Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

{"title":"Phylogenetic and morphological re-evaluation of Camptophora","authors":"Akira Hashimoto,&nbsp;Saho Shibata,&nbsp;Yuuri Hirooka,&nbsp;Moriya Ohkuma","doi":"10.1007/s10482-024-01990-w","DOIUrl":"10.1007/s10482-024-01990-w","url":null,"abstract":"<div><p>The genetic variety and habitats of <i>Camptophora</i> species, generally known as black yeast, have not been clarified. In this study, we re-evaluated <i>Camptophora</i> based on morphological observations and phylogenetic analyses. Because prior investigations on <i>Camptophora</i> only included a few strains/specimens, 24 <i>Camptophora</i>-related strains were newly obtained from 13 leaf samples of various plant species to redefine the genetic and species concepts of <i>Camptophora</i>. Their molecular phylogenetic relationships were examined using small subunit nuclear ribosomal DNA (nSSU, 18S rDNA), the internal transcribed spacer (ITS) rDNA operon, the large subunit nuclear ribosomal DNA (LSU, 28S rDNA), β-tubulin, the second largest subunit of RNA polymerase II (<i>rpb2</i>), and mitochondrial small subunit DNA (mtSSU). Single- and multi-locus analyses using nSSU-ITS-LSU-<i>rpb2</i>-mtSSU revealed a robust phylogenetic relationship among <i>Camptophora</i> species within <i>Chaetothyriaceae</i>. <i>Camptophora</i> species could be distinguished from other chaetothyriaceous genera by their snake-shaped conidia with microcyclic conidiation and loosely interwoven mycelial masses. Based on the results of phylogenetic analyses, two undescribed lineages were recognized, and <i>Ca. schimae</i> was excluded from the genus. ITS sequence comparison with environmental DNA sequences revealed that the distribution of the genus is restricted to the Asia–Pacific region. <i>Camptophora</i> has been isolated or detected from abrupt sources, and this was attributed to its microcycle. The mechanisms driving genetic diversity within species are discussed with respect to their phyllosphere habitats.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Desertibaculum subflavum gen. nov., sp. nov., a novel member of the family Sneathiellaceae isolated from the Kumtag Desert soil","authors":"Chu-Ying Feng,&nbsp;Huan-Huan He,&nbsp;Shuai Li,&nbsp;Zhuo-Huan Zheng,&nbsp;Yi-Jun Mo,&nbsp;Wen-Hui Lian,&nbsp;Chun-Yan Lu,&nbsp;Dong-Ya Zhang,&nbsp;Wen-Jun Li,&nbsp;Lei Dong","doi":"10.1007/s10482-024-02003-6","DOIUrl":"10.1007/s10482-024-02003-6","url":null,"abstract":"<div><p>A novel rod-shaped bacterium, designated as strain SYSU D60015^T that formed yellowish colonies was isolated from a sandy soil collected from the Kumtag Desert in Xinjiang, China. Cells were Gram-stain-negative, oxidase-positive, catalase-negative and motile with a single polar flagellum. Growth optimum occurred between 28 and 37 °C, pH 7.0 and with 0–0.5% (W/V) NaCl. The predominant cellular fatty acids (&gt; 5%) were summed feature 8 (C_18:1 <i>ω</i>7<i>c</i> and/or C_18:1 <i>ω</i>6<i>c</i>), C_19:0 cyclo <i>ω</i>8<i>c</i>, C_18:1 <i>ω</i>7<i>c</i> 11-methyl and C_16:0. The polar lipid profile contained one phosphatidylethanolamine, one diphosphatidylglycerol, one phosphatidylglycerol, one unidentified phospholipid, three unidentified aminolipids, two unidentified aminophospholipids and seven unidentified lipids. The only respiratory quinone was ubiquinone-10. Based on 16S rRNA gene sequence phylogenetic analysis, strain SYSU D60015^T was found to form a distinct linage within the family <i>Sneathiellaceae</i>, and had 16S rRNA gene sequence similarities of 90.8% to <i>Taonella mepensis</i> H1^T, and 90.2% to <i>Ferrovibrio denitrificans</i> S3^T. The genome of SYSU D60015^T was 5.66 Mb in size with 68.2% of DNA G + C content. The low digital DNA-DNA hybridization (dDDH, 18.0%), average nucleotide identity (ANI, 77.5%) and amino acid identity (AAI, 56.0%) values between SYSU D60015^T and <i>Ferrovibrio terrae</i> K5^T indicated that SYSU D60015^T might represent a distinct genus. Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose <i>Desertibaculum subflavum</i> gen. nov., sp. nov. as a novel species of a new genus within the family <i>Sneathiellaceae</i>. The type strain is SYSU D60015^T (= NBRC 112952^T = CGMCC 1.16256^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella","authors":"Yea-Lin Moon,&nbsp;Kyung Hyun Kim,&nbsp;Jin-Sook Park","doi":"10.1007/s10482-024-01998-2","DOIUrl":"10.1007/s10482-024-01998-2","url":null,"abstract":"<div><p>A Gram-stain-positive, strictly aerobic, creamy-white colored, endospore-forming and non-motile rods strain, designated as strain 2205SS18-9^T, was isolated from a marine sponge, <i>Axinella</i> sp. collected from Seopseom Island, Republic of Korea. Optimal growth of strain 2205SS18-9^T was observed at 25–30 °C, pH 6.5–7.0, and in the presence of 3.0% (w/v) NaCl. Cells were oxidase-positive and catalase-negative. Negative for nitrate reduction and indole production. Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2205SS18-9^T formed a distinct phyletic lineage in the genus <i>Chengkuizengella</i>, and it was most closely related to <i>Chengkuizengella marina</i> YPA3-1-1^T and <i>Chengkuizengella sediminis</i> J15A17^T with 97.1 and 96.6% 16S rRNA gene sequence similarities, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205SS18-9^T and <i>Chengkuizengella marina</i> YPA3-1-1^T were 79.0 and 21.6%, respectively. The genomic DNA G + C content was 34.1%. The genome harbors a number of host-adhesion and transporter genes, suggested that strain 2205SS18-9^T may interact with its sponge host as a symbiont. Menaquinone-7 was the sole isoprenoid quinone and antieiso-C_15:0 (28.5%), iso-C_16:0 (25.8%), C_16:1 <i>ω</i>7c alcohol (15.0%), and iso-C_15:0 (11.2%) were detected as the major fatty acids. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, and an unidentified lipid. The cell-wall peptidoglycan contained lysine, alanine, glutamate, and aspartate. Based on these analyses, strain 2205SS18-9^T represents a novel species of the genus <i>Chengkuizengella</i>, for which the name <i>Chengkuizengella axinellae</i> sp. nov. is proposed. The type strain is 2205SS18-9^T (= KACC 23238^T = LMG 33063^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141767920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ubiquity of methanogenic archaea in the trunk of coniferous and broadleaved tree species in a mountain forest","authors":"Mikitoshi Harada,&nbsp;Atsuya Endo,&nbsp;Shuji Wada,&nbsp;Takeshi Watanabe,&nbsp;Daniel Epron,&nbsp;Susumu Asakawa","doi":"10.1007/s10482-024-02004-5","DOIUrl":"10.1007/s10482-024-02004-5","url":null,"abstract":"<div><p>Wetwood of living trees is a habitat of methanogenic archaea, but the ubiquity of methanogenic archaea in the trunk of various trees has not been revealed. The present study analysed methanogenic archaeal communities inside coniferous and broadleaved trees in a cold temperate mountain forest by culture-dependent or independent techniques. Heartwood and sapwood segments were obtained from the trunk of seven tree species, <i>Cryptomeria japonica</i>, <i>Quercus crispula</i>, <i>Fraxinus mandshurica</i>, <i>Acer pictum</i>, <i>Aesculus turbinata</i>, <i>Magnolia obovata</i>, and <i>Populus tremula</i>. Amplicon sequencing analysis of 16S rRNA genes showed that <i>Methanobacteriaceae</i> predominated the archaeal communities and <i>Methanomassiliicoccaceae</i> also inhabited some trees. Real-time PCR analysis detected methanogenic archaeal <i>mcrA</i> genes from all the tree species, with a maximum of 10⁷ copies g⁻¹ dry wood. Digital PCR analysis also detected <i>mcrA</i> genes derived from <i>Methanobacterium</i> spp. and <i>Methanobrevibacter</i> spp. from several samples, with a maximum of 10⁵ and 10⁴ copies g⁻¹ dry wood. The enumeration by the most probable number method demonstrated the inhabitation of viable methanogenic archaea inside the trees; 10⁶ cells g⁻¹ dry wood was enumerated from a heartwood sample of <i>C. japonica</i>. Methanogenic archaea related to <i>Methanobacterium beijingense</i> were cultivated from a heartwood sample of <i>Q. crispula</i> and <i>F. mandshurica</i>. The present study demonstrated that the inside of various trees is a common habitat for methanogenic archaeal communities and a potential source of methane in forest ecosystems.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141767921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomics and taxonomy of the glyphosate-degrading, copper-tolerant rhizospheric bacterium Achromobacter insolitus LCu2","authors":"Yelena V. Kryuchkova,&nbsp;Alexandra A. Neshko,&nbsp;Natalia E. Gogoleva,&nbsp;Alexander S. Balkin,&nbsp;Vera I. Safronova,&nbsp;Kristina Yu. Kargapolova,&nbsp;Elena I. Shagimardanova,&nbsp;Yuri V. Gogolev,&nbsp;Gennady L. Burygin","doi":"10.1007/s10482-024-01989-3","DOIUrl":"10.1007/s10482-024-01989-3","url":null,"abstract":"<div><p>A rhizosphere strain, <i>Achromobacter insolitus</i> LCu2, was isolated from alfalfa (<i>Medicago sativa</i> L.) roots. It was able to degrade of 50% glyphosate as the sole phosphorus source, and was found resistant to 10 mM copper (II) chloride, and 5 mM glyphosate–copper complexes. Inoculation of alfalfa seedlings and potato microplants with strain LCu2 promoted plant growth by 30–50%. In inoculated plants, the toxicity of the glyphosate–copper complexes to alfalfa seedlings was decreased, as compared with the noninoculated controls. The genome of <i>A. insolitus</i> LCu2 consisted of one circular chromosome (6,428,890 bp) and encoded 5843 protein genes and 76 RNA genes. Polyphasic taxonomic analysis showed that <i>A. insolitus</i> LCu2 was closely related to <i>A. insolitus</i> DSM23807^T on the basis of the average nucleotide identity of the genomes of 22 type strains and the multilocus sequence analysis. Genome analysis revealed genes putatively responsible for (1) plant growth promotion (osmolyte, siderophore, and 1-aminocyclopropane-1-carboxylate deaminase biosynthesis and auxin metabolism); (2) degradation of organophosphonates (glyphosate oxidoreductase and multiple <i>phn</i> clusters responsible for the transport, regulation and C–P lyase cleavage of phosphonates); and (3) tolerance to copper and other heavy metals, effected by the CopAB–CueO system, responsible for the oxidation of copper (I) in the periplasm, and by the efflux Cus system. The putative catabolic pathways involved in the breakdown of phosphonates are predicted. <i>A. insolitus</i> LCu2 is promising in the production of crops and the remediation of soils contaminated with organophosphonates and heavy metals.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria","authors":"Wouter B. Lenferink,&nbsp;Theo A. van Alen,&nbsp;Mike S. M. Jetten,&nbsp;Huub J. M. Op den Camp,&nbsp;Maartje A. H. J. van Kessel,&nbsp;Sebastian Lücker","doi":"10.1007/s10482-024-02002-7","DOIUrl":"10.1007/s10482-024-02002-7","url":null,"abstract":"<div><p>Bacteria of the phylum <i>Planctomycetota</i> have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class <i>Phycisphaerae</i> have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality <i>Phycisphaerae</i> genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird’s eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any <i>Phycisphaerae</i> genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by <i>Phycisphaerae</i> families.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11266412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China","authors":"Inam Ullah Khan,&nbsp;Muhammad Saqib,&nbsp;Arshia Amin,&nbsp;Sadia Manzoor,&nbsp;Iftikhar Ahmed,&nbsp;Rui-Rui Liu,&nbsp;Jian-Yu Jiao,&nbsp;Xiao-Yang Zhi,&nbsp;Wen-Jun Li","doi":"10.1007/s10482-024-02001-8","DOIUrl":"10.1007/s10482-024-02001-8","url":null,"abstract":"&lt;div&gt;&lt;p&gt;Genus &lt;i&gt;Thermus&lt;/i&gt; is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus &lt;i&gt;Thermus&lt;/i&gt; in geographically different thermal springs. Sixteen &lt;i&gt;Thermus&lt;/i&gt; strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the &lt;i&gt;Thermus&lt;/i&gt; strains. Whole genome based phylogenetic analysis showed, all 16 &lt;i&gt;Thermus&lt;/i&gt; strains belong to five species; &lt;i&gt;Thermus &lt;/i&gt;&lt;i&gt;oshimai&lt;/i&gt; (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), &lt;i&gt;Thermus&lt;/i&gt; &lt;i&gt;antranikianii&lt;/i&gt; (YIM 73052, 77412, 77311, 71206), &lt;i&gt;Thermus &lt;/i&gt; &lt;i&gt;brokianus&lt;/i&gt; (YIM 73518, 71318, 72351), &lt;i&gt;Thermus &lt;/i&gt; &lt;i&gt;hydrothermalis&lt;/i&gt; (YIM 730264 and 77927) and one potential novel species 77420 forming clade with &lt;i&gt;Thermus &lt;/i&gt;&lt;i&gt;thalpophilus&lt;/i&gt; SYSU G00506&lt;sup&gt;T&lt;/sup&gt;. Although the genomes of different strains of &lt;i&gt;Thermus&lt;/i&gt; of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that &lt;i&gt;Thermus&lt;/i&gt; isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the &lt;i&gt;Thermus&lt;/i&gt; genomes which could be helpful to acquire DNA from environment. In the present study it was found that &lt;i&gt;Thermus&lt;/i&gt; isolates use two mechanism of incomplete denitrification pathway, some &lt;i&gt;Thermus&lt;/i&gt; strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of &lt;i&gt;Thermus&lt;/i&gt; genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of &lt;i&gt;T&lt;/i&gt;. &lt;i&gt;oshimai&lt;/i&gt; and &lt;i&gt;T&lt;/i&gt;. &lt;i&gt;antranikianii&lt;/i&gt; strains, while genomes of all &lt;i&gt;T&lt;/i&gt;. &lt;i&gt;brokianus&lt;/i&gt; strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced &lt;i&gt;Thermus&lt;/i&gt; strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequen","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A detailed analysis of 16S rRNA gene sequencing and conventional PCR-based testing for the diagnosis of bacterial pathogens and discovery of novel bacteria","authors":"Mei-Na Li,&nbsp;Ting Wang,&nbsp;Nan Wang,&nbsp;Qiang Han,&nbsp;Xue-Ming You,&nbsp;Shuai Zhang,&nbsp;Cui-Cui Zhang,&nbsp;Yong-Qiang Shi,&nbsp;Pei-Zhuang Qiao,&nbsp;Cheng-Lian Man,&nbsp;Teng Feng,&nbsp;Yue-Yue Li,&nbsp;Zhuang Zhu,&nbsp;Ke-Ji Quan,&nbsp;Teng-Lin Xu,&nbsp;George Fei Zhang","doi":"10.1007/s10482-024-01999-1","DOIUrl":"10.1007/s10482-024-01999-1","url":null,"abstract":"<div><p>This study represents the first analysis of the bacterial community in chickens affected by swollen head syndrome, utilizing 16S rRNA gene sequencing. Samples were obtained from clinical laying chickens and were examined for the presence of <i>Avibacterium paragallinarum</i> (APG) and <i>Ornithobacterium rhinotracheale</i> (ORT) using conventional polymerase chain reaction (PCR). From the samples, five APG-positive (APG) and APG-negative (N-APG) samples were chosen, along with five specific pathogen-free chickens, for 16S rRNA gene sequencing. Results showed that APG and ORT were widely detected in the chicken samples with swollen head syndrome (SHS, 9/10), while APG was detected in all five specific pathogen-free (SPF) samples. In contrast, conventional PCR sensitivity was found to be inadequate for diagnosis, with only 35.7% (5/14) and 11.1% (1/9) sensitivity for APG and ORT, respectively, based on 16S rRNA gene sequencing data. Furthermore, 16S rRNA gene sequencing was able to quantify the bacteria in the samples, revealing that the relative abundance of APG in the APG group ranged from 2.7 to 81.3%, while the relative abundance of APG in the N-APG group ranged from 0.1 to 21.0%. Notably, a low level of APG was also detected in all 5 SPF samples. The study also identified a significant number of animal and human common bacterial pathogens, including but not limited to <i>Gallibacterium anatis</i>, <i>Riemerella columbina</i>, <i>Enterococcus cecorum</i>, <i>Mycoplasma synoviae</i>, <i>Helicobacter hepaticus</i>, and <i>Staphylococcus lentus</i>. In conclusion, 16S rRNA gene sequencing is a valuable tool for bacterial pathogen diagnosis and the discovery of novel bacterial pathogens, while conventional PCR is not reliable for diagnosis.</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thalassospira aquimaris sp. nov. and Winogradskyella marincola sp. nov. two marine bacteria isolated from an agar-degrading co-culture","authors":"Zi-Yue Fu,&nbsp;Dao-Feng Zhang,&nbsp;Meng-Han Huang,&nbsp;Hong-Chuan Wang,&nbsp;Xiao-Ye Chen,&nbsp;Yu-Fang Yao,&nbsp;Yang Yuan,&nbsp;Wen-Jun Li","doi":"10.1007/s10482-024-02000-9","DOIUrl":"10.1007/s10482-024-02000-9","url":null,"abstract":"<div><p>Two novel Gram-stain-negative, aerobic, and non-motile strains, designated FZY0004^T and YYF002^T, were isolated from an agar-degrading co-culture, which was obtained from seawater of the intertidal zone of Yancheng City, the Yellow Sea of China. Strain FZY0004^T optimally grew at 28 °C, pH 7.0, and 2–6% NaCl, while strain YYF002^T optimally grew at 28 °C, pH 7.5, and 2–4% NaCl. Strain FZY0004^T possessed Q-9 as the major respiratory quinone, and its major fatty acids (&gt; 10%) were summed feature 8 (C_18:1 <i>ω</i>7<i>c</i>), C_16:0, and summed feature 3 (C_16:1 <i>ω</i>7<i>c</i>/C_16:1 <i>ω</i>6<i>c</i>). The polar lipids identified in strain FZY0004^T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and several unidentified phospholipids (PL) and lipids (L). On the other hand, strain YYF002^T had MK-6 as the predominant respiratory quinone and its major fatty acids consisted of iso-C_15:0, iso-C_15:1 G, and iso-C_15:0 3-OH. The polar lipids identified in strain YYF002^T were aminolipid (AL), PE, and several unidentified lipids. Strain FZY0004^T shared 99.5% 16S rRNA gene sequence similarity and 90.1% average nucleotide identity (ANI) with <i>T. povalilytica</i> Zumi 95^T, and strain YYF002^T shared 99.2% 16S rRNA gene sequence similarity and 88.2% ANI with <i>W. poriferorum</i> JCM 12885^T. The genomic DNA G + C contents of strains FZY0004^T and YYF002^T were 54.5% and 33.5%, respectively. The phylogenetic, phenotypic, and physiological characteristics permitted the distinction of the two strains from their neighbors, and we thus propose the names <i>Thalassospira aquimaris</i> sp. nov. (type strain FZY0004^T = JCM 35895^T = MCCC 1K08380^T) and <i>Winogradskyella marincola</i> sp. nov. (type strain YYF002^T = JCM 35950^T = MCCC 1K08382^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity","authors":"Christopher A. Dunlap,&nbsp;Eric T. Johnson,&nbsp;Marleny Burkett-Cadena,&nbsp;Johanna Cadena,&nbsp;Ephantus J. Muturi","doi":"10.1007/s10482-024-01993-7","DOIUrl":"10.1007/s10482-024-01993-7","url":null,"abstract":"<div><p>An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to <i>Lysinibacillus fusiformis</i> NRRL NRS-350^T (99.7%) and <i>Lysinibacillus sphaericus</i> NRRL B-23268^T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C_15: 0 (52.3%), anteiso-C_15: 0 (14.8%), C_16:1ω7C alcohol (11.2%), and C_16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of <i>Lysinibacillus</i> revealed this strain formed a distinct monophyletic clade with the nearest neighbor being <i>Lysinibacillus fusiformis</i>. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus <i>Lysinibacillus</i>, for which the name <i>Lysinibacillus pinottii</i> sp. nov. is proposed, with type strain PB211^T (= NRRL B-65672^T, = CCUG 77181^T).</p></div>","PeriodicalId":50746,"journal":{"name":"Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology","volume":"117 1","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}