International journal of systematic and evolutionary microbiology最新文献

{"title":"The dynamic history of prokaryotic phyla: discovery, diversity and division.","authors":"Mark J Pallen","doi":"10.1099/ijsem.0.006508","DOIUrl":"10.1099/ijsem.0.006508","url":null,"abstract":"<p><p>Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The <i>Candidatus</i> designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11382960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation List no. 219. Valid publication of new names and new combinations effectively published outside the IJSEM.","authors":"Aharon Oren, Markus Göker","doi":"10.1099/ijsem.0.006452","DOIUrl":"10.1099/ijsem.0.006452","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum: <i>Nicoliella lavandulae</i> sp. nov., a novel fructophilic <i>Nicoliella</i> species isolated from flowers of <i>Lavandula angustifolia</i>.","authors":"Cristina Alcántara, Ángela Peirotén, Luis A Ramón-Nuñez, José M Landete, Manuel Zúñiga, Vicente Monedero","doi":"10.1099/ijsem.0.006538","DOIUrl":"https://doi.org/10.1099/ijsem.0.006538","url":null,"abstract":"","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142346744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Luteipulveratus flavus</i> sp. nov. isolated from two lichen species.","authors":"Lian-Shuang Xiong, Ming-Qun Fan, Zu-Zhen Yang, Shu-Ya Zuo, Qing Yuan, Li-Song Wang, Cheng-Lin Jiang, Xin-Yu Wang, Yi Jiang","doi":"10.1099/ijsem.0.006518","DOIUrl":"https://doi.org/10.1099/ijsem.0.006518","url":null,"abstract":"<p><p>Two novel strains, YIM 133132^T and YIM 133296, were isolated from lichen samples collected from Yunnan Province, Southwest PR China. YIM 133132^T and YIM 133296 are aerobic, Gram-staining-positive, non-motile actinomycetes. They are also catalase-positive and oxidase-negative, and YIM 133132^T formed flat yellowish colonies that were relatively dry on YIM38 agar medium. Flat yellowish colonies of YIM 133296 were also observed on YIM38 agar medium. YIM 133132^T grew at 25-35 °C (optimum 25-30 °C), pH 6.0-9.0 (optimum pH 7.0) and in the presence of 0-8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains YIM 133132^T and YIM 133296 represented members of the genus <i>Luteipulveratus</i> and exhibited high sequence similarity (96.93%) with <i>Luteipulveratus halotolerans</i> C296001^T. The genomic DNA G+C content of both strains was 71.8%. The DNA-DNA hybridisation (dDDH) values between YIM 133132^T and YIM 133296 were 85.1%, and the DNA-DNA hybridisation value between YIM 133132^T and YIM 133296 and <i>L. halotolerans</i> C296001^T was 23.4%. On the basis of the draft genome sequences, the average nucleotide identity (ANI) between strains YIM 133132^T and YIM 133296 and <i>L. halotolerans</i> C296001^T was 80.8%. The major menaquinones that were identified were MK-8(H₄), MK-9 and MK-8(H₂). The polar lipids were diphosphatidylglycerol and phosphatidylinositol. On the basis of the morphological, physiological, biochemical, genomic, phylogenetic and chemotaxonomic characteristics, strains YIM 133132^T and YIM 133296 can be clearly distinguished from <i>L. halotolerans</i> C296001^T, and the two strains represent a novel species for which the name <i>L. flavus</i> sp. nov. is proposed. The type strain is YIM 133132^T (CGMCC= 1.61357^T and KCTC= 49824^T).</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Hyphobacterium marinum</i> sp. nov. and <i>Hyphobacterium lacteum</i> sp. nov., isolated from marine sediment.","authors":"Shi-Bo Zhao, Le Liu, Feng-Bai Lian, Zong-Jun Du","doi":"10.1099/ijsem.0.006512","DOIUrl":"10.1099/ijsem.0.006512","url":null,"abstract":"<p><p>Two bacterial strains, Y60-23^T and HN-65^T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23^T exhibited 96.0% similarity to its most related type strain <i>Hyphobacterium vulgare</i> KCTC 52487^T, while strain HN-65^T exhibited 97.3% similarity to its most related type strain <i>Hyphobacterium indicum</i> 2ED5^T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23^T and HN-65^T belonged to the genus <i>Hyphobacterium</i>. Cells of strains Y60-23^T and HN-65^T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23^T were C_18 : 1 <i> ω</i>7<i>c</i> and C_17 : 0, while those of strain HN-65^T were iso-C_17 : 1 <i> ω</i>9<i>c</i>, iso-C_17 : 0 and C_18 : 1 <i> ω</i>7<i>c</i>. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23^T and HN-65^T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus <i>Hyphobacterium</i>, for which the names <i>Hyphobacterium marinum</i> sp. nov. and <i>Hyphobacterium lacteum</i> sp. nov. were proposed with the type strains Y60-23^T (=MCCC 1H01433^T=KCTC 8172^T) and HN-65^T (=MCCC 1H01434^T=KCTC 8169^T), respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 <i>Lactobacillus amylovorus</i> subsp. <i>animalis</i> subsp. nov. and an emended description of <i>Lactobacillus amylovorus</i>.","authors":"Kenji Yamane, Yasuhiro Tanizawa, Hisami Kobayashi, Tomomi Kamizono, Yoichiro Kojima, Hiroki Takagi, Masanori Tohno","doi":"10.1099/ijsem.0.006517","DOIUrl":"10.1099/ijsem.0.006517","url":null,"abstract":"<p><p>Seven novel lactic acid bacterial strains (BF125^T, BF186, TKL145, YK3, YK6, YK10 and NSK) were isolated from the fresh faeces of Japanese black beef cattle and weanling piglets, spent mushroom substrates, or steeping water of a corn starch production plant. These strains are rod-shaped, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, cytochrome oxidase-negative, facultatively anaerobic, and homofermentative. Strain BF125^T did not produce any gas from glucose; both d- and l-lactate were produced as end-products of glucose (D/L, 40 : 60). Growth occurred at 30-45 °C (optimum, 37 °C), pH 5.0-8.0 (optimum, pH 6.0), and with NaCl concentration of 1.0-3.0% (w/v). The G+C content of genomic DNA of strain BF125^T was 37.8 mol% (whole-genome analysis). The major fatty acids were C_16 : 0, C_18 : 1 ω9<i>c</i>, C₁₉ cyclopropane 9, 10<i>,</i> and summed feature 10. The 16S rRNA gene in strain BF125^T showed high similarity to that of the type strain of <i>Lactobacillus amylovorus</i> (99.93%), and the other isolates were also identified as <i>L. amylovorus</i> based on these similarities. A phylogenetic tree based on the core genomes of <i>L. amylovorus</i> strains (<i>n</i>=54), including the seven isolates, showed that they could be divided into two clusters. Strains YK3, YK6, YK10, and NSK were in the first cluster, along with the type strain DSM 20531^T, while the second cluster included isolates BF125^T, BF186, TKL145, and other strains isolated from various animal origins. Phenotypic differences in fermentability were observed for lactose, salicin, and gentiobiose between these two groups. The intergroup digital DNA-DNA hybridization values (72.9-78.6%) and intergroup average nucleotide identity values (95.64-96.92%) were comparable to values calculated using datasets of other valid subspecies of the genus (ex-) <i>Lactobacillus</i>. In light of the physiological, genotypic, and phylogenetic evidence, we propose a novel subspecies of <i>L. amylovorus</i>, named <i>Lactobacillus amylovorus</i> subsp. <i>animalis</i> subsp. nov. (type strain BF125^T=MAFF 212522^T=DSM 115528^T). Our findings also led to the automatic creation of <i>Lactobacillus amylovorus</i> subsp. <i>amylovorus</i> subsp. nov. and an emended description of the species <i>L. amylovorus</i>.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reclassification of <i>Halomicroarcula saliterrae</i> Straková <i>et al</i>. 2024 and <i>Halomicroarcula onubensis</i> Straková <i>et al</i>. 2024 into the genus <i>Haloarcula</i>, as <i>Haloarcula saliterrae</i> comb. nov. and <i>Haloarcula onubensis</i> comb. nov., respectively.","authors":"Dáša Straková, Cristina Sánchez-Porro, Rafael R de la Haba, Antonio Ventosa","doi":"10.1099/ijsem.0.006510","DOIUrl":"https://doi.org/10.1099/ijsem.0.006510","url":null,"abstract":"<p><p>The haloarchaeal genera <i>Halomicroarcula</i> and <i>Haloarcula</i>, belonging to the family <i>Haloarculaceae</i>, order <i>Halobacteriales</i>, class <i>Halobacteria</i>, within the phylum <i>Methanobacteriota</i>, have previously exhibited significant phylogenetic and taxonomic overlaps. This issue was recently resolved by merging the two genera into a single genus, <i>Haloarcula</i>. However, <i>Halomicroarcula saliterrae</i> and <i>Halomicroarcula onubensis</i> were described almost simultaneously with the proposal to unify the genera <i>Haloarcula</i> and <i>Halomicroarcula</i>. Their names were validly published under the International Code of Nomenclature of Prokaryotes (ICNP) according to Validation List no. 217, alongside six <i>Haloarcula</i> species and the transfer of the existing <i>Halomicroarcula</i> species into the genus <i>Haloarcula</i>. Therefore a phylogenetic, phylogenomic, and comparative genomic analysis was carried out to clarify the taxonomic status of these two haloarchaeal species, <i>Halomicroarcula saliterrae</i> and <i>Halomicroarcula onubensis</i>, with lower priority than the six new species of the genus <i>Haloarcula</i>. Phylogenetic studies of 16S rRNA and <i>rpoB'</i> gene sequences, along with phylogenomic reconstructions using single-copy core-orthologous proteins, indicated that the two species clustered with the members of the genus <i>Haloarcula</i>. The overall genome relatedness indexes (OGRIs), comparative analyses of phenotypic features, and polar lipid profiles further supported their taxonomic reassignment as two separate species within the genus <i>Haloarcula</i>. Consequently, we propose the reclassification of <i>Halomicroarcula saliterrae</i> Straková <i>et al</i>. 2024 and <i>Halomicroarcula onubensis</i> Straková <i>et al</i>. 2024 into the genus <i>Haloarcula</i>, as <i>Haloarcula saliterrae</i> comb. nov. and <i>Haloarcula onubensis</i> comb. nov., respectively, in accordance with the ICNP.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonogenomic analysis of the <i>Xanthomonas translucens</i> complex leads to the descriptions of <i>Xanthomonas cerealis</i> sp. nov. and <i>Xanthomonas graminis</i> sp. nov.","authors":"James T Tambong, Renlin Xu, Maria Constanza Fleitas, Randy Kutcher","doi":"10.1099/ijsem.0.006523","DOIUrl":"https://doi.org/10.1099/ijsem.0.006523","url":null,"abstract":"<p><p>The pathovar-based taxonomy of the <i>Xanthomonas translucens</i> group is very confusing due to an overlap of plant host ranges and level of host specificity. Here, whole-genome sequence-based parameters (digital DNA-DNA hybridization and blast-based average nucleotide identity), phylogenomic, biochemical and phenotypical data were used to taxonomically analyse the 11 known pathovars of the <i>X. translucens</i> complex. This polyphasic approach taxonomically assigned the 11 pathovars of <i>X. translucens</i> complex into three distinct species, two of which are new: <i>X. translucens</i>, <i>X. cerealis</i> sp. nov. and <i>X. graminis</i> sp. nov. <i>X. translucens</i> consists of three pathovars: pv. <i>translucens</i> (=pv. <i>hordei</i>), pv. <i>pistaciae</i> strain A ICMP 16316^PT and pv. <i>undulosa</i> (=pv. <i>secalis</i>). <i>X. cerealis</i> sp. nov. encompasses the pv. <i>cerealis</i> strain LMG 679^PT and pv. <i>pistaciae</i> strain B ICMP 16317^PT with genome similarity of 92.7% (dDDH) and 99.0% (ANIb) suggesting taxonomically similar genotypes. The other new species, <i>X. graminis</i> sp. nov., consists of the remaining five designated pathovars (pv. <i>graminis</i>, pv. <i>arrhenatheri,</i> pv. <i>poae</i>, pv. <i>phleipratensis</i> and pv. <i>phlei</i>) with highly variable dDDH and ANIb values ranging from 74.5 to 93.0% and from 96.7 to 99.2%, respectively, an indication of a very divergent taxonomic group. Only strains of pvs. <i>phlei</i> and <i>phleipratensis</i> showed the highest genomic similarities of 93.0% (dDDH) and 99.2% (ANIb), suggesting synonymic pathovars as both infect the same plant hosts. The dDDH and ANI data were corroborated by phylogenomics clustering. The fatty acid contents were similar but the type strain of <i>X. graminis</i> sp. nov. exhibited 20% less C_15 : 0 iso and 40% more C_17 : 0 iso fatty acids than the other species. Based on phenotypic, biochemical and whole-genome sequence data, we propose two new species, <i>Xanthomonas cerealis</i> sp. nov. and <i>Xanthomonas graminis</i> sp. nov. with type strains LMG 679^T (=NCPPB 1944^T) and LMG 726^T (=NCPPB 2700^T), respectively.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Nitrosotalea devaniterrae</i> gen. nov., sp. nov. and <i>Nitrosotalea sinensis</i> sp. nov., two acidophilic ammonia oxidising archaea isolated from acidic soil, and proposal of the new order <i>Nitrosotaleales</i> ord. nov. within the class <i>Nitrososphaeria</i> of the phylum <i>Nitrososphaerota</i>.","authors":"Laura E Lehtovirta-Morley, Chaorong Ge, Jenna Ross, Huaiying Yao, Christina Hazard, Cécile Gubry-Rangin, James I Prosser, Graeme W Nicol","doi":"10.1099/ijsem.0.006387","DOIUrl":"https://doi.org/10.1099/ijsem.0.006387","url":null,"abstract":"<p><p>Two obligately acidophilic, mesophilic and aerobic soil ammonia-oxidising archaea were isolated from a pH 4.5 arable sandy loam (UK) and pH 4.7 acidic sulphate paddy soil (PR China) and designated strains Nd1^T and Nd2^T, respectively. The strains shared more than 99 % 16S rRNA gene sequence identity and their genomes were both less than 2 Mb in length, sharing 79 % average nucleotide identity, 81 % average amino acid identity and a DNA G+C content of approximately 37 mol%. Both strains were chemolithotrophs that fixed carbon dioxide and gained energy by oxidising ammonia to nitrite, with no evidence of mixotrophic growth. Neither strain was capable of using urea as a source of ammonia. Both strains were non-motile in culture, although Nd1^T does possess genes encoding flagella components and therefore may be motile under certain conditions. Cells of Nd1^T were small angular rods 0.5-1 µm in length and grew at pH 4.2-5.6 and at 20-30 °C. Cells of Nd1^T were small angular rods 0.5-1 µm in length and grew at pH 4.0-6.1 and at 20-42 °C. Nd1^T and Nd2^T are distinct with respect to genomic and physiological features and are assigned as the type strains for the species <i>Nitrosotalea devaniterrae</i> sp. nov. (type strain, Nd1^T=NCIMB 15248^T=DSM 110862^T) and <i>Nitrosotalea sinensis</i> sp. nov. (type strain, Nd2^T=NCIMB 15249^T=DSM 110863^T), respectively, within the genus <i>Nitrosotalea</i> gen. nov. The family <i>Nitrosotaleaceae</i> fam. nov. and order <i>Nitrosotaleales</i> ord. nov. are also proposed officially.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142346741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic and molecular marker based studies to clarify the evolutionary relationships amongst <i>Anoxybacillus</i> species and demarcation of the family <i>Anoxybacillaceae</i> and some of its constituent genera.","authors":"Isha Patel, Sarah Bello, Radhey S Gupta","doi":"10.1099/ijsem.0.006528","DOIUrl":"10.1099/ijsem.0.006528","url":null,"abstract":"<p><p>The family <i>Anoxybacillaceae</i> was recently proposed encompassing the genera <i>Anoxybacillus</i>, <i>Geobacillus</i>, <i>Parageobacillus</i>, <i>Saccharococcus</i> and <i>Thermolongibacillus</i>. Of these genera, <i>Anoxybacillus</i> contains >50% of the <i>Anoxybacillaceae</i> species. However, <i>Anoxybacillus</i> species form multiple unrelated clades in phylogenetic trees and their evolutionary relationships are unclear. To clarify the evolutionary relationships of <i>Anoxybacillus</i> and other <i>Anoxybacillaceae</i> species, detailed phylogenomic and comparative analyses were conducted on 38 <i>Anoxybacillaceae</i> species with available genomes. In a phylogenomic tree based on 1148 core proteins, all <i>Anoxybacillus</i>, <i>Geobacillus</i>, <i>Parageobacillus</i>, <i>Saccharococcus</i> and <i>Thermolongibacillus</i> species, excepting <i>Anoxybacillus sediminis</i>, formed a strongly supported clade representing the family <i>Anoxybacillaceae</i>. Five conserved signature indels (CSIs) reported here are also uniquely found in these species, providing robust means for the demarcation of family <i>Anoxybacillaceae</i> in molecular terms. In our phylogenomic tree and in the Genomic Taxonomy Database, <i>Anoxybacillus</i> species formed four distinct clades designated as <i>Anoxybacillus sensu stricto</i> (containing the type species <i>A. pushchinoensis</i>), <i>Anoxybacillus</i>_A, <i>Anoxybacillus</i>_B and <i>Anoxybacillus</i>_C. Our analyses have identified 17 novel CSIs which offer means to reliably distinguish species from these clades based upon multiple uniquely shared molecular characteristics. Additionally, we have identified three and seven CSIs specific for the genera <i>Geobacillus</i> and <i>Brevibacillus</i>, respectively. All seven <i>Brevibacillus</i>-specific CSIs are also shared by <i>Anoxybacillus sediminis</i>, which branches reliably with this genus. Based on the strong phylogenetic and molecular evidence presented here, we are proposing that the genus <i>Anoxybacillus</i> should be restricted to only the species from <i>Anoxybacillus sensu stricto</i> clade, whereas the species from <i>Anoxybacillus</i>_A, <i>Anoxybacillus</i>_B, and <i>Anoxybacillus</i>_C clades should be transferred into three novel genera <i>Anoxybacteroides</i> gen. nov., <i>Paranoxybacillus</i> gen. nov. and <i>Thermaerobacillus</i> gen. nov., respectively. Additionally, we are also proposing the transfer of <i>Anoxybacillus sediminis</i> to the genus <i>Brevibacillus</i>. The proposed changes, which reliably depict the evolutionary relationships among <i>Anoxybacillaceae</i> species, should be helpful in the studies of these organisms.</p>","PeriodicalId":14390,"journal":{"name":"International journal of systematic and evolutionary microbiology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11407518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142287295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}