Pub Date : 2023-10-07DOI: 10.1016/j.syapm.2023.126472
Ana S. Ramírez , José B. Poveda , Remco Dijkman , Carlos Poveda , Alejandro Suárez-Pérez , Rubén S. Rosales , Anneke Feberwee , Michael P. Szostak , Lorenzo Ressel , Tomeu Viver , Pascual Calabuig , Salvatore Catania , Federica Gobbo , Dorina Timofte , Joachim Spergser
In the search for mollicutes in wild birds, six Mycoplasma strains were isolated from tracheal swabs taken from four different species of seabirds. Four strains originated from three Yellow-legged gulls (Larus michahellis) and a Cory’s shearwater (Calonectris borealis) from Spain, one from a South African Kelp gull (Larus dominicanus), and one from an Italian Black-headed gull (Chroicocephalus ridibundus). These Mycoplasma strains presented 99 % 16S rRNA gene sequence similarity values with Mycoplasma (M.) gallisepticum. Phylogenetic analyses of marker genes (16S rRNA gene and rpoB) confirmed the close relationship of the strains to M. gallisepticum and M. tullyi. 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 hydrolyze arginine or urea. Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas, presenting spherical to flask-shaped cells with an attachment organelle. Gliding motility was also observed. Furthermore, serological tests, MALDI-ToF mass spectrometry and genomic studies demonstrated that the strains were different to any known Mycoplasma species, for which the name Mycoplasma bradburyae sp. nov. is proposed; the type strain is T158T (DSM 110708 = NCTC 14398).
{"title":"Mycoplasma bradburyae sp. nov. isolated from the trachea of sea birds","authors":"Ana S. Ramírez , José B. Poveda , Remco Dijkman , Carlos Poveda , Alejandro Suárez-Pérez , Rubén S. Rosales , Anneke Feberwee , Michael P. Szostak , Lorenzo Ressel , Tomeu Viver , Pascual Calabuig , Salvatore Catania , Federica Gobbo , Dorina Timofte , 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<sup>T</sup> (DSM 110708 = NCTC 14398).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"46 6","pages":"Article 126472"},"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}
Pub Date : 2023-09-23DOI: 10.1016/j.syapm.2023.126468
Helen R. Davison, Gregory D.D. Hurst
Chlamydiota 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 Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae 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 “Sacchlamyda saccharinae” (Family Rhabdochlamydiaceae) and “Amphrikana amoebophyrae” (Family Simkaniaceae), as well as a third new clade of environmental MAGs “Acheromyda pituitae” (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae 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 Parachlamydiales 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.
{"title":"Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data","authors":"Helen R. Davison, 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":"46 6","pages":"Article 126468"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126451
Galina Slobodkina , Alexander Merkel , Nataliya Ratnikova , Alexandra Kuchierskaya , Alexander Slobodkin
Chemolithoautotrophic microorganisms can play a significant role in the biogeochemical cycling of elements in deep-subsurface-associated environments. A novel facultatively anaerobic lithoautotrophic bacteria (strains SB48T and SN1189) were isolated from terrestrial mud volcanoes (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 CO2/HCO3− as a carbon source. They also grew with organic acids, ethanol, yeast extract and peptone. The isolates were capable of either anaerobic respiration with nitrate or nitrous oxide as the electron acceptors or aerobic respiration under microaerobic condition. The total size of the genome of strains SB48T and SN1189 was 4.71 and 5.13 Mbp, respectively. Based on phenotypic and phylogenetic characteristics, strains SB48T and SN1189 represent a novel species of the genus Sedimenticola, S. hydrogenitrophicus (the type strain is SB48T = KCTC 25568 T = VKM B-3680 T). The new isolates are the first representatives of the genus Sedimenticola isolated from a terrestrial ecosystem. Based on phylogenomic reconstruction we propose to include the genus Sedimenticola and the related genera into a new family Sedimenticolaceae fam. nov. within the order Chromatiales.
{"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 , Alexander Merkel , Nataliya Ratnikova , Alexandra Kuchierskaya , 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><sup>T</sup><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><sub>2</sub>/HCO<sub>3</sub><sup>−</sup><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><sup>T</sup><span> and SN1189 was 4.71 and 5.13 Mbp, respectively. Based on phenotypic and phylogenetic characteristics, strains SB48</span><sup>T</sup> and SN1189 represent a novel species of the genus <em>Sedimenticola</em>, <em>S. hydrogenitrophicus</em> (the type strain is SB48<sup>T</sup> = KCTC 25568 <sup>T</sup> = VKM B-3680 <sup>T</sup>). 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":"46 5","pages":"Article 126451"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126452
Ricu Claassens , Stephanus N. Venter , Chrizelle W. Beukes , Tomasz Stępkowski , Wai Y. Chan , Emma T. Steenkamp
A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) 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 nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.
{"title":"Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa","authors":"Ricu Claassens , Stephanus N. Venter , Chrizelle W. Beukes , Tomasz Stępkowski , Wai Y. Chan , 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<sup>T</sup>, <em>B. betae</em> PL7HG1<sup>T</sup>, <em>B. ganzhouense</em> CCBAU 51670 <sup>T</sup>, <em>B. cytisi</em> CTAW11<sup>T</sup> and <em>B. rifense</em> CTAW71<sup>T</sup>) 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<sup>T</sup> (=LMG 31415 <sup>T</sup> = SARCC-753 <sup>T</sup>) 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":"46 5","pages":"Article 126452"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126453
Eva Grabner , Eva Stare , Lijana Fanedl , Maša Zorec , Dakota S. Jones , Christopher D. Johnston , Gorazd Avguštin , Tomaž Accetto
{"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 , Eva Stare , Lijana Fanedl , Maša Zorec , Dakota S. Jones , Christopher D. Johnston , Gorazd Avguštin , 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":"46 5","pages":"Article 126453"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126439
Svetlana N. Dedysh
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.
{"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":"46 5","pages":"Article 126439"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126440
Atena Sadat Sombolestani , Dries Bongaerts , Eliza Depoorter , Ilse Cleenwerck , Anneleen D. Wieme , Scott J. Britton , Stefan Weckx , Luc De Vuyst , Peter Vandamme
Polyphasic taxonomic and comparative genomic analyses revealed that a series of lambic beer isolates including strain LMG 32668T and the kombucha isolate LMG 32879 represent a novel species among the acetic acid bacteria, with Acidomonas methanolica 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 Brytella acorum gen. nov., sp. nov., with LMG 32668T (=CECT 30723T) as the type strain. The B. acorum genomes encode a complete but modified tricarboxylic acid cycle, and complete pentose phosphate, pyruvate oxidation and gluconeogenesis 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 nitrate reduction genes, but both genomes encode genes for the biosynthesis of a broad range of amino acids. Antibiotic resistance genes or virulence factors are absent.
{"title":"Brytella acorum gen. nov., sp. nov., a novel acetic acid bacterium from sour beverages","authors":"Atena Sadat Sombolestani , Dries Bongaerts , Eliza Depoorter , Ilse Cleenwerck , Anneleen D. Wieme , Scott J. Britton , Stefan Weckx , Luc De Vuyst , 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<sup>T</sup><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<sup>T</sup> (=CECT 30723<sup>T</sup>) 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":"46 5","pages":"Article 126440"},"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}
Pub Date : 2023-09-01DOI: 10.1016/j.syapm.2023.126454
José David Flores-Félix , Fernando Sánchez-Juanes , Juan Araujo , César Antonio Díaz-Alcántara , Encarna Velázquez , Fernando González-Andrés
Cajanus cajan L. (guandul) is commonly cultivated in Dominican Republic where this legume is a subsistence crop. Here we identified through MALDI-TOF MS several rhizobial strains nodulating C. cajan in two Dominican locations as Bradyrhizobium yuanmingense. The phylogenetic analysis of recA and glnII housekeeping genes showed that these strains belong to a wide cluster together with the type strain of B. yuanmingense and other C. cajan 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 B. yuanmingense, which is the major microsymbiont of C. cajan in Dominican Republic where it is also nodulated by Bradyrhizobium cajani and Bradyrhizobium pachyrhizi. The analysis of the symbiotic nodC gene showed that the C. cajan nodulating strains from the B. yuanmingense complex belong to two clusters with less than 90% similarity between them. The strains from these two clusters showed nodC gene similarity values lower than 90% with respect to the remaining Bradyrhizobium symbiovars and then they correspond to two new symbiovars for which we propose the names americaense and caribense. The results of the nodC gene analysis also showed that C. cajan is nodulated by the symbiovar tropici, which has been found by first time in this work within the species Bradyrhizobium pachyrhizi. These results confirmed the high promiscuity degree of C. cajan, which is also nodulated by the symbiovar cajani of Bradyrhizobium cajani in Dominican Republic.
{"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 , Fernando Sánchez-Juanes , Juan Araujo , César Antonio Díaz-Alcántara , Encarna Velázquez , 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":"46 5","pages":"Article 126454"},"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}
Pub Date : 2023-07-01DOI: 10.1016/j.syapm.2023.126437
Eva Grabner , Eva Stare , Lijana Fanedl , Maša Zorec , Dakota S. Jones , Christopher D. Johnston , Gorazd Avguštin , Tomaž Accetto
27 strains representing eight new Prevotella species were isolated from rumen 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 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 Prevotella species are strictly saccharolytic as is usual for rumen Prevotella, and use plant cell-wall xylans and pectins for growth. However, the range of cell-wall polysaccharides utilised for growth is rather limited compared to rumen generalists such as Prevotella bryantii or Prevotella ruminicola and this extends also to the inability to utilise starch, which is unexpected for the members of the genus Prevotella. Based on the data obtained, we propose Prevotella communis sp. nov. to accommodate strain E1-9T as well as other strains with the similar properties. The proposed species is widespread: two other strains were previously isolated from sheep in Japan and is also common in metagenomic 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.
在8周的时间间隔内从一只羊的瘤胃中分离出8个新的普雷沃氏菌种27株。其中一个假定的物种包含最高数量的分离菌株,并且在初步数据中也表现出一些遗传变异,然后被选择用于描述一个新种。我们在基因组和表型细节上检查了六株菌株,其中两株实际上可能是相隔近三周分离的同一株菌株。其他菌株形成了明显分化的种内谱系,核心基因组系统发育和表型差异证明了这一点。与通常的瘤胃普雷沃特菌一样,提出的新普雷沃特菌株严格地具有糖溶性,并利用植物细胞壁木聚糖和果胶进行生长。然而,用于生长的细胞壁多糖的范围与瘤胃通才(如bryantii普雷沃氏菌或ruminicola普雷沃氏菌)相比相当有限,这也延伸到无法利用淀粉,这对普雷沃氏菌属的成员来说是意想不到的。根据获得的数据,我们提出了普雷沃氏菌(Prevotella communis sp. 11 .)来容纳菌株E1-9T以及其他具有类似性质的菌株。该物种分布广泛:之前从日本的绵羊中分离出另外两种菌株,在苏格兰和新西兰的牛和羊瘤胃样本的元基因组数据中也很常见。它也被发现在一组来自苏格兰牛的宏基因组组装基因组中。因此,它是一种在驯养反刍动物中普遍存在的细菌,专门降解某种程度上有限的植物细胞壁成分。
{"title":"Expanding the rumen Prevotella collection: The description of Prevotella communis, sp. nov. of ovine origin","authors":"Eva Grabner , Eva Stare , Lijana Fanedl , Maša Zorec , Dakota S. Jones , Christopher D. Johnston , Gorazd Avguštin , 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<sup>T</sup> 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":"46 4","pages":"Article 126437"},"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}