Systematic and applied microbiology最新文献

{"title":"Description and genomic characterization of Mesorhizobium marinum sp. nov., a bacterium isolated from sea sediment","authors":"Chengshao Zan ,&nbsp;Xiao Ma ,&nbsp;Zhouqing Zheng ,&nbsp;Feina Li ,&nbsp;Xian Yang ,&nbsp;Yifen Luo ,&nbsp;Li Tuo","doi":"10.1016/j.syapm.2025.126589","DOIUrl":"10.1016/j.syapm.2025.126589","url":null,"abstract":"<div><div>Two Gram-stain-negative, aerobic strains, designed ZMM04-4^T and ZMM04–5, were isolated from sea sediment collected from Qinzhou Bay, Guangxi Zhuang Automous Region, China. The predominant respiratory quinone was ubiquinone-10. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, aminophospholipid and phospholipid. The predominant fatty acids were C_18:1<em>ω</em>7c, C_19:0 cyclo <em>ω</em>8c and C_16:0. Strain ZMM04-4^T shared 99.7 % similarity of 16S rRNA gene sequence with ZMM04–5. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZMM04-4^T and ZMM04–5 were 92.9 % and 98.6 %, respectively, indicating that strains ZMM04-4^T, ZMM04–5 belong to the same species. Phylogenetic and phylogenomic analysis indicated that strains ZMM04-4^T and ZMM04–5 belong to the genus <em>Mesorhizobium</em> and showed the highest sequence similarity to <em>Mesorhizobium qingshengii</em> CGMCC 1.12097^T (97.7 %–97.8 % sequence similarity) and <em>Mesorhizobium shangrilense</em> DSM 21850^T (97.7 %–97.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between strains ZMM04-4^T, ZMM04–5 and their closely related species were within the ranges of 76.5 %–77.2 % and 20.9 %–21.8 %, respectively, indicating that strains ZMM04-4^T, ZMM04–5 were novel species. In accordance with phylogenetic and genomic as well as phenotypic and chemotaxonomic characterizations, strains ZMM04-4^T and ZMM04–5 should be assigned to the genus <em>Mesorhizobium</em> and indentified as a novel species, for which the name <em>Mesorhizobium marinum</em> sp. nov., is proposed. The type strain is ZMM04-4^T (=MCCC 1K08883^T = KCTC 8273^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126589"},"PeriodicalIF":3.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080997","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":"Flavobacterium plantiphilum sp. nov., Flavobacterium rhizophilum sp. nov., Flavobacterium rhizosphaerae sp. nov., Chryseobacterium terrae sp. nov., and Sphingomonas plantiphila sp. nov. isolated from salty soil showing plant growth promoting potential","authors":"Peter Kämpfer ,&nbsp;André Lipski ,&nbsp;Kathy S. Lawrence ,&nbsp;Walker R. Olive ,&nbsp;Molli M. Newman ,&nbsp;John A. McInroy ,&nbsp;Tomeu Viver","doi":"10.1016/j.syapm.2025.126588","DOIUrl":"10.1016/j.syapm.2025.126588","url":null,"abstract":"<div><div>Members of the genera <em>Flavobacterium</em>, <em>Chryseobacterium</em> and <em>Sphingomonas</em> constitute a group of microorganisms in the rhizosphere associated with plant growth promoting (PGP) features. A polyphasic approach was employed to ascertain the taxonomic status of five selected strains. Overall genome relatedness indices of digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) between the strains and the other members of the genera <em>Flavobacterium</em>, <em>Chryseobacterium</em> and <em>Sphingomonas</em> were found to be below the established thresholds, respectively. Morphological, physiological, and biochemical characteristics of the strains confirmed their status as five novel species. A large variety of genes involved in plant growth promotion and carbohydrate utilization were found in all strains suggesting a contribution of all strains to PGP.</div><div>Based on the result of the polyphasic characterization, the following names are proposed: <em>Chryseobacterium terrae</em> sp. nov., with the strain ST-37^T as the type strain (= CCM 9260^T = LMG 32728^T); <em>Flavobacterium plantiphilum</em> sp. nov., with the strain ST-87^T as the type strain CIP 112180^T = DSM 114790^T = LMG 32757^T); <em>Flavobacterium rhizophilum</em> sp. nov., with the strain ST-75^T as the type strain (= CIP 112185^T = DSM 114831^T = LMG 32758^T); <em>Flavobacterium rhizosphaerae</em> sp. nov., with the strain ST-119^T as the type strain (CIP 112181^T = DSM 114832^T = LMG 32756^T); and <em>Sphingomonas plantiphila</em> sp. nov. with the strain ST-64 ^T as the type strain (= CCM 9261^T = CIP 112178^T = DSM 114515^T = LMG 32729^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126588"},"PeriodicalIF":3.3,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067773","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":"MIRRI-ERIC's position on the recent evolution of the international code of nomenclature of prokaryotes","authors":"Rosa Aznar ,&nbsp;Michel-Yves Mistou ,&nbsp;Praveen Rahi ,&nbsp;Jean-Luc Legras ,&nbsp;Anete Boroduske ,&nbsp;Amalia Stefaniu ,&nbsp;Nelson Lima ,&nbsp;Amalia D. Karagouni ,&nbsp;Vincent Van de Perre ,&nbsp;Ana M.P. Melo","doi":"10.1016/j.syapm.2025.126587","DOIUrl":"10.1016/j.syapm.2025.126587","url":null,"abstract":"","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 2","pages":"Article 126587"},"PeriodicalIF":3.3,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029840","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 Hyphococcus formosus sp. nov. and Hyphococcus lacteus sp. nov., isolated from coastal sediment, and reclassification of Marinicaulis flavus as Hyphococcus luteus nom. nov. and Marinicaulis aureus as Hyphococcus aureus comb. nov","authors":"Yu-Qi Ye ,&nbsp;Xin-Yue Zhang ,&nbsp;Hong-Nan Gong ,&nbsp;Meng-Qi Ye ,&nbsp;Zong-Jun Du","doi":"10.1016/j.syapm.2024.126575","DOIUrl":"10.1016/j.syapm.2024.126575","url":null,"abstract":"<div><div>During a study on sediment bacterial diversity in coastal China, three bacterial strains, DH-69^T, EH-24, and ECK-19^T, were isolated from coastal sediments off Xiaoshi Island, Weihai. These strains were Gram-staining-negative, aerobic, and coccoid to rod-shaped with prosthecae and flagella. Comparison of the 16S rRNA gene showed that they shared the highest identity values with <em>Hyphococcus flavus</em> MCCC 1K03223^T (96.2–97.6 %), followed by <em>Marinicaulis flavus</em> SY-3-19^T (95.2–96.8 %) and <em>Marinicaulis aureus</em> HHTR114^T (95.2–96.2 %). Genome comparisons using average nucleotide identity (ANI) and average amino acid identity (AAI) suggested that the three novel strains and the three related strains belonged to the same genus, with strains DH-69^T, EH-24, and ECK-19^T identified as two distinct novel species. Pan-genome analysis revealed that 995 core genes were shared among 23 <em>Hyphococcus</em> genomes/MAGs. Secondary metabolites analysis identified a biosynthesis gene cluster for microsclerodermin, a potent antifungal peptide, in the novel strains. Moreover, these newly isolated strains were detected in various ecosystems, with a particular prevalence in marine environments, based on analysis of 500,048 amplicon datasets, underscoring their ecological preference. Based on polyphasic characterizations, strains DH-69^T and EH-24 represent a novel species of the genus <em>Hyphococcus</em>, for which the name <em>Hyphococcus formosus</em> sp. nov. is proposed with the type strain DH-69^T (= MCCC 1H00436^T = KCTC 8010^T). Strain ECK-19^T represents another novel <em>Hyphococcus</em> species, for which the name <em>Hyphococcus lacteus</em> sp. nov. is proposed with the type strain ECK-19^T (= MCCC 1H00435^T = KCTC 8009^T). Furthermore, <em>Marinicaulis flavus</em> and <em>Marinicaulis aureus</em> are proposed to be reclassified as <em>Hyphococcus luteus</em> nom. nov. and <em>Hyphococcus aureus</em> comb. nov., respectively, accompanied by an emended description of the genus <em>Hyphococcus</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126575"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814030","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":"Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland","authors":"Eva Pouder,&nbsp;Erwann Vince,&nbsp;Karen Jacquot,&nbsp;Maimouna batoma Traoré,&nbsp;Ashley Grosche,&nbsp;Maria Ludwig,&nbsp;Mohamed Jebbar,&nbsp;Loïs Maignien,&nbsp;Karine Alain,&nbsp;Sophie Mieszkin","doi":"10.1016/j.syapm.2024.126578","DOIUrl":"10.1016/j.syapm.2024.126578","url":null,"abstract":"<div><div>A novel bacterial strain, HK31-G^T, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus <em>Phenylobacterium</em>. Cells are motile Gram-negative thin rods. Physiological characterization showed that strain HK31-G^T is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 6 and 8 and at NaCl concentrations between 0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-G^T is chemoorganoheterotroph and its major saturated fatty acids are C_18:1<em>ω7c</em>, C₁₆_:1<em>ω6c</em> and C_16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-G^T was estimated to be 4.46 Mbp in size with a DNA G + C content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from groundwater have been assigned to the same species as the new strain HK31-G^T. Furthermore, OGRI values between the genome of strain HK31-G^T and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-G^T represents a novel species of the genus <em>Phenylobacterium</em>, for which the name <em>Phenylobacterium ferrooxidans</em> sp. nov. is proposed. The type strain is HK31-G^T (DSM 116432^T = UBOCC-M-3429^T = LMG 33376^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126578"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883026","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":"Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems","authors":"Jette F. Petersen ,&nbsp;Laura C. Valk ,&nbsp;Maarten D. Verhoeven,&nbsp;Marta A. Nierychlo,&nbsp;Caitlin M. Singleton,&nbsp;Morten K.D. Dueholm,&nbsp;Per H. Nielsen","doi":"10.1016/j.syapm.2024.126574","DOIUrl":"10.1016/j.syapm.2024.126574","url":null,"abstract":"<div><div>Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is <em>Rhodoferax,</em> an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of <em>Rhodoferax</em> species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of “<em>Rhodoferax</em>” revealed that species previously assigned to <em>Rhodoferax</em> in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the <em>Rhodoferax</em> genus.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126574"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865414","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":"Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans","authors":"Isabella Wilkie,&nbsp;Luis H. Orellana","doi":"10.1016/j.syapm.2024.126562","DOIUrl":"10.1016/j.syapm.2024.126562","url":null,"abstract":"<div><div>Members of the phylum <em>Verrucomicrobiota</em> play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (<em>Seribacter</em> gen. Nov., <em>Chordibacter</em> gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, <em>Seribacteraceae</em>. Our findings shed light on the ecological significance and metabolic potential of <em>Verrucomicrobiota</em> populations in spring bloom events.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126562"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787057","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":"Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria","authors":"Ya-Ling Mao ,&nbsp;Xin-Yue Dong ,&nbsp;Cong-Qi Tao,&nbsp;Zhang-Ping Wu,&nbsp;Xiao-Wei Shi,&nbsp;Jing Hou,&nbsp;Heng-Lin Cui","doi":"10.1016/j.syapm.2024.126577","DOIUrl":"10.1016/j.syapm.2024.126577","url":null,"abstract":"<div><div>Four novel halophilic archaeal strains CGA53^T, CG83^T, FCH27^T, and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53^T showed the highest 16S rRNA gene similarity (92.6%) to <em>Salinilacihabitans rarus</em> AD-4^T, and the other three strains were found to be related to <em>Halalkalicoccus</em> species with similarities of 97.6–98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus <em>Halalkalicoccus</em>. Their growth occurred at 20–60 °C (optima, 42, 37, 37–42, and 35 °C), 0.9–5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0–1.0 M MgCl₂ (optima, 0.5, 0.7, and 0.1) and pH 5.5–10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83^T, FCH27^T, and SEDH24 cluster with the current species of the genus <em>Halalkalicoccus</em>, and strain CGA53^T forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53^T, CG83^T, FCH27^T, SEDH24, and the type species of the current genera within the class <em>Halobacteria</em> were 67.4–81.6%, 16.5–28.6% and 49.7–74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53^T may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H₂S formation, were found among these four strains and <em>Halalkalicoccus</em> species. Genome-based classification supported that strains CGA53^T, CG83^T, FCH27^T, SEDH24, and the current species of <em>Halalkalicoccus</em> represent a novel family of the order <em>Halobacteriales</em> within the class <em>Halobacteria</em>.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126577"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865417","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":"Phylogenetic characterization of Bifidobacterium kimbladii sp. nov., a novel species from the honey stomach of the honeybee Apis mellifera","authors":"M. Modesto ,&nbsp;D. Scarafile ,&nbsp;A. Vásquez ,&nbsp;R. Pukall ,&nbsp;M. Neumann-Schaal ,&nbsp;S. Pascarelli ,&nbsp;B. Sgorbati ,&nbsp;M. Ancora ,&nbsp;C. Cammà ,&nbsp;P. Mattarelli ,&nbsp;T.C. Olofsson","doi":"10.1016/j.syapm.2025.126579","DOIUrl":"10.1016/j.syapm.2025.126579","url":null,"abstract":"<div><div>Six novel <em>Bifidobacterium</em> strains H1HS16N^T, Bin2N, Hma3N, H6bp22N, H1HS10N, and H6bp9N, were isolated from the honey stomach of <em>Apis mellifera</em>. Cells are Gram-positive, non-motile, non-sporulating, facultatively anaerobic, and fructose 6-phosphate phosphoketolase-positive. Optimal growth conditions occur at 37 °C in anaerobiosis in MRS medium added with 2 % fructose and 0.1 % L-cysteine. The 16S rRNA gene sequences analysis revealed clustering with <em>Bifidobacterium</em> species found in honeybees. Strains Hma3N, H6bp22N, and H1HS16N^T showed significant similarity to <em>Bifidobacterium polysaccharolyticum</em> JCM 34588^T, with an average similarity of 99.63 %. In contrast, strains Bin2N, H1HS10N, and H6bp9N were closely related to <em>Bifidobacterium apousia</em> JCM 34587^T, with an average similarity of 99.22 %. Moreover, strains Hma3N and H6bp22N exhibited ANI values of 96.65 % and 96.53 % when compared to <em>Bifidobacterium polysaccharolyticum</em> JCM 34588^T, while strains H1HS16N^T, Bin2N, H6bp9N, and H1HS10N revealed ANI values of 94.18 %, 94.33 %, 94.22 %, and 95.50 % respectively when compared to <em>B. apousia</em> JCM 34587^T. dDDH analysis confirmed that strains Hma3N and H6bp22N belong to <em>B. polysaccharolyticum</em>, whereas strains H1HS16N^T, Bin2N, H6bp9N, and H1HS10N represent a novel species. The peptidoglycan of the novel species is of the A4α type (L-Lys-D-Asp). The main cellular fatty acids of the type strain H1HS16N^T are C_16:0, C_14:0, C_19:0 cyclo ω9c, and C_18:1 ω9c. The DNA G + C content of the type strain is 60.8 mol%.</div><div>Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, probiotic features, and ecological distribution patterns.</div><div>Phenotypic and genotypic characterization show that strain H1HS16N^T is distinct from the type strains of other recognized <em>Bifidobacterium</em> species. Thus, <em>Bifidobacterium kimbladii</em> sp. nov. (H1HS16N^T = DSM 115187^T = CCUG 76695^T) is proposed as a novel <em>Bifidobacterium</em> species.</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126579"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971952","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 Albidovulum litorale sp. nov., Albidovulum marisflavi sp. nov., Albidovulum salinarum sp. nov., and Albidovulum sediminicola sp. nov., and proposal for reclassification of the genus Defluviimonas as a later heterotypic synonym of Albidovulum","authors":"Wei He ,&nbsp;Dao-Feng Zhang ,&nbsp;Xing-Jie Li ,&nbsp;Hong-Chuan Wang ,&nbsp;Lin-Qiong Wang ,&nbsp;Yang Yuan","doi":"10.1016/j.syapm.2024.126576","DOIUrl":"10.1016/j.syapm.2024.126576","url":null,"abstract":"<div><div>Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002^T, WL0024^T, WL0050^T, and WL0075^T, were isolated from sediment in the coastal areas of Nantong City, China. Metagenomic analysis revealed higher relative abundance of taxa closely related to the four strains in sediment (0.79–2.0 %) than in water (0.34–1.3 %) (Mann-Whitney <em>U</em> test: <em>p</em> &lt; 0.001). Phylogenetic analysis based on 16S rRNA gene and the bac120 gene set both suggested that the four strains are closely related to the genus <em>Defluviimonas</em>. Additionally, <em>Albidovulum inexpectatum</em> DSM 12048^T formed a distinct branch within <em>Defluviimonas</em>. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of <em>Albidovulum</em> and <em>Defluviimonas</em> should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera <em>Albidovulum</em> and <em>Defluviimonas</em> was below species delimitation thresholds, except for strains WL0024^T and “<em>D. salinarum</em>” CAU 1641^T, which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in <em>Albidovulum</em>, and it is reasonable to reclassify the genus <em>Defluviimonas</em> as a later heterotypic synonym of <em>Albidovulum</em>, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: <em>Albidovulum marisflavi</em> sp. nov. (type strain WL0002^T = MCCC 1K06013^T = JCM 34653^T = GDMCC 1.2437^T), <em>Albidovulum salinarum</em> sp. nov. (WL0024^T = MCCC 1K06062^T = JCM 34656^T = GDMCC 1.2438^T), <em>Albidovulum litorale</em> sp. nov. (WL0050^T = MCCC 1K07524^T = JCM 35566^T = GDMCC 1.3084^T), and <em>Albidovulum sediminicola</em> sp. nov. (WL0075^T = MCCC 1K06064^T = JCM 34660^T = GDMCC 1.2419^T).</div></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"48 1","pages":"Article 126576"},"PeriodicalIF":3.3,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819250","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}