Systematic and applied microbiology最新文献

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Inconsistent identification of Apilactobacillus kunkeei-related strains obtained by well-developed overall genome-related indices. 通过完善的整体基因组相关指数获得的昆明杏杆菌相关菌株的鉴定结果不一致。
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-11-04 DOI: 10.1016/j.syapm.2024.126559
Shintaro Maeno, Akihito Endo
{"title":"Inconsistent identification of Apilactobacillus kunkeei-related strains obtained by well-developed overall genome-related indices.","authors":"Shintaro Maeno, Akihito Endo","doi":"10.1016/j.syapm.2024.126559","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126559","url":null,"abstract":"<p><p>During a decade, overall genome related indices, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), have been used as standards for the classification and identification of bacteria. On the other hand, a former study suggested that ANI-based classification is difficult for fructophilic lactic acid bacterium Apilactobacillus kunkeei. In the present study, the classification of Apilactobacillus spp., including A. kunkeei, was evaluated by multiple genome-based analyses. ANIb-based classification appropriately identified strains of Apilactobacillus spp., except for A. kunkeei-related strains. A number of strain pairings in A. kunkeei-related strains showed ANIb values around the threshold value of 95 %, based on which they were unable to be identified. On the other hand, dDDH provided clearer identification results for A. kunkeei-related strains but segmentalized them into a number of groups, while the validity of this segmentation was unclear. Certain strains shared similarities over the threshold with multiple species-level taxonomic groups in ANIb and dDDH. GTDB-Tk classifies the A. kunkeei-related strains into six species-level taxonomic groups without marked confusion, while the classification results differed from those obtained by ANIb and dDDH. The present study highlighted the inconsistent identification of A. kunkeei-related strains by the well-developed overall genome related indices, which would be a significant concern for bacterial taxonomy. Moreover, the rule adopted in GTDB-Tk, i.e., the classification of strains to taxa containing type strains showing the highest similarity, is recommended for introduction into ANIb- and GGDC-based classifications.</p>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606530","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}
引用次数: 0
Corrigendum to "Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili" [Syst. Appl. Microbiol. 45(5) (2022) 126344]. 两个新型戊糖发酵和 GABA 产物的特征:Levilactobacillus tujiorum sp:从固态发酵的辣椒中分离出的 Levilactobacillus tujiorum sp.
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-10-21 DOI: 10.1016/j.syapm.2024.126558
Chun Tao Gu
{"title":"Corrigendum to \"Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili\" [Syst. Appl. Microbiol. 45(5) (2022) 126344].","authors":"Chun Tao Gu","doi":"10.1016/j.syapm.2024.126558","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126558","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142508428","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}
引用次数: 0
Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species 来自蜥蜴的卡帕多慈氏螺旋杆菌新种(Helicobacter cappadocius sp:第一个精神滋养型螺旋杆菌物种
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-10-14 DOI: 10.1016/j.syapm.2024.126557
Fuat Aydin , Serdal Tarhane , Emre Karakaya , Seçil Abay , Tuba Kayman , Özgür Güran , Emin Bozkurt , Nazan Üzüm , Aziz Avci , Kurtuluş Olgun , Daniel Jablonski , Cansu Güran , İzzet Burçin Saticioğlu
{"title":"Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species","authors":"Fuat Aydin ,&nbsp;Serdal Tarhane ,&nbsp;Emre Karakaya ,&nbsp;Seçil Abay ,&nbsp;Tuba Kayman ,&nbsp;Özgür Güran ,&nbsp;Emin Bozkurt ,&nbsp;Nazan Üzüm ,&nbsp;Aziz Avci ,&nbsp;Kurtuluş Olgun ,&nbsp;Daniel Jablonski ,&nbsp;Cansu Güran ,&nbsp;İzzet Burçin Saticioğlu","doi":"10.1016/j.syapm.2024.126557","DOIUrl":"10.1016/j.syapm.2024.126557","url":null,"abstract":"<div><div>It was aimed to determine the prevalence of <em>Helicobacter</em> in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus <em>Helicobacter</em>. These isolates were found to be in a distinct group from other <em>Helicobacter</em> species. However, the 16S rRNA sequence did not match any identified species, with the closest match being <em>Helicobacter mustelae</em> strain R85-13-6<sup>T</sup>, which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75<sup>T</sup> and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75<sup>T</sup> and their close neighbors <em>H.anseris</em> ATCC BAA-1299<sup>T</sup> shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75<sup>T</sup> in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name <em>Helicobacter cappadocius</em> with faydin-H75<sup>T</sup> (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first <em>Helicobacter</em> species to exhibit a psychrotrophic feature.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441607","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}
引用次数: 0
Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs 从野猪粪便样本中分离出的新物种 Limosilactobacillus allomucosae sp.
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-25 DOI: 10.1016/j.syapm.2024.126556
Binbin Chen, Shaktheeshwari Silvaraju, Sharifah Nora Ahmad Almunawar, Yu Chyuan Heng, Jolie Kar Yi Lee, Sandra Kittelmann
{"title":"Limosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs","authors":"Binbin Chen,&nbsp;Shaktheeshwari Silvaraju,&nbsp;Sharifah Nora Ahmad Almunawar,&nbsp;Yu Chyuan Heng,&nbsp;Jolie Kar Yi Lee,&nbsp;Sandra Kittelmann","doi":"10.1016/j.syapm.2024.126556","DOIUrl":"10.1016/j.syapm.2024.126556","url":null,"abstract":"<div><div>Six strains, WILCCON 0050, WILCCON 0051, WILCCON 0052, WILCCON 0053, WILCCON 0054, WILCCON 0055<sup>T</sup>, were isolated from four different faecal samples of wild boars on Pulau Ubin, Singapore, Singapore. Based on core genome phylogenetic analysis, the six strains formed a distinct clade within the genus <em>Limosilactobacillus</em> (<em>Lm</em>.), with the most closely related type strain being <em>Lm. mucosae</em> DSM 13345<sup>T</sup><em>.</em> The minimum ANI, dDDH, and AAI values within these six strains were 97.8%, 78.8%, and 98.6%, respectively. In contrast, the ANI, dDDH, and AAI values with <em>Lm. mucosae</em> DSM 13345<sup>T</sup> were lower, ranging between 94.8–95.1%, 57.1–59.0%, and 95.9–97.0%, respectively. While ANI and AAI were close to the thresholds of 95% and 97% for bacterial species delineation, respectively, dDDH was significantly lower than the threshold value of 70%. Based on our phylogenomic, phenotypic and chemotaxonomic analyses, we propose a novel species with the name <em>Limosilactobacillus allomucosae</em> sp. nov., with WILCCON 0055<sup>T</sup> (DSM 117632<sup>T</sup> = LMG 33563<sup>T</sup>) as the designated type strain. <em>In vitro</em> investigations revealed the strains’ ability to break down raffinose-family oligosaccharides, and to utilize prebiotics such as <em>xylo</em>-oligosaccharides and galacturonic acid, thereby enhancing fibre digestion and nutrient absorption. Moreover, strong auto-aggregation properties, as well as resistance to low pH and porcine bile were observed, suggesting their potential survival and persistence during passage through the gut. The high bile tolerance of these strains appears to be attributed to their ability to deconjugate a wide range of conjugated bile compounds. <em>In silico</em> analysis indicated a strong potential for mucin-binding activity, which aids their colonization in the gut. These characteristics indicate the potential suitability of strains of <em>Lm. allomucosae</em> as probiotics for domestic pigs.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142523161","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}
引用次数: 0
Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential 酸性微生物,沿海海洋沉积物中的放线菌群:丰度、分类和基因组潜力。
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-24 DOI: 10.1016/j.syapm.2024.126555
Sebastián Silva-Solar, Tomeu Viver, Yueqing Wang, Luis H. Orellana, Katrin Knittel, Rudolf Amann
{"title":"Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential","authors":"Sebastián Silva-Solar,&nbsp;Tomeu Viver,&nbsp;Yueqing Wang,&nbsp;Luis H. Orellana,&nbsp;Katrin Knittel,&nbsp;Rudolf Amann","doi":"10.1016/j.syapm.2024.126555","DOIUrl":"10.1016/j.syapm.2024.126555","url":null,"abstract":"<div><div>Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class <em>Acidimicrobiia</em>, within the phylum <em>Actinomycetota</em>, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available <em>Acidimicrobiia</em> genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class <em>Acidimicrobiia</em> and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of <em>Actinomycetota</em> 16S rRNA gene sequences, and 3–7% of <em>Bacteria</em>. We propose <em>Benthobacter isfjordensis</em> gen. nov., sp. nov., <em>Hadalibacter litoralis</em> gen. nov., sp. nov., and two new species from <em>Ilumatobacter</em>, following SeqCode guidelines. In addition, we report the first <em>in situ</em> quantification of the family <em>Ilumatobacteraceae</em>, revealing its substantial presence (1–6%) in coastal sediments. This work highlights the need of refining the taxonomy of <em>Acidimicrobiia</em> to better understand their ecological contributions.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354249","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}
引用次数: 0
Options and considerations for validation of prokaryotic names under the SeqCode 根据 SeqCode 验证原核生物名称的选项和注意事项
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-19 DOI: 10.1016/j.syapm.2024.126554
Stephanus N. Venter , Luis M. Rodriguez-R , Maria Chuvochina , Marike Palmer , Philip Hugenholtz , Emma T. Steenkamp
{"title":"Options and considerations for validation of prokaryotic names under the SeqCode","authors":"Stephanus N. Venter ,&nbsp;Luis M. Rodriguez-R ,&nbsp;Maria Chuvochina ,&nbsp;Marike Palmer ,&nbsp;Philip Hugenholtz ,&nbsp;Emma T. Steenkamp","doi":"10.1016/j.syapm.2024.126554","DOIUrl":"10.1016/j.syapm.2024.126554","url":null,"abstract":"<div><p>Stable taxon names for <em>Bacteria</em> and <em>Archaea</em> are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as <em>Candidatus</em> or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established <em>Code of Nomenclature of Prokaryotes Described from Sequence Data</em> (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000687/pdfft?md5=5b5372d92c75bdd6040b1f983f546de1&pid=1-s2.0-S0723202024000687-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274062","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}
引用次数: 0
Description of three new Pseudomonas species isolated from aquarium fish: Pseudomonas auratipiscis sp. nov., Pseudomonas carassii sp. nov. and Pseudomonas ulcerans sp. nov 描述从水族鱼类中分离出的三种新假单胞菌:Pseudomonas auratipiscis sp.
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-19 DOI: 10.1016/j.syapm.2024.126552
Muhammed Duman , Jorge Lalucat , Izzet Burcin Saticioglu , Magdalena Mulet , Margarita Gomila , Soner Altun , Nihed Ajmi , Elena García-Valdés
{"title":"Description of three new Pseudomonas species isolated from aquarium fish: Pseudomonas auratipiscis sp. nov., Pseudomonas carassii sp. nov. and Pseudomonas ulcerans sp. nov","authors":"Muhammed Duman ,&nbsp;Jorge Lalucat ,&nbsp;Izzet Burcin Saticioglu ,&nbsp;Magdalena Mulet ,&nbsp;Margarita Gomila ,&nbsp;Soner Altun ,&nbsp;Nihed Ajmi ,&nbsp;Elena García-Valdés","doi":"10.1016/j.syapm.2024.126552","DOIUrl":"10.1016/j.syapm.2024.126552","url":null,"abstract":"<div><div><em>Pseudomonas</em> species constitute a significant group of pathogens in aquarium fish and frequently cause haemorrhagic septicaemia. This study conducted a taxonomic characterization of <em>Pseudomonas</em> isolates from aquarium fish exhibiting deep ulceration and general disease signs. A polyphasic approach was employed to ascertain the taxonomic affiliation of the strains. The overall genome relatedness indices of digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genus <em>Pseudomonas</em> were found to be below the established thresholds of 70 and 95–96%, respectively. Whole-genome based phylogenetic analysis revealed that strains 119P<sup>T</sup> and 120P were closely related to <em>P. arcuscaelestis.</em> Strain 137P<sup>T</sup> was related to <em>P. peradeniyensis,</em> while strains 147P<sup>T</sup> and 148P were closely related to <em>P. japonica</em>. The morphological, physiological, and biochemical characteristics of the strains and the genome relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as three novel species. Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, virulence features and ecological distribution patterns. Based on polyphasic characterization, the strains 119P<sup>T</sup>, 120P, 137P<sup>T</sup>, 147P<sup>T</sup>, and 148P are novel species within the genus <em>Pseudomonas</em>, for which the following names are proposed: <em>Pseudomonas auratipiscis</em> sp. nov., with the strain 119P<sup>T</sup> as the type strain (=DSM 117162 <sup>T</sup>, =LMG 33381<sup>T</sup>); <em>Pseudomonas carassii</em> sp. nov., with the strain 137P<sup>T</sup> as the type strain (=DSM 117060<sup>T</sup>, =LMG 33378<sup>T</sup>); and <em>Pseudomonas ulcerans</em> sp. nov. 147P<sup>T</sup>, as the type strain (=DSM 117163<sup>T</sup>, =LMG 33377<sup>T</sup>).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142327103","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}
引用次数: 0
Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal Halorubrum miltondacostae sp.
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-17 DOI: 10.1016/j.syapm.2024.126553
Luciana Albuquerque , Tomeu Viver , Cristina Barroso , Ricardo Claudino , Mariana Galvan , Gabriela Simões , Alexandre Lobo-da-Cunha , Conceição Egas
{"title":"Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal","authors":"Luciana Albuquerque ,&nbsp;Tomeu Viver ,&nbsp;Cristina Barroso ,&nbsp;Ricardo Claudino ,&nbsp;Mariana Galvan ,&nbsp;Gabriela Simões ,&nbsp;Alexandre Lobo-da-Cunha ,&nbsp;Conceição Egas","doi":"10.1016/j.syapm.2024.126553","DOIUrl":"10.1016/j.syapm.2024.126553","url":null,"abstract":"<div><p>One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the <em>Archaea</em> domain within the genus <em>Halorubrum</em>. Two strains, RMP-11<sup>T</sup> and RMP-47, showed 99.1 % sequence similarity with the species <em>Halorubrum californiense</em> based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, <em>atpB</em>, <em>EF-2</em>, <em>glnA</em>, <em>ppsA</em> and <em>rpoB</em>’, showed <em>Halorubrum coriense</em> as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11<sup>T</sup>, RMP-47 and species <em>Hrr. coriense</em> were within the range of 90.0–90.5 %, supporting that strains RMP-11<sup>T</sup> and RMP-47 represent a novel species of the genus <em>Halorubrum</em>. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25–50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus <em>Halorubrum</em>. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel <em>Halorubrum</em> species but distinct from the species represented by strains RMP-11<sup>T</sup> and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus <em>Halorubrum</em> represented by strains RMP-11<sup>T</sup> (=CECT 30760<sup>T</sup> = DSM 115521<sup>T</sup>) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name <em>Halorubrum miltondacostae</em> sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000675/pdfft?md5=23869e81b22a25eff38705095178ebb6&pid=1-s2.0-S0723202024000675-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274040","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}
引用次数: 0
Evidence for the occurrence of Acinetobacter faecalis in cattle feces and its emended description 牛粪便中存在粪杆菌的证据及其修订描述。
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-01 DOI: 10.1016/j.syapm.2024.126545
Martina Kyselková , Kyriaki Xanthopoulou , Violetta Shestivska , Petra Španělová , Martina Maixnerová , Paul G. Higgins , Alexandr Nemec
{"title":"Evidence for the occurrence of Acinetobacter faecalis in cattle feces and its emended description","authors":"Martina Kyselková ,&nbsp;Kyriaki Xanthopoulou ,&nbsp;Violetta Shestivska ,&nbsp;Petra Španělová ,&nbsp;Martina Maixnerová ,&nbsp;Paul G. Higgins ,&nbsp;Alexandr Nemec","doi":"10.1016/j.syapm.2024.126545","DOIUrl":"10.1016/j.syapm.2024.126545","url":null,"abstract":"<div><p>This study provides an emended description of <em>Acinetobacter faecalis</em>, a species previously described based on a single isolate (YIM 103518<sup>T</sup>) from elephant feces in China. Our emended description is based on 15 novel isolates conspecific with the <em>A. faecalis</em> type strain, obtained from eight cattle farms in the Czech Republic. The <em>A. faecalis</em> strains have relatively small genomes (≈2.5−2.7 Mbp), with a GC content of 36.3−36.7 mol%. Core genome-based phylogenetic analysis showed that the 15 strains, together with the type strain of <em>A. faecalis</em>, form a distinct and internally coherent phylogroup within the genus. Pairwise genomic ANIb values for the 16 <em>A. faecalis</em> strains were 97.32−99.04 %, while ANIb values between the genomes of the 16 strains and those of the other <em>Acinetobacter</em> spp. were ≤ 86.2 %. Analysis of whole-cell MALDI-TOF mass spectra supported the distinctness and cohesiveness of the taxon. The <em>A. faecalis</em> strains could be differentiated from the other validly named <em>Acinetobacter</em> spp. by the absence of hemolytic activity along with their ability to grow at 37 °C and on L-aspartate, ethanol, and L-glutamate but not at 41 °C or on adipate or 2,3-butanediol. Reduced susceptibility to sulfamethoxazole, trimethoprim and/or streptomycin was shown in eight strains, along with the presence of corresponding antibiotic resistance genes. In conclusion, this study provides a comprehensive description of <em>A. faecalis</em> and demonstrates its occurrence in cattle feces. Though the ecological role of <em>A. faecalis</em> remains unknown, our results show its ability to acquire antibiotic resistance genes, likely as an adaptation to antibiotic selection pressure in livestock farms.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142146384","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}
引用次数: 0
Corrigendum to “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” [Syst. Appl. Microbiol. 47 (2024) 126519] 对 "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 "的更正 [Syst.
IF 3.3 2区 生物学
Systematic and applied microbiology Pub Date : 2024-09-01 DOI: 10.1016/j.syapm.2024.126526
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引用次数: 0
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