首页 > 最新文献

Systematic and applied microbiology最新文献

英文 中文
Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode 马略卡岛两个热异常含水层的元基因组学,以及根据 SeqCode 规则命名的新的未栽培类群的建议
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-04-09 DOI: 10.1016/j.syapm.2024.126506
Juan F. Gago , Tomeu Viver , Mercedes Urdiain , Elaine Ferreira , Pedro Robledo , Ramon Rossello-Mora

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

地下水融合了独特的物理和化学条件,对微生物生命构成了挑战。马略卡岛是巴利阿里群岛中最大的岛屿,岛上有多种热异常现象(即地表含水层温度超过地区平均温度的地热表现)。该岛中部和南部两个含水层的元基因组显示,利用提取的 16S rRNA 基因序列,假单胞菌是最具代表性的门类。不过,含水层内部和含水层之间的微生物结构具有显著的多样性,但元基因组组装基因组(MAGs)显示,其代谢特征相似,尤其是在 Llucmajor 含水层中,需氧化学自养和异养代谢普遍存在。此外,还发现了一些厌氧生活方式的证据,这表明这些环境可能会出现缺氧现象,或者厌氧菌是从更深的水域迁移过来的。我们认为,当地环境因素(温度、外部输入或化学)似乎比含水层内微生物细胞的连接和最终迁移更能决定高度分化的结构。值得注意的是,大部分重建的基因组属于未被描述的细菌系,其中两个高质量的 MAGs 可根据序列数据描述的原核生物命名规则(SeqCode)被归类为新类群。因此,我们提出了新种和属 Costitxia debesea gen.
{"title":"Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode","authors":"Juan F. Gago ,&nbsp;Tomeu Viver ,&nbsp;Mercedes Urdiain ,&nbsp;Elaine Ferreira ,&nbsp;Pedro Robledo ,&nbsp;Ramon Rossello-Mora","doi":"10.1016/j.syapm.2024.126506","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126506","url":null,"abstract":"<div><p>Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed <em>Pseudomonadota</em> to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus <em>Costitxia debesea</em> gen. nov., sp. nov., affiliated with the novel family <em>Costitxiaceae</em> fam. nov<em>.</em>, order <em>Costitxiales</em> ord. nov. and class <em>Costitxiia</em> class. nov.; and the new new species and genus <em>Lloretia debesea</em> gen. nov. sp. nov. affiliated with the novel family <em>Lloretiaceae</em> fam. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126506"},"PeriodicalIF":3.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000201/pdfft?md5=1a25fb9ae3fca24ad4164b29088d3762&pid=1-s2.0-S0723202024000201-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140606939","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
SeqCode facilitates naming of South African rhizobia left in limbo SeqCode 为南非根瘤菌的命名提供便利
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-03-25 DOI: 10.1016/j.syapm.2024.126504
Melandré van Lill , Stephanus N. Venter , Esther K. Muema , Marike Palmer , Wai Y. Chan , Chrizelle W. Beukes , Emma T. Steenkamp

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa’s current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.

南非因其豆科植物及其固氮细菌共生体的多样性而闻名于世。然而,与它们的植物伙伴相比,南非的这些微生物(统称为根瘤菌)却鲜有特征描述和正式描述。这是因为《国际原核生物命名法》(ICNP)的规则与南非的《国家环境管理:生物多样性法》及其相关法规相抵触。国际原核生物命名法》规定,一个新细菌物种的拟议模式菌株的培养物必须存放在两个国际培养物保藏中心,并应要求不受限制地提供,而南非目前的国家法规不可能做到这一点。在这里,我们描述了从一种分布于南部非洲不同生物群落的标志性树豆科植物--Vachellia karroo 的根瘤中获得的七个新的中生孢子菌物种。为此,我们利用系谱一致法将 18 个根瘤菌分离物划分为推定物种,然后利用表型特征和平均基因组亲缘关系探讨了它们的可信性。在命名这些新物种时,我们采用了最近出版的《根据序列数据描述的原核生物命名法则》(SeqCode)的规则,该法则利用基因组序列作为命名类型。因此,本研究中介绍的工作提供了一个示例,说明 SeqCode 是如何为栽培生物提供标准化命名方法的,而目前在国际栽培菌种库中存放模式菌株是个问题。
{"title":"SeqCode facilitates naming of South African rhizobia left in limbo","authors":"Melandré van Lill ,&nbsp;Stephanus N. Venter ,&nbsp;Esther K. Muema ,&nbsp;Marike Palmer ,&nbsp;Wai Y. Chan ,&nbsp;Chrizelle W. Beukes ,&nbsp;Emma T. Steenkamp","doi":"10.1016/j.syapm.2024.126504","DOIUrl":"10.1016/j.syapm.2024.126504","url":null,"abstract":"<div><p>South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa’s current national regulations. Here, we describe seven new <em>Mesorhizobium</em> species obtained from root nodules of <em>Vachellia karroo</em>, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126504"},"PeriodicalIF":3.4,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000183/pdfft?md5=885b47be2491e2918543c1a10b18b6fa&pid=1-s2.0-S0723202024000183-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140403534","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
A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees 来自熊蜂的 Fructobacillus evanidus sp.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-03-22 DOI: 10.1016/j.syapm.2024.126505
Juliana Botero , Charlotte Peeters , Evelien De Canck , David Laureys , Anneleen D. Wieme , Ilse Cleenwerck , Eliza Depoorter , Jessy Praet , Denis Michez , Guy Smagghe , Peter Vandamme

The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of Fructobacillus in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with Fructobacillus bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 Fructobacillus isolates from bumble bees demonstrated that they represented four species, i.e. Fructobacillus cardui, Fructobacillus fructosus, Fructobacillus tropaeoli, and the novel species Fructobacillus evanidus sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct Fructobacillus species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with F. evanidus and F. tropaeoli genomes featuring a higher number of complete metabolic pathways. While Fructobacillus genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple Fructobacillus species from several bumble bee gut samples in the present study also argued against a specific partnership between Fructobacillus species and their bumble bee hosts.

对蜜蜂微生物组研究的增加是由于对全球授粉者减少的担忧。大黄蜂寄生的核心和非核心微生物群可能有助于提高其一生的适应能力。大黄蜂工蜂肠道微生物组中果酸杆菌的存在,或果酸杆菌对核心共生菌的替代,一直被认为是菌群失调的标志。对从大黄蜂中分离出的 21 个果酸杆菌基因组进行的系统发生组分析和功能基因组鉴定表明,它们代表了 4 个物种,即卡氏果酸杆菌(Fructobacillus cardui)、果寡糖果酸杆菌(Fructobacillus fructosus)、滋养果酸杆菌(Fructobacillus tropaeoli)和新物种埃瓦尼德果酸杆菌(Fructobacillus evanidus sp.nov)。我们的研究结果证实了两个在系统发育和功能上截然不同的果酸杆菌物种支系的存在,它们在基因组大小、G + C 含量百分比、编码 DNA 序列数量和代谢特征上都有所不同。支系 1 和支系 2 的物种在氨基酸代谢方面存在差异,在碳水化合物代谢方面差异较小,其中 F. evanidus 和 F. tropaeoli 的基因组具有较多的完整代谢途径。虽然果杆菌基因组编码的基因可以实现粘附、生物膜形成、抗菌活性和解毒,但从大黄蜂肠道中分离出的其他细菌似乎更适合与大黄蜂宿主共存。本研究从几种大黄蜂肠道样本中分离并鉴定出多种果酸杆菌,这也证明果酸杆菌与大黄蜂宿主之间并不存在特定的伙伴关系。
{"title":"A comparative genomic analysis of Fructobacillus evanidus sp. nov. from bumble bees","authors":"Juliana Botero ,&nbsp;Charlotte Peeters ,&nbsp;Evelien De Canck ,&nbsp;David Laureys ,&nbsp;Anneleen D. Wieme ,&nbsp;Ilse Cleenwerck ,&nbsp;Eliza Depoorter ,&nbsp;Jessy Praet ,&nbsp;Denis Michez ,&nbsp;Guy Smagghe ,&nbsp;Peter Vandamme","doi":"10.1016/j.syapm.2024.126505","DOIUrl":"10.1016/j.syapm.2024.126505","url":null,"abstract":"<div><p>The increase in studies on bee microbiomes is prompted by concerns over global pollinator declines. Bumble bees host core and non-core microbiota which may contribute to increased lifetime fitness. The presence of <em>Fructobacillus</em> in the gut microbiomes of bumble bee workers, or the replacement of core symbionts with <em>Fructobacillus</em> bacteria, has been considered a marker of dysbiosis. A phylogenomic analysis and functional genomic characterization of the genomes of 21 <em>Fructobacillus</em> isolates from bumble bees demonstrated that they represented four species, i.e. <em>Fructobacillus cardui</em>, <em>Fructobacillus fructosus, Fructobacillus tropaeoli</em>, and the novel species <em>Fructobacillus evanidus</em> sp. nov. Our results confirmed and substantiated the presence of two phylogenetically and functionally distinct <em>Fructobacillus</em> species clades that differ in genome size, percentage G + C content, the number of coding DNA sequences and metabolic characteristics. Clade 1 and clade 2 species differed in amino acid and, to a lesser extent, in carbohydrate metabolism, with <em>F. evanidus</em> and <em>F. tropaeoli</em> genomes featuring a higher number of complete metabolic pathways. While <em>Fructobacillus</em> genomes encoded genes that allow adhesion, biofilm formation, antibacterial activity and detoxification, other bacteria isolated from the bumble bee gut appeared better equipped to co-exist with the bumble bee host. The isolation and identification of multiple <em>Fructobacillus</em> species from several bumble bee gut samples in the present study also argued against a specific partnership between <em>Fructobacillus</em> species and their bumble bee hosts.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126505"},"PeriodicalIF":3.4,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140279708","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
Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil 来自污染土壤的壳斗科四个新成员 Paraflavitalea pollutisoli sp.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-03-12 DOI: 10.1016/j.syapm.2024.126503
Ze-Shen Liu , Xiao-Kang Wang , Ke-Huan Wang , Mei-Ling Yang , De-Feng Li , Shuang-Jiang Liu

A taxonomic investigation was conducted on four bacterial strains isolated from soil contaminated with polycyclic aromatic hydrocarbons and heavy metals. Phylogenetic analysis revealed that these strains belonged to the family Chitinophagaceae. Examination of the 16S rRNA genes indicated that their sequence identities were below 97.6 % compared to any known and validly nominated bacterial species. The genomes of the four strains ranged from 4.12 to 8.76 Mb, with overall G + C molar contents varying from 41.28 % to 50.39 %. Predominant cellular fatty acids included iso-C15:0, iso-C15:1 G, and iso-C17:0 3-OH. The average nucleotide identity ranged from 66.90 % to 74.63 %, and digital DNA-DNA hybridization was 12.5–12.8 %. Based on the genomic and phenotypic features of the new strains, four novel species and two new genera were proposed within the family Chitinophagaceae. The ecological distributions were investigated by data-mining of NCBI databases, and results showed that additional strains or species of the newly proposed taxa were widely distributed in various environments, including polluted soil and waters. Functional analysis demonstrated that strains H1-2-19XT, JS81T, and JY13-12T exhibited resistance to arsenite (III) and chromate (VI). The proposed names for the four novel species are Paraflavitalea pollutisoli (type strain H1-2-19XT = JCM 36460T = CGMCC 1.61321T), Terrimonas pollutisoli (type strain H1YJ31T = JCM 36215T = CGMCC 1.61343T), Pollutibacter soli (type strain JS81T = JCM 36462T = CGMCC 1.61338T), and Polluticoccus soli (type strain JY13-12T = JCM 36463T = CGMCC 1.61341T).

对从受多环芳烃和重金属污染的土壤中分离出的四种细菌菌株进行了分类研究。系统进化分析表明,这些菌株属于......科。对 16S rRNA 基因的研究表明,与任何已知和有效命名的细菌物种相比,它们的序列相同度低于 97.6%。四株菌株的基因组大小从 4.12 到 8.76 Mb 不等,总的 G + C 摩尔含量从 41.28 % 到 50.39 % 不等。主要的细胞脂肪酸包括-C、-C G和-C 3-OH。平均核苷酸同一性从 66.90 % 到 74.63 % 不等,数字 DNA-DNA 杂交率为 12.5-12.8%。根据新菌株的基因组和表型特征,提出了甲壳素噬菌科中的 4 个新种和 2 个新属。通过对 NCBI 数据库进行数据挖掘,对其生态分布进行了研究,结果表明新提出的类群中的新菌株或新菌种广泛分布于各种环境中,包括受污染的土壤和水域。功能分析表明,菌株 H1-2-19X、JS81 和 JY13-12 对亚砷酸盐(III)和铬酸盐(VI)具有抗性。这四个新物种的拟命名为:(模式菌株 H1-2-19X = JCM 36460 = CGMCC 1.61321)、(模式菌株 H1YJ31 = JCM 36215 = CGMCC 1.61343)、(模式菌株 JS81 = JCM 36462 = CGMCC 1.61338)和(模式菌株 JY13-12 = JCM 36463 = CGMCC 1.61341)。
{"title":"Paraflavitalea pollutisoli sp. nov., Pollutibacter soli gen. nov. sp. nov., Polluticoccus soli gen. nov. sp. nov., and Terrimonas pollutisoli sp. nov., four new members of the family Chitinophagaceae from polluted soil","authors":"Ze-Shen Liu ,&nbsp;Xiao-Kang Wang ,&nbsp;Ke-Huan Wang ,&nbsp;Mei-Ling Yang ,&nbsp;De-Feng Li ,&nbsp;Shuang-Jiang Liu","doi":"10.1016/j.syapm.2024.126503","DOIUrl":"10.1016/j.syapm.2024.126503","url":null,"abstract":"<div><p>A taxonomic investigation was conducted on four bacterial strains isolated from soil contaminated with polycyclic aromatic hydrocarbons and heavy metals. Phylogenetic analysis revealed that these strains belonged to the family <em>Chitinophagaceae</em>. Examination of the 16S rRNA genes indicated that their sequence identities were below 97.6 % compared to any known and validly nominated bacterial species. The genomes of the four strains ranged from 4.12 to 8.76 Mb, with overall G + C molar contents varying from 41.28 % to 50.39 %. Predominant cellular fatty acids included <em>iso</em>-C<sub>15:0</sub>, <em>iso</em>-C<sub>15:1</sub> G, and <em>iso</em>-C<sub>17:0</sub> 3-OH. The average nucleotide identity ranged from 66.90 % to 74.63 %, and digital DNA-DNA hybridization was 12.5–12.8 %. Based on the genomic and phenotypic features of the new strains, four novel species and two new genera were proposed within the family Chitinophagaceae. The ecological distributions were investigated by data-mining of NCBI databases, and results showed that additional strains or species of the newly proposed taxa were widely distributed in various environments, including polluted soil and waters. Functional analysis demonstrated that strains H1-2-19X<sup>T</sup>, JS81<sup>T</sup>, and JY13-12<sup>T</sup> exhibited resistance to arsenite (III) and chromate (VI). The proposed names for the four novel species are <em>Paraflavitalea pollutisoli</em> (type strain H1-2-19X<sup>T</sup> = JCM 36460<sup>T</sup> = CGMCC 1.61321<sup>T</sup>), <em>Terrimonas pollutisoli</em> (type strain H1YJ31<sup>T</sup> = JCM 36215<sup>T</sup> = CGMCC 1.61343<sup>T</sup>), <em>Pollutibacter soli</em> (type strain JS81<sup>T</sup> = JCM 36462<sup>T</sup> = CGMCC 1.61338<sup>T</sup>), and <em>Polluticoccus soli</em> (type strain JY13-12<sup>T</sup> = JCM 36463<sup>T</sup> = CGMCC 1.61341<sup>T</sup>).</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126503"},"PeriodicalIF":3.4,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127464","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
Stomatohabitans albus gen. nov., sp. nov., an oral living facultative anaerobic actinobacteria isolated form Steller sea lion, and proposal of Stomatohabitantaceae fam. nov. and Stomatohabitantales ord. nov 分离自斯特勒海狮的口腔生活兼性厌氧放线菌 Stomatohabitans albus gen.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-03-07 DOI: 10.1016/j.syapm.2024.126501
Zi-Wen Yang , Wen-Li Liu , Peng Zhang , Dan-Yuan Guo , Hong-Chuan Wang , Jia-Ling Li , Pan-Deng Wang , Gui-Xin Dong , Guo-Xing Nie , Wen-Jun Li

Two novel actinobacteria, designated as SYSU M7M538T and SYSU M7M531, were isolated from oral of Eumetopias jubatus in Zhuhai Chimelong Ocean Kingdom, China. The cells of these microorganisms stained Gram-positive and were rod shaped. These strains were facultative anaerobic, and catalase-positive. Optimal growth occurred at 37 °C and pH 7.0 over 7 days of cultivation. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol and phosphocholine as the major polar lipids. The main menaquinone was MK-9(H4). The major fatty acids were C16:0, C17:1 w8c, C17:0, C18:1 w9c and C18:0. Analyses of genome sequences revealed that the genome size of SYSU M7M538T was 2.1 Mbp with G + C content of 52.5 %, while the genome size of SYSU M7M531 was 2.3 Mbp with G + C content of 52.7 %. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains and other recognized Nitriliruptoria species were less than 64.9 % and 89.0 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains SYSU M7M538T and SYSU M7M531 formed a well-separated phylogenetic branch distinct from other orders of Nitriliruptoria. Based on the data presented here, these two strains are considered to represent a novel species of a novel genus, for which the name Stomatohabitans albus gen. nov., sp. nov., with the type strain SYSU M7M538T (=KCTC 59113T = GDMCC 1.4286T), are proposed. We also propose that these organisms represent a novel family named Stomatohabitantaceae fam. nov. of a novel order Stomatohabitantales ord. nov.

从中国珠海长隆海洋王国的大鳞蜥口腔中分离出两种新型放线菌,分别命名为 SYSU M7M538T 和 SYSU M7M531。这些微生物的细胞呈革兰氏阳性,呈杆状。这些菌株为兼性厌氧菌,过氧化氢酶阳性。在 37 °C、pH 值为 7.0 的条件下培养 7 天,可达到最佳生长状态。两种菌株的主要极性脂质为二磷脂酰甘油、磷脂酰甘油和磷脂酰胆碱。主要的甲萘醌是 MK-9(H4)。主要脂肪酸为 C16:0、C17:1 w8c、C17:0、C18:1 w9c 和 C18:0。基因组序列分析表明,SYSU M7M538T 的基因组大小为 2.1 Mbp,G + C 含量为 52.5 %,而 SYSU M7M531 的基因组大小为 2.3 Mbp,G + C 含量为 52.7 %。ANI 和 16S rRNA 基因分析结果表明,两株菌株与其他已知 Nitriliruptoria 物种的配对相似度分别小于 64.9 % 和 89.0 %。16S rRNA基因序列的系统进化分析表明,SYSU M7M538T和SYSU M7M531菌株形成了一个与其他Nitriliruptoria目截然不同的系统进化分支。根据本文提供的数据,我们认为这两株菌株代表了一个新属的新种,并将其命名为 Stomatohabitans albus gen.我们还提出这些生物代表一个新科,命名为 Stomatohabitantaceae fam.
{"title":"Stomatohabitans albus gen. nov., sp. nov., an oral living facultative anaerobic actinobacteria isolated form Steller sea lion, and proposal of Stomatohabitantaceae fam. nov. and Stomatohabitantales ord. nov","authors":"Zi-Wen Yang ,&nbsp;Wen-Li Liu ,&nbsp;Peng Zhang ,&nbsp;Dan-Yuan Guo ,&nbsp;Hong-Chuan Wang ,&nbsp;Jia-Ling Li ,&nbsp;Pan-Deng Wang ,&nbsp;Gui-Xin Dong ,&nbsp;Guo-Xing Nie ,&nbsp;Wen-Jun Li","doi":"10.1016/j.syapm.2024.126501","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126501","url":null,"abstract":"<div><p>Two novel actinobacteria, designated as SYSU M7M538<sup>T</sup> and SYSU M7M531, were isolated from oral of <em>Eumetopias jubatus</em> in Zhuhai Chimelong Ocean Kingdom, China. The cells of these microorganisms stained Gram-positive and were rod shaped. These strains were facultative anaerobic, and catalase-positive. Optimal growth occurred at 37 °C and pH 7.0 over 7 days of cultivation. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol and phosphocholine as the major polar lipids. The main menaquinone was MK-9(H<sub>4</sub>). The major fatty acids were C<sub>16:0</sub>, C<sub>17:1</sub> <em><sub>w</sub></em><sub>8</sub><em><sub>c</sub></em>, C<sub>17:0</sub>, C<sub>18:1</sub> <em><sub>w</sub></em><sub>9</sub><em><sub>c</sub></em> and C<sub>18:0</sub>. Analyses of genome sequences revealed that the genome size of SYSU M7M538<sup>T</sup> was 2.1 Mbp with G + C content of 52.5 %, while the genome size of SYSU M7M531 was 2.3 Mbp with G + C content of 52.7 %. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains and other recognized <em>Nitriliruptoria</em> species were less than 64.9 % and 89.0 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains SYSU M7M538<sup>T</sup> and SYSU M7M531 formed a well-separated phylogenetic branch distinct from other orders of <em>Nitriliruptoria</em>. Based on the data presented here, these two strains are considered to represent a novel species of a novel genus, for which the name <em>Stomatohabitans albus</em> gen. nov., sp. nov., with the type strain SYSU M7M538<sup>T</sup> (=KCTC 59113<sup>T</sup> = GDMCC 1.4286<sup>T</sup>), are proposed. We also propose that these organisms represent a novel family named <em>Stomatohabitantaceae</em> fam. nov. of a novel order <em>Stomatohabitantales</em> ord. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126501"},"PeriodicalIF":3.4,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140066881","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
Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds 元基因组组装基因组的系统进化分析表明 Spirochaetales 目中的新类群以及 Thalassospirochaeta sargassi gen.Nov.来自海藻
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-03-02 DOI: 10.1016/j.syapm.2024.126502
Kohli Pragya , Pannikurungottu Sreya , Lakshmanan Vighnesh , Dhurka Mahima , Mallick Sushmita , Chintalapati Sasikala , Chintalapati Venkata Ramana

Six metagenome-assembled genomes (JB008Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order Spirochaetales were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2–93.4 %, respectively with uncultivated Spirochaetaceae family members, and < 90 % identity with Marispirochaeta aestuari JC444T. While, the bin JB015 showed 99.1 % identity with Pleomorphochaeta naphthae SEBR 4209T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008Ts confirmed that these members belong to the family Spirochaetaceae and bins JB015, JB002, JB003, and JB004 belong to the genus Pleomorphochaeta within the family Sphaerochaetaceae. The AAI values of the binned genomes JB007 and JB008Ts compared to other members of the Spirochaetaceae family were between 53.9- 56.8 % and 53.8–57.1 %, respectively. Furthermore, the comparison of ANI, dDDH, and POCP metrics of the binned genomes JB007 and JB008Ts, both among themselves and with the members of Spirochaetaceae, was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name Thalassospirochaeta sargassi gen. nov. sp. nov., in the family Spirochaetaceae while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other Pleomorphochaeta members.

从印度马纳尔湾采集的海藻样本中生成了属于该目六种元基因组(JB008、JB007、JB015、JB003、JB004 和 JB002)。JB008 和 JB007 的 16S rRNA 基因与未培养的家族成员具有最高的一致性,分别为 94.9 % 和 92.2-93.4 %,与 JC444 的一致性小于 90 %。而 bin JB015 与 SEBR 4209 的同一性为 99.1%。对分选基因组 JB007 和 JB008 的系统发生组和基于 16S rRNA 基因的系统发生分析证实,这些成员属于科,而分选基因组 JB015、JB002、JB003 和 JB004 属于科内的属。与该科其他成员相比,JB007 和 JB008 分类基因组的 AAI 值分别为 53.9 % 至 56.8 % 和 53.8 % 至 57.1 %。此外,分选基因组 JB007 和 JB008 的 ANI、DDH 和 POCP 指标之间以及与其他成员之间的比较也低于建议的属划分阈值。因此,根据根据序列数据描述的原核生物命名准则(SeqCode),建议将分选基因组 JB008 作为科中的一个新属,命名为 gen.JB015类群及其附加基因组形成了一个独特的支系,但由于缺乏其他成员的基因组证据,其分类地位仍不明确。
{"title":"Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds","authors":"Kohli Pragya ,&nbsp;Pannikurungottu Sreya ,&nbsp;Lakshmanan Vighnesh ,&nbsp;Dhurka Mahima ,&nbsp;Mallick Sushmita ,&nbsp;Chintalapati Sasikala ,&nbsp;Chintalapati Venkata Ramana","doi":"10.1016/j.syapm.2024.126502","DOIUrl":"10.1016/j.syapm.2024.126502","url":null,"abstract":"<div><p>Six metagenome-assembled genomes (JB008<sup>Ts</sup>, JB007, JB015, JB003, JB004, and JB002) belonging to the order <em>Spirochaetales</em> were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008<sup>Ts</sup> and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2–93.4 %, respectively with uncultivated <em>Spirochaetaceae</em> family members, and &lt; 90 % identity with <em>Marispirochaeta aestuari</em> JC444<sup>T</sup>. While, the bin JB015 showed 99.1 % identity with <em>Pleomorphochaeta naphthae</em> SEBR 4209<sup>T</sup>. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008<sup>Ts</sup> confirmed that these members belong to the family <em>Spirochaetaceae</em> and bins JB015, JB002, JB003, and JB004 belong to the genus <em>Pleomorphochaeta</em> within the family <em>Sphaerochaetaceae</em>. The AAI values of the binned genomes JB007 and JB008<sup>Ts</sup> compared to other members of the <em>Spirochaetaceae</em> family were between 53.9- 56.8 % and 53.8–57.1 %, respectively. Furthermore, the comparison of ANI, <em>d</em>DDH, and POCP metrics of the binned genomes JB007 and JB008<sup>Ts</sup>, both among themselves and with the members of <em>Spirochaetaceae,</em> was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008<sup>Ts</sup> is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name <em>Thalassospirochaeta sargassi</em> gen. nov. sp. nov., in the family <em>Spirochaetaceae</em> while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other <em>Pleomorphochaeta</em> members.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126502"},"PeriodicalIF":3.4,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140044344","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
Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang Plateau 来自青藏高原盐湖的嗜卤古菌 Halomontanus rarus gen.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-02-24 DOI: 10.1016/j.syapm.2024.126500
Ya-Ling Mao, Bei-Bei Wang, Xue-Meng Yin, Jing Hou, Heng-Lin Cui

Two halophilic archaeal strains TS33T and KZCA124 were isolated from two distant salt lakes on the Qinghai-Xizang Plateau, respectively. Culture-independent analysis indicated that these two strains were original inhabitants but low abundant taxa in respective salt lakes. Strains TS33T and KZCA124 were able to grow at 20–60 °C (optimum were 42 and 35 °C, respectively), with 0.9–4.8 M NaCl (optimum were 3.0 and 2.6 M, respectively), with 0–0.7 M MgCl2 (optimum, 0.3 M) and at pH 5.0–9.5 (optimum were pH 7.5 and pH 7, respectively). The 16S rRNA and rpoB' gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33T, KZCA124, and existing species of the family Natrialbaceae were 90.6–95.5% and 84.4–89.3%, respectively. Phylogenetic and phylogenomic analyses indicated that strains TS33T and KZCA124 formed an independent branch separated from neighboring genera, Saliphagus, Natronosalvus, and Natronobiforma. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between strains TS33T and KZCA124 were 96.4%, 73.1%, and 96.7%, respectively, higher than the thresholds for species demarcation. The overall genome-related indexes between these two strains and existing species of family Natrialbaceae were 73–77%, 21–25%, and 63–70%, respectively, significantly lower than the species boundary thresholds. Strains TS33T and KZCA124 may represent a novel species of a new genus within the family Natrialbaceae judged by the cutoff value of AAI (≤76%) proposed to differentiate genera within the family Natrialbaceae. The major polar lipids of strains TS33T and KZCA124 were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated mannosyl glucosyl diether, and sulfated galactosyl mannosyl glucosyl diether. These two strains could be distinguished from the related genera according to differential phenotypic characteristics. These phenotypic, phylogenetic, and genomic analyses revealed that strains TS33T (=KCTC 4310T = MCCC 4K00132T) and KZCA124 (=CGMCC 1.17432 = JCM 34316) represent a novel species of a new genus of the family Natrialbaceae and were named Halomontanus rarus gen. nov., sp. nov.

研究人员分别从青藏高原两个遥远的盐湖中分离出两株嗜卤古细菌TS33T和KZCA124。独立培养分析表明,这两株菌株是各自盐湖中的原始居民,但含量较低。TS33T 和 KZCA124 菌株能在 20-60 °C(最适温度分别为 42 和 35 °C)、0.9-4.8 M NaCl(最适温度分别为 3.0 和 2.6 M)、0-0.7 M MgCl2(最适温度为 0.3 M)和 pH 5.0-9.5 (最适温度分别为 pH 7.5 和 pH 7)条件下生长。这两株菌株的 16S rRNA 和 rpoB'基因相似度分别为 99.7% 和 99.4%,而 TS33T、KZCA124 菌株与 Natrialbaceae 现有物种的 16S rRNA 和 rpoB'基因相似度分别为 90.6-95.5% 和 84.4-89.3%。系统发育和系统组学分析表明,TS33T 和 KZCA124 菌株与邻近的 Saliphagus 属、Natronosalvus 属和 Natronobiforma 属形成了一个独立的分支。TS33T和KZCA124之间的平均核苷酸同一性(ANI)、数字DNA-DNA杂交(dDDH)和平均氨基酸同一性(AAI)值分别为96.4%、73.1%和96.7%,高于物种划分的阈值。这两个菌株与 Natrialbaceae 家族现有物种之间的总体基因组相关指数分别为 73-77%、21-25% 和 63-70%,明显低于物种界限阈值。根据Natrialbaceae科属区分的AAI临界值(≤76%)判断,TS33T和KZCA124菌株可能代表Natrialbaceae科中一个新属的新种。TS33T 株和 KZCA124 株的主要极性脂质为磷脂酸、磷脂酰甘油、磷脂酰甘油磷酸甲酯、硫酸化甘露糖基二醚和硫酸化半乳糖基甘露糖基二醚。根据不同的表型特征,这两种菌株可与相关属区分开来。这些表型、系统发育和基因组分析表明,TS33T(=KCTC 4310T = MCCC 4K00132T)和 KZCA124(=CGMCC 1.17432 = JCM 34316)菌株代表了 Natrialbaceae 科一个新属的新种,并被命名为 Halomontanus rarus gen.
{"title":"Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang Plateau","authors":"Ya-Ling Mao,&nbsp;Bei-Bei Wang,&nbsp;Xue-Meng Yin,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2024.126500","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126500","url":null,"abstract":"<div><p>Two halophilic archaeal strains TS33<sup>T</sup> and KZCA124 were isolated from two distant salt lakes on the Qinghai-Xizang Plateau, respectively. Culture-independent analysis indicated that these two strains were original inhabitants but low abundant taxa in respective salt lakes. Strains TS33<sup>T</sup> and KZCA124 were able to grow at 20–60 °C (optimum were 42 and 35 °C, respectively), with 0.9–4.8 M NaCl (optimum were 3.0 and 2.6 M, respectively), with 0–0.7 M MgCl<sub>2</sub> (optimum, 0.3 M) and at pH 5.0–9.5 (optimum were pH 7.5 and pH 7, respectively). The 16S rRNA and <em>rpoB'</em> gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33<sup>T</sup>, KZCA124, and existing species of the family <em>Natrialbaceae</em> were 90.6–95.5% and 84.4–89.3%, respectively. Phylogenetic and phylogenomic analyses indicated that strains TS33<sup>T</sup> and KZCA124 formed an independent branch separated from neighboring genera, <em>Saliphagus</em>, <em>Natronosalvus</em>, and <em>Natronobiforma</em>. The average<!--> <!-->nucleotide<!--> <!-->identity (ANI), digital DNA-DNA<!--> <!-->hybridization (dDDH), and average amino acid identity (AAI) values between strains TS33<sup>T</sup> and KZCA124 were 96.4%, 73.1%, and 96.7%, respectively, higher than the thresholds for species demarcation. The overall genome-related indexes between these two strains and existing species of family <em>Natrialbaceae</em> were 73–77%, 21–25%, and 63–70%, respectively, significantly lower than the species boundary thresholds. Strains TS33<sup>T</sup> and KZCA124 may represent a novel species of a new genus within the family <em>Natrialbaceae</em> judged by the cutoff value of AAI (≤76%) proposed to differentiate genera within the family <em>Natrialbaceae</em>. The major polar lipids of strains TS33<sup>T</sup> and KZCA124 were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated mannosyl glucosyl diether, and sulfated galactosyl mannosyl glucosyl diether. These two strains could be distinguished from the related genera according to differential phenotypic characteristics. These phenotypic, phylogenetic, and genomic analyses revealed that strains TS33<sup>T</sup> (=KCTC 4310<sup>T</sup> = MCCC 4K00132<sup>T</sup>) and KZCA124 (=CGMCC 1.17432 = JCM 34316) represent a novel species of a new genus of the family <em>Natrialbaceae</em> and were named <em>Halomontanus rarus</em> gen. nov., sp. nov.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126500"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139975705","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
Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode Quis custodiet ipsos custodes?呼吁社区参与 SeqCode 的管理
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-02-24 DOI: 10.1016/j.syapm.2024.126498
Iain C. Sutcliffe , Luis M. Rodriguez-R , Stephanus N. Venter , William B. Whitman

Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of Archaea and Bacteria using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.

为分类群命名提供规范和稳定框架的命名法是生物研究的基础。这些规范本身需要有管理、解释和修订的制度。在此,我们回顾了最近推出的《序列数据描述的原核生物命名规范》(SeqCode)的管理规定,该规范为有效公布以分离基因组、元基因组组装基因组或单一扩增基因组序列为类型材料的名称提供了命名框架。支持 SeqCode 的管理结构旨在实现开放性和包容性。我们鼓励对原核生物系统学感兴趣的人加入 SeqCode 社区。
{"title":"Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode","authors":"Iain C. Sutcliffe ,&nbsp;Luis M. Rodriguez-R ,&nbsp;Stephanus N. Venter ,&nbsp;William B. Whitman","doi":"10.1016/j.syapm.2024.126498","DOIUrl":"10.1016/j.syapm.2024.126498","url":null,"abstract":"<div><p>Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of <em>Archaea</em> and <em>Bacteria</em> using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126498"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000122/pdfft?md5=762a11d283f0db1e74c77527e4520630&pid=1-s2.0-S0723202024000122-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140007964","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
Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus 基于系统发生组和分子标记的研究,以澄清 Peptoniphilus 物种之间的进化关系。鉴定 Peptoniphilus 物种的几个属级支系,并将一些 Peptoniphilus 物种归入 Aedoeadaptatus 属
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-02-24 DOI: 10.1016/j.syapm.2024.126499
Megha Malhotra , Sarah Bello , Radhey S. Gupta

To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.

Peptoniphilus物种的成员与前列腺癌风险增加有关,为了弄清这些物种之间的进化关系,我们对它们的基因组序列进行了详细的系统发生学和比较分析。在基于核心基因组蛋白和 16S rRNA 基因序列的系统发生树中,Peptoniphilus 物种形成了八个不同的支系,Aedoeadaptatus 和 Anaerosphaera 物种在它们之间形成分支。根据 16S rRNA 相似度和平均氨基酸相同度(AAI),观察到的支系被命名为严格意义上的 Peptoniphilus(包括其模式种)、Harei、Lacrimalis、Duerdenii、Mikwangii、Stercorisuis、Catoniae 和 Aedoeadaptatus,显示出属一级的分化。基因组分类数据库(Genome Taxonomy Database)也将这些支系中的大多数归入不同的类群。根据 16S rRNA 相似性、AAI 和多个唯一共享的分子特征,几个 Peptoniphilus 物种(即 P. coxii、P. ivorii、P. nemausensis 和一些未有效发表的物种)与 Aedoeadaptatus 的模式种(A. acetigenes)可靠分组,并隶属于该属。因此,我们建议将这些物种转入修正后的 Aedoeadaptatus 属。我们对 Peptoniphilus 基因组蛋白质序列的分析还发现了 54 个新的分子标记,这些标记由保守的特征性嵌段(CSIs)组成,对不同的 Peptoniphilus 物种支系具有特异性,为从分子角度划分这些支系提供了可靠的方法。最后,我们还表明,根据这些 CSIs 在未定性的 Peptoniphilus 属(培养的和未培养的)基因组中的共同存在,可以准确预测它们隶属于特定的 Peptoniphilus 支系。这些结果将有助于了解与 Peptoniphilus 相关的物种在疾病中的潜在参与。
{"title":"Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus","authors":"Megha Malhotra ,&nbsp;Sarah Bello ,&nbsp;Radhey S. Gupta","doi":"10.1016/j.syapm.2024.126499","DOIUrl":"https://doi.org/10.1016/j.syapm.2024.126499","url":null,"abstract":"<div><p>To clarify the evolutionary relationships among <em>Peptoniphilus</em> species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, <em>Peptoniphilus</em> species formed eight distinct clades, with <em>Aedoeadaptatus</em> and <em>Anaerosphaera</em> species branching between them. The observed clades designated as <em>Peptoniphilus sensu stricto</em> (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several <em>Peptoniphilus</em> species (viz. <em>P. coxii</em>, <em>P</em>. <em>ivorii</em>, <em>P</em>. <em>nemausensis</em> and some non-validly published species) grouped reliably with the type species of <em>Aedoeadaptatus</em> (<em>A. acetigenes</em>) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence<em>,</em> we are proposing the transfer of these species into the emended genus <em>Aedoeadaptatus</em>. Our analyses on protein sequences from <em>Peptoniphilus</em> genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different <em>Peptoniphilus</em> species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized <em>Peptoniphilus</em> spp. (cultured and uncultured), their affiliations to the specific <em>Peptoniphilus</em> clades can be accurately predicted. These results should prove useful in understanding the potential involvement of <em>Peptoniphilus</em>-related species in diseases.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126499"},"PeriodicalIF":3.4,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139999227","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
Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov 描述从法国卡马格地区沿海咸水湿地水中分离出的果胶杆菌科新属 Prodigiosinella gen.
IF 3.4 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-02-21 DOI: 10.1016/j.syapm.2024.126497
Nicole Hugouvieux-Cotte-Pattat , Jean-Pierre Flandrois , Jérôme Briolay , Sylvie Reverchon , Céline Brochier-Armanet

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of Pectobacteriaceae that branches at the basis of the group encompassing the genera Lonsdalea, Musicola, and Dickeya. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101T (CFBP 8826T = LMG 32072T) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA–DNA relatedness: digital DNA–DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name Prodigiosinella aquatilis sp. nov. Four strains previously designated as Serratia sp. (ATCC 39006), Brenneriaulupoensis” (K61) or Erwinia sp. (MK01 and MK09) belong to the new genus Prodigiosinella.

果胶杆菌科植物病原体能够引发多种疾病,包括由于产生果胶酶破坏植物细胞壁而导致植物浸渍。为了更好地了解它们的多样性,我们对地中海附近法国卡马格地区的咸水湖中的果胶溶解菌进行了调查。对六个非典型分离菌的基因组进行了测序;它们的大小约为 4.8 至 5.0 Mb,包括一个 59 至 61 kb 的质粒;它们的 G+C 值在 49.1 至 49.3 mol% 之间。系统发育分析表明,这些新菌株形成了果胶杆菌科的一个新支系,该支系在包括龙须菜属、Musicola 属和 Dickeya 属的基础上分支。根据表型、基因组和系统发育特征,我们提议建立一个新属,命名为 Prodigiosinella gen.表型和系统发育分析都将菌株分为两个不同的亚群,即 G1 和 G2。模式菌株 LS101T(CFBP 8826T = LMG 32072T)和菌株 CE70(CFBP 9054 = LMG 32867)分别是具有代表性的 G1 和 G2 成员。分析 DNA-DNA 亲缘关系使用了三种基因组学方法:数字 DNA-DNA 杂交(isDDH)、平均核苷酸同一性(ANI)和基因组比对分数(AF)。结果表明,这两个群体的基因组之间关系密切,支持它们属于同一物种,我们将其命名为 Prodigiosinella aquatilis sp.之前被命名为 Serratia sp. (ATCC 39006)、Brenneria "ulupoensis" (K61) 或 Erwinia sp. (MK01 和 MK09) 的四株菌株属于新的 Prodigiosinella 属。
{"title":"Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov","authors":"Nicole Hugouvieux-Cotte-Pattat ,&nbsp;Jean-Pierre Flandrois ,&nbsp;Jérôme Briolay ,&nbsp;Sylvie Reverchon ,&nbsp;Céline Brochier-Armanet","doi":"10.1016/j.syapm.2024.126497","DOIUrl":"10.1016/j.syapm.2024.126497","url":null,"abstract":"<div><p>The <em>Pectobacteriaceae</em> family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of <em>Pectobacteriaceae</em> that branches at the basis of the group encompassing the genera <em>Lonsdalea</em>, <em>Musicola</em>, and <em>Dickeya</em>. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name <em>Prodigiosinella</em> gen. nov<em>.</em> Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101<sup>T</sup> (CFBP 8826<sup>T</sup> = LMG 32072<sup>T</sup>) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA–DNA relatedness: digital DNA–DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name <em>Prodigiosinella aquatilis</em> sp. nov. Four strains previously designated as <em>Serratia</em> sp. (ATCC 39006), <em>Brenneria</em> “<em>ulupoensis”</em> (K61) or <em>Erwinia</em> sp. (MK01 and MK09) belong to the new genus <em>Prodigiosinella</em>.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126497"},"PeriodicalIF":3.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0723202024000110/pdfft?md5=80fdafebb6872b34e10a36ad1568139f&pid=1-s2.0-S0723202024000110-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139919668","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
期刊
Systematic and applied microbiology
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1