Systematic and applied microbiology最新文献

{"title":"Methyloraptor flagellatus gen. Nov., sp. nov., novel Ancalomicrobiaceae-affiliated facultatively methylotrophic bacteria that feed on methanotrophs of the genus Methylococcus","authors":"Victoria A. Saltykova ,&nbsp;Olga V. Danilova ,&nbsp;Igor Y. Oshkin ,&nbsp;Svetlana E. Belova ,&nbsp;Natalia E. Suzina ,&nbsp;Nikolai V. Pimenov ,&nbsp;Svetlana N. Dedysh","doi":"10.1016/j.syapm.2024.126565","DOIUrl":"10.1016/j.syapm.2024.126565","url":null,"abstract":"<div><div>A morphologically conspicuous microbial association was detected in a bioreactor running in a continuous mode with methanotrophic bacteria of the genus <em>Methylococcus</em> and natural gas as a growth substrate. The association consisted of spherical <em>Methylococcus</em> cells colonized by elongated rods, which produced rosette-like aggregates and inhibited the cultivation process. An isolate of these bacteria, strain S20^T, was obtained and identified as belonging to the alphaproteobacterial family <em>Ancalomicrobiaceae</em> but displaying only a distant relationship (93.9–95.1 % 16S rRNA gene sequence similarity) to characterized members of this family. Strain S20^T was represented by aerobic, motile, facultatively methylotrophic bacteria, which grew between 10 and 45 °C (optimum 30–35 °C) in a pH range of 4.5–8.5 (optimum pH 6.0). These bacteria were capable of attaching to <em>Methylococcus</em> cells and breaking the integrity of methanotroph cell walls, presumably to feed on methanol. The same interaction was observed with <em>Methylomonas</em> species. The finished genome sequence of strain S20^T consisted of a 5.0 Mb chromosome and one plasmid, 0.26 Mb in size; the DNA G + C content was 68.4 %. The genome encoded 3 rRNA operons and ~ 4400 proteins including MxaFI- and XoxF-like methanol dehydrogenases, all enzymes of the serine pathway as well as a complete chemotaxis pathway, a unipolar polysaccharide adhesin, and a wide range of peptidases. The genome sequence displayed 67.20–69.56 % average amino acid identity to those of earlier described <em>Ancalomicrobiaceae</em> species. We propose to classify these bacteria as representing a novel genus and species, <em>Methyloraptor flagellatus</em> gen. Nov., sp. nov., with the type strain S20^T (=KCTC 8649^T = VKM B-3853^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126565"},"PeriodicalIF":3.3,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700550","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":"Parafrigoribacterium soli sp. nov. and Parafrigoribacterium humi sp. nov., two novel siderophore-synthesizing species isolated from black soil","authors":"Yu-Ting OuYang ,&nbsp;Le-Bin Chen ,&nbsp;Jian-Yu Jiao ,&nbsp;Zi-Xuan Hu ,&nbsp;Jiong-Shan Wang ,&nbsp;Tian-Hang Yang ,&nbsp;Jun Xiao ,&nbsp;Ting-Ting She ,&nbsp;Pin-Jiao Jin ,&nbsp;Shuang Wang ,&nbsp;Lan Liu ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2024.126564","DOIUrl":"10.1016/j.syapm.2024.126564","url":null,"abstract":"<div><div>Two siderophore-synthesizing species SYSU BS000078^T and SYSU BS000231^T were isolated from the black soil collected from fields located in Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these two strains showed the highest sequence similarity to <em>Parafrigoribacterium mesophilum</em> KCTC 19311^T (98.61 % and 98.68 %, respectively). The average nucleotide identity (ANI) values between the two strains and other members of the genus <em>Parafrigoribacterium</em> were lower than 95 %, recommended for distinguishing novel prokaryotic species. Cells of strains SYSU BS000078^T and SYSU BS000231^T were aerobic, motile, Gram-stain-positive and non-spore-forming rods. The colonies of these two strains exhibited a cream pigment, with tidy edges and smooth surfaces. Growth was observed within the temperature range of 4–37 °C (optimal growth at 28 °C) and pH range of 6.0–8.0 (optimal growth at pH 7.0). The predominant polar lipids detected in these two strains included diphosphatidylglycerol and phosphatidylglycerol. The predominant respiratory quinones was MK-9. The major cellular fatty acids (&gt;10 %) were iso-C_16:0, anteiso-C_15:0, and anteiso-C_17:0. The genome size and G + C content of strain SYSU BS000078^T were determined to be 2.89 Mbp and 66.5 %, respectively. Meanwhile, SYSU BS000231^T exhibited a genome size of 2.81 Mbp, accompanied by a G + C content of 65.8 %. Based on the phenotypic, physiological, genotypic, and phylogenetic data, these two strains represent two novel species of the genus <em>Parafrigoribacterium</em>, which are proposed as <em>Parafrigoribacterium soli</em> sp. nov. SYSU BS000078^T (=GDMCC 1.4599^T = KCTC 59245^T), and <em>Parafrigoribacterium humi</em> sp. nov. SYSU BS000231^T (=GDMCC 1.3816^T = KCTC 59001^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126564"},"PeriodicalIF":3.3,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142744184","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 five new strains in the family Woeseiaceae and emended description of the order Woeseiales with genomic features related to environmental adaptation","authors":"Feng-Bai Lian ,&nbsp;Bing-Jun Zhou ,&nbsp;Zi-Yang Zhou ,&nbsp;Alejandro P. Rooney ,&nbsp;Zhen-Xing Xu ,&nbsp;Zong-Jun Du","doi":"10.1016/j.syapm.2024.126563","DOIUrl":"10.1016/j.syapm.2024.126563","url":null,"abstract":"<div><div>The family <em>Woeseiaceae</em>, also known as the JTB255 bacterial group, are ubiquitous and abundant core members of microbial communities in marine surface sediments. However, to date, only one <em>Woeseiaceae</em> strain isolated from marine sediments has been described, and the phylogeny and environmental adaptation mechanisms of this group have been little explored. Here, we isolated five novel <em>Woeseiaceae</em> strains from the marine solar saltern in Weihai, China. Multiple genomic, physiological, and chemotaxonomic characteristics supported that these five isolates represent three novel species within a novel genus, for which <em>Lentisalinibacter</em> gen. nov. and three species <em>Lentisalinibacter sediminis</em> sp. nov., <em>Lentisalinibacter salinarum</em> sp. nov. and <em>Lentisalinibacter orientalis</em> sp. nov. are proposed. Moreover, phylogenetic analysis based on the 16S rRNA genes and genome sequences revealed that <em>Woeseiaceae</em> is most closely related to <em>Steroidobacterales</em>. Further comparative genomics analysis indicated the separate evolution of <em>Woeseiaceae</em> and <em>Steroidobacterales</em>, supporting the emended description of the order <em>Woeseiales</em>. <em>Woeseiales</em> representitives showed facultatively anaerobic characteristics and small genome sizes in contrast to their phylogenetic relatives. They primarily inhabit surface marine sediment environments using multiple metabolic and ecological strategies to adapt to the changing microenvironments. Our results demonstrate the novel representatives of <em>Woeseiales</em> and their environmental adaptation mechanisms in marine environments.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126563"},"PeriodicalIF":3.3,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142700552","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":"Thermodesulfovibrio autotrophicus sp. nov., the first autotrophic representative of the widespread sulfate-reducing genus Thermodesulfovibrio, and Thermodesulfovibrio obliviosus sp. nov. that has lost this ability","authors":"Anastasia I. Maltseva ,&nbsp;Alexander G. Elcheninov ,&nbsp;Alexandra A. Klyukina ,&nbsp;Nikolay V. Pimenov ,&nbsp;Andrei A. Novikov ,&nbsp;Alexander V. Lebedinsky ,&nbsp;Evgenii N. Frolov","doi":"10.1016/j.syapm.2024.126561","DOIUrl":"10.1016/j.syapm.2024.126561","url":null,"abstract":"<div><div>Representatives of the genus <em>Thermodesulfovibrio</em> are widespread thermophilic sulfate-reducing bacteria. The genus currently includes five species with validly published names. Two new <em>Thermodesulfovibrio</em> strains, 3907-1M ^T and 3462-1^T, were isolated with molecular hydrogen as an electron donor, sulfate as an electron acceptor and acetate as the carbon source from hot springs of Kunashir Island and Kamchatka Peninsula. Similar to other <em>Thermodesulfovibrio</em> species, the new isolates grew by reduction of sulfate, thiosulfate or Fe (III) with a limited range of electron donors, such as hydrogen (in the presence of acetate), formate (in the presence of acetate), pyruvate and lactate. Surprisingly, strain 3907-1M^T proved to be capable of autotrophic growth as well. Up to now, the genus <em>Thermodesulfovibrio</em> was represented by heterotrophic species only. Genome analysis revealed the presence of a gene cluster encoding enzymes of form III RubisCO-mediated transaldolase variant of the Calvin cycle in both strains, but genes encoding ribulose-1,5-bisphosphate carboxylase and phosphoribulokinase in the genome of the strain 3462-1^T contained internal stop codons in their sequences. On the basis of phylogenomic analysis, as well as distinct phenotypic and genomic properties, strain 3907-1M^T (=DSM 112797^T =JCM 39445^T =VKM B-3594^T =UQM 41601^T) is proposed to be classified as <em>Thermodesulfovibrio autotrophicus</em> sp. nov., and strain 3462-1^T (=JCM 39444^T =VKM B-3714^T =UQM 41602^T) – as <em>Thermodesulfovibrio obliviosus</em> sp. nov. Our results demonstrate a chemolithoautotrophic lifestyle in <em>Thermodesulfovibrio</em> representatives, suggesting greater ecological flexibility of this genus than previously assumed.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126561"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648455","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":"Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C","authors":"Violetta Shestivska ,&nbsp;Petra Španělová ,&nbsp;Marcela Krůtová ,&nbsp;Martina Maixnerová ,&nbsp;Priscila Thiago Dobbler ,&nbsp;Tomáš Větrovský ,&nbsp;Alexandr Nemec ,&nbsp;Martina Kyselková","doi":"10.1016/j.syapm.2024.126560","DOIUrl":"10.1016/j.syapm.2024.126560","url":null,"abstract":"<div><div>This study aimed to determine the taxonomic status of a new group of bovine strains of the genus <em>Acinetobacter</em> characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and <em>rpoB</em> gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome <em>de novo</em> sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known <em>Acinetobacter</em> species were &lt; 83%. Each of the 12 genomes consisted of a circular chromosome (3.05−3.28 Mb) and 1−6 extrachromosomal elements (1.43−122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37–46 °C differed from that of <em>Acinetobacter baumannii</em>. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of <em>strA</em>/<em>strB</em>, <em>tet</em>(Y), and <em>sul2</em> genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name <em>Acinetobacter thermotolerans</em> sp. nov. The type strain is ANC 7454^T (= CCM 9356^T = CCUG 77195^T = CNCTC 8200^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126560"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676834","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 “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":"10.1016/j.syapm.2024.126558","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126558"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","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}

{"title":"Inconsistent identification of Apilactobacillus kunkeei-related strains obtained by well-developed overall genome-related indices","authors":"Shintaro Maeno ,&nbsp;Akihito Endo","doi":"10.1016/j.syapm.2024.126559","DOIUrl":"10.1016/j.syapm.2024.126559","url":null,"abstract":"<div><div>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 <em>Apilactobacillus kunkeei</em>. In the present study, the classification of <em>Apilactobacillus</em> spp., including <em>A. kunkeei</em>, was evaluated by multiple genome-based analyses. ANIb-based classification appropriately identified strains of <em>Apilactobacillus</em> spp., except for <em>A. kunkeei</em>-related strains. A number of strain pairings in <em>A. kunkeei</em>-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 <em>A. kunkeei</em>-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 <em>A. kunkeei</em>-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 <em>A. kunkeei</em>-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.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 6","pages":"Article 126559"},"PeriodicalIF":3.3,"publicationDate":"2024-11-01","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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^T, which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75^T 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^T and their close neighbors <em>H.anseris</em> ATCC BAA-1299^T 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^T 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^T (=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":"47 6","pages":"Article 126557"},"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}

{"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^T, 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^T<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^T 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^T (DSM 117632^T = LMG 33563^T) 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":"47 6","pages":"Article 126556"},"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}

{"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":"47 6","pages":"Article 126555"},"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}