em></span>) from Spain<em>,</em><span> one from a South African Kelp gull (</span><em>Larus dominicanus</em>)<em>,</em> and one from an Italian Black-headed gull (<span><em>Chroicocephalus</em><em> ridibundus</em></span>). These <em>Mycoplasma</em><span> strains presented 99 % 16S rRNA gene sequence similarity values with </span><em>Mycoplasma</em> (<em>M.</em>) <em>gallisepticum</em><span>. Phylogenetic analyses of marker genes (16S rRNA gene and </span><em>rpoB</em>) confirmed the close relationship of the strains to <em>M. gallisepticum</em> and <em>M. tullyi</em><span><span><span><span><span>. The seabirds’ strains grew well in modified Hayflick medium, and colonies showed typical fried egg morphology. They produced acid from glucose and mannose but did not </span>hydrolyze arginine or urea. </span>Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas, presenting spherical to flask-shaped cells with an attachment </span>organelle. </span>Gliding motility<span> was also observed. Furthermore, serological tests, MALDI-ToF mass spectrometry and genomic studies demonstrated that the strains were different to any known </span></span><em>Mycoplasma</em> species, for which the name <em>Mycoplasma bradburyae</em> sp. nov. is proposed; the type strain is T158^T (DSM 110708 = NCTC 14398).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41238684","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":"Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data","authors":"Helen R. Davison,&nbsp;Gregory D.D. Hurst","doi":"10.1016/j.syapm.2023.126468","DOIUrl":"10.1016/j.syapm.2023.126468","url":null,"abstract":"<div><p><em>Chlamydiota</em> are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic <em>Chlamydiota</em> are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of <em>Chlamydiota</em> diversity and its hosts, in particular the Order <em>Parachlamydiales</em>. We extract one <em>Rhabdochlamydiaceae</em> and three <em>Simkaniaceae</em> Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names “<em>Sacchlamyda saccharinae”</em> (Family <em>Rhabdochlamydiaceae)</em> and “<em>Amphrikana amoebophyrae”</em> (Family <em>Simkaniaceae</em>), as well as a third new clade of environmental MAGs “<em>Acheromyda pituitae</em>” (Family <em>Rhabdochlamydiaceae</em>). The extent of uncharacterized diversity within the <em>Rhabdochlamydiaceae</em> and <em>Simkaniaceae</em> is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in <em>Parachlamydiales</em> metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41238683","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":"Sedimenticola hydrogenitrophicus sp. nov. a chemolithoautotrophic bacterium isolated from a terrestrial mud volcano, and proposal of Sedimenticolaceae fam. nov. in the order Chromatiales","authors":"Galina Slobodkina ,&nbsp;Alexander Merkel ,&nbsp;Nataliya Ratnikova ,&nbsp;Alexandra Kuchierskaya ,&nbsp;Alexander Slobodkin","doi":"10.1016/j.syapm.2023.126451","DOIUrl":"10.1016/j.syapm.2023.126451","url":null,"abstract":"<div><p><span>Chemolithoautotrophic microorganisms<span> can play a significant role in the biogeochemical cycling of elements in deep-subsurface-associated environments. A novel facultatively anaerobic lithoautotrophic bacteria (strains SB48</span></span>^T<span> and SN1189) were isolated from terrestrial mud volcanoes<span> (Krasnodar Krai, Russia). Cells of the strains were straight motile rods. Growth was observed at temperatures up to 35 °C (optimum at 30 °C), pH 6.0–8.5 (optimum at pH 7.5) and NaCl concentrations of 0.5–4.0% (w/v) (optimum at 1.5–2.0% (w/v)). The isolates grew chemolithoautotrophically with molecular hydrogen or thiosulfate as an electron donor, nitrate as an electron acceptor and CO</span></span>₂/HCO₃⁻<span><span><span> as a carbon source. They also grew with organic acids, ethanol, yeast extract and peptone. The isolates were capable of either </span>anaerobic respiration with nitrate or </span>nitrous oxide as the electron acceptors or aerobic respiration under microaerobic condition. The total size of the genome of strains SB48</span>^T<span> and SN1189 was 4.71 and 5.13 Mbp, respectively. Based on phenotypic and phylogenetic characteristics, strains SB48</span>^T and SN1189 represent a novel species of the genus <em>Sedimenticola</em>, <em>S. hydrogenitrophicus</em> (the type strain is SB48^T = KCTC 25568 ^T = VKM B-3680 ^T). The new isolates are the first representatives of the genus <em>Sedimenticola</em><span> isolated from a terrestrial ecosystem<span>. Based on phylogenomic reconstruction we propose to include the genus </span></span><em>Sedimenticola</em> and the related genera into a new family <em>Sedimenticolaceae</em> fam. nov. within the order <em>Chromatiales</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9973839","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":"Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa","authors":"Ricu Claassens ,&nbsp;Stephanus N. Venter ,&nbsp;Chrizelle W. Beukes ,&nbsp;Tomasz Stępkowski ,&nbsp;Wai Y. Chan ,&nbsp;Emma T. Steenkamp","doi":"10.1016/j.syapm.2023.126452","DOIUrl":"10.1016/j.syapm.2023.126452","url":null,"abstract":"<div><p>A genealogical concordance approach was used to delineate strains isolated from <em>Acacia dealbata</em> and <em>Acacia mearnsii</em> root nodules in South Africa. These isolates form part of <em>Bradyrhizobium</em> based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (<em>atpD, dnaK, glnII, gyrB, recA</em> and <em>rpoB</em>) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (<em>B. cosmicum</em> 58S1^T, <em>B. betae</em> PL7HG1^T, <em>B. ganzhouense</em> CCBAU 51670 ^T, <em>B. cytisi</em> CTAW11^T and <em>B. rifense</em> CTAW71^T) resulted in values well below 95–96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the <em>nodA</em> and <em>nifD</em> loci indicated that the symbiotic loci of the strains are closely related to those of <em>Bradyrhizobium</em> isolates with an Australian origin. Strain 14AB^T (=LMG 31415 ^T = SARCC-753 ^T) is designated as the type strain of the novel species for which we propose the name <em>Bradyrhizobium xenonodulans</em> sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10083922","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":"Corrigendum to “Expanding the rumen Prevotella collection: the description of Prevotella communis, sp. nov. of ovine origin” [Syst. Appl. Microbiol. 46(4) (2023) 126437]","authors":"Eva Grabner ,&nbsp;Eva Stare ,&nbsp;Lijana Fanedl ,&nbsp;Maša Zorec ,&nbsp;Dakota S. Jones ,&nbsp;Christopher D. Johnston ,&nbsp;Gorazd Avguštin ,&nbsp;Tomaž Accetto","doi":"10.1016/j.syapm.2023.126453","DOIUrl":"10.1016/j.syapm.2023.126453","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10153009","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":"Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new?","authors":"Svetlana N. Dedysh","doi":"10.1016/j.syapm.2023.126439","DOIUrl":"10.1016/j.syapm.2023.126439","url":null,"abstract":"<div><p>Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9759497","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":"Corrigendum to “Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis” [Syst. Appl. Microbiol. 42(3) (2019) 334–342]","authors":"Rahul R. Menon ,&nbsp;Sunitha Kumari ,&nbsp;Pravin Kumar ,&nbsp;Ashish Verma ,&nbsp;Srinivasan Krishnamurthi ,&nbsp;N. Rameshkumar","doi":"10.1016/j.syapm.2023.126450","DOIUrl":"10.1016/j.syapm.2023.126450","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9941224","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":"Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages","authors":"Atena Sadat Sombolestani ,&nbsp;Dries Bongaerts ,&nbsp;Eliza Depoorter ,&nbsp;Ilse Cleenwerck ,&nbsp;Anneleen D. Wieme ,&nbsp;Scott J. Britton ,&nbsp;Stefan Weckx ,&nbsp;Luc De Vuyst ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2023.126440","DOIUrl":"10.1016/j.syapm.2023.126440","url":null,"abstract":"<div><p>Polyphasic taxonomic and comparative genomic analyses revealed that a series of lambic beer isolates including strain LMG 32668^T<span><span> and the kombucha isolate LMG 32879 represent a novel species among the </span>acetic acid bacteria, with </span><em>Acidomonas methanolica</em><span> as the nearest phylogenomic neighbor with a valid name. Overall genomic relatedness indices and phylogenomic and physiological analyses revealed that this novel species was best classified in a novel genus for which we propose the name </span><em>Brytella acorum</em> gen. nov., sp. nov., with LMG 32668^T (=CECT 30723^T) as the type strain. The <em>B. acorum</em><span><span> genomes encode a complete but modified tricarboxylic acid cycle<span>, and complete pentose phosphate, </span></span>pyruvate<span> oxidation<span><span><span> and gluconeogenesis<span> pathways. The absence of 6-phosphofructokinase which rendered the glycolysis pathway non-functional, and an energy metabolism that included both aerobic respiration and oxidative fermentation are typical metabolic characteristics of acetic acid bacteria. Neither genome encodes nitrogen fixation or </span></span>nitrate reduction genes, but both genomes encode genes for the </span>biosynthesis<span> of a broad range of amino acids<span>. Antibiotic resistance<span> genes or virulence factors are absent.</span></span></span></span></span></span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10143785","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":"Two novel symbiovars of Bradyrhizobium yuanmingense, americaense and caribense, the symbiovar tropici of Bradyrhizobium pachyrhizi and the symbiovar cajani of Bradyrhizobium cajani are microsymbionts of the legume Cajanus cajan in Dominican Republic","authors":"José David Flores-Félix ,&nbsp;Fernando Sánchez-Juanes ,&nbsp;Juan Araujo ,&nbsp;César Antonio Díaz-Alcántara ,&nbsp;Encarna Velázquez ,&nbsp;Fernando González-Andrés","doi":"10.1016/j.syapm.2023.126454","DOIUrl":"10.1016/j.syapm.2023.126454","url":null,"abstract":"<div><p><span><em>Cajanus</em><em> cajan</em></span> L. (guandul) is commonly cultivated in Dominican Republic where this legume is a subsistence crop<em>.</em> Here we identified through MALDI-TOF MS several rhizobial strains nodulating <em>C. cajan</em> in two Dominican locations as <span><em>Bradyrhizobium</em><em> yuanmingense</em></span><span>. The phylogenetic analysis of </span><em>recA</em> and <em>glnII</em><span> housekeeping genes showed that these strains belong to a wide cluster together with the type strain of </span><em>B. yuanmingense</em> and other <em>C. cajan</em><span> nodulating strains previously isolated in Dominican Republic. The comparison of genomes from strains representative of different lineages within this cluster support the existence of several genospecies within </span><em>B. yuanmingense</em><span>, which is the major microsymbiont of </span><em>C. cajan</em> in Dominican Republic where it is also nodulated by <em>Bradyrhizobium cajani</em> and <em>Bradyrhizobium pachyrhizi</em>. The analysis of the symbiotic <em>nodC</em> gene showed that the <em>C. cajan</em> nodulating strains from the <em>B. yuanmingense</em> complex belong to two clusters with less than 90% similarity between them. The strains from these two clusters showed <em>nodC</em> gene similarity values lower than 90% with respect to the remaining <em>Bradyrhizobium</em> symbiovars and then they correspond to two new symbiovars for which we propose the names americaense and caribense. The results of the <em>nodC</em> gene analysis also showed that <em>C. cajan</em> is nodulated by the symbiovar tropici, which has been found by first time in this work within the species <em>Bradyrhizobium pachyrhizi</em>. These results confirmed the high promiscuity degree of <em>C. cajan</em>, which is also nodulated by the symbiovar cajani of <em>Bradyrhizobium cajani</em> in Dominican Republic.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10230913","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":"Expanding the rumen Prevotella collection: The description of Prevotella communis, sp. nov. of ovine origin","authors":"Eva Grabner ,&nbsp;Eva Stare ,&nbsp;Lijana Fanedl ,&nbsp;Maša Zorec ,&nbsp;Dakota S. Jones ,&nbsp;Christopher D. Johnston ,&nbsp;Gorazd Avguštin ,&nbsp;Tomaž Accetto","doi":"10.1016/j.syapm.2023.126437","DOIUrl":"10.1016/j.syapm.2023.126437","url":null,"abstract":"<div><p>27 strains representing eight new <span><em>Prevotella</em></span><span> species were isolated from rumen<span> of a single sheep in eight weeks interval. One of the putative species encompassing the highest number of isolated strains which also exhibited some genetic variability<span> in preliminary data, was then selected for description of a novel species. We examined six strains in genomic and phenotypic detail, two of which may actually be the same strain isolated nearly three weeks apart. Other strains formed clearly diverged intraspecies lineages as evidenced by core genome phylogeny and phenotypic differences. Strains of the proposed new </span></span></span><em>Prevotella</em> species are strictly saccharolytic as is usual for rumen <em>Prevotella</em><span><span>, and use plant cell-wall xylans and pectins for growth. However, the range of cell-wall </span>polysaccharides<span> utilised for growth is rather limited compared to rumen generalists such as </span></span><em>Prevotella bryantii</em> or <span><em>Prevotella ruminicola</em></span> and this extends also to the inability to utilise starch, which is unexpected for the members of the genus <em>Prevotella</em>. Based on the data obtained, we propose <em>Prevotella communis</em> sp. nov. to accommodate strain E1-9^T as well as other strains with the similar properties<em>.</em><span> The proposed species is widespread: two other strains were previously isolated from sheep in Japan and is also common in metagenomic<span> data of cattle and sheep rumen samples from Scotland and New Zealand. It was also found in a collection of metagenome-assembled genomes originating from cattle in Scotland. Thus, it is a ubiquitous bacterium of domesticated ruminants specialising in degradation of a somewhat restricted set of plant cell wall components.</span></span></p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10158346","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}