Systematic and applied microbiology最新文献

{"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}

{"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}

{"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}

{"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_15:0, <em>iso</em>-C_15:1 G, and <em>iso</em>-C_17:0 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 H1-2-19X^T, JS81^T, and JY13-12^T 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^T = JCM 36460^T = CGMCC 1.61321^T), <em>Terrimonas pollutisoli</em> (type strain H1YJ31^T = JCM 36215^T = CGMCC 1.61343^T), <em>Pollutibacter soli</em> (type strain JS81^T = JCM 36462^T = CGMCC 1.61338^T), and <em>Polluticoccus soli</em> (type strain JY13-12^T = JCM 36463^T = CGMCC 1.61341^T).</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}

{"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^T 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(H₄). The major fatty acids were C_16:0, C_17:1 <em>_w</em>₈<em>_c</em>, C_17:0, C_18:1 <em>_w</em>₉<em>_c</em> and C_18:0. Analyses of genome sequences revealed that the genome size of SYSU M7M538^T 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^T 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^T (=KCTC 59113^T = GDMCC 1.4286^T), 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}

{"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^Ts, 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^Ts 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^T. While, the bin JB015 showed 99.1 % identity with <em>Pleomorphochaeta naphthae</em> SEBR 4209^T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008^Ts 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^Ts 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^Ts, 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^Ts 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}

{"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^T 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^T 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 <em>rpoB'</em> gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33^T, 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^T 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^T 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^T 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^T 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^T (=KCTC 4310^T = MCCC 4K00132^T) 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}

{"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}

{"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}

{"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^T (CFBP 8826^T = LMG 32072^T) 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}