Journal of Genomics最新文献

{"title":"Whole Genome Sequence of <i>Marinobacter salarius</i> Strain SMR5, Shown to Promote Growth in its Diatom Host.","authors":"Mats Töpel, Matthew I M Pinder, Oskar N Johansson, Olga Kourtchenko, Anna Godhe, Adrian K Clarke","doi":"10.7150/jgen.39039","DOIUrl":"10.7150/jgen.39039","url":null,"abstract":"<p><p>Attempts to obtain axenic cultures of the marine diatom <i>Skeletonema marinoi</i> often result in poor growth, indicating the importance of the microbiome to the growth of its host. In order to identify the precise roles played by these associated bacteria, individual strains were isolated, cultured and sequenced. We report the genome of one such strain - SMR5, isolated from a culture of <i>S. marinoi</i> strain R05AC sampled from top layer sediments of the Swedish west coast. Its genome of 4,630,160 bp consists of a circular chromosome and one circular plasmid, and 4,263 CDSs were inferred in the annotation. Comparison of 16S rRNA sequences and other markers, along with phylotaxonomic analysis, leads us to place strain SMR5 in the taxon <i>Marinobacter salarius</i>. Pathway analysis and previous experimental work suggest that this strain may produce a growth factor, as well as improve iron availability for its host via siderophores.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 1","pages":"60-63"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46087322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Draft Genome of a Hydrogen-producing Cyanobacterium, Arthrospira platensis NIES-46","authors":"Shigekatsu Suzuki, Haruyo Yamaguchi, M. Kawachi","doi":"10.7150/jgen.38149","DOIUrl":"https://doi.org/10.7150/jgen.38149","url":null,"abstract":"Arthrospira is an economically important cyanobacterium that contains many useful products, including proteins, vitamins, lipids, and pigments, and it is distributed in several alkaline soda lakes. Arthrospira platensis NIES-46 produces large amounts of hydrogen. In this study, we sequenced the NIES-46 draft genome and performed comparative analyses among Arthrospira species to elucidate the genomic background of this strain. The genome consists of 5.7 Mbp with a GC% of 44.5% and encodes 5,008 proteins. Our phylogenetic analysis using multiple orthologous proteins shows that Arthrospira is divided into two clades and that NIES-46 is closely related to A. platensis NIES-39. The genome structure and protein functions are highly conserved between A. platensis NIES-39 and NIES-46, suggesting that these two strains have recently diverged. Genes involved in hydrogen production are well-conserved among Arthrospira species, indicating conserved abilities to produce hydrogen.","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 1","pages":"56 - 59"},"PeriodicalIF":0.0,"publicationDate":"2019-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.38149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48699673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft genome sequences for three unisolated <i>Alnus</i>-infective <i>Frankia</i> Sp+ strains, AgTrS, AiOr and AvVan, the first sequenced <i>Frankia</i> strains able to sporulate <i>in-planta</i>.","authors":"Lorine Bethencourt,&nbsp;Florian Vautrin,&nbsp;Najwa Taib,&nbsp;Audrey Dubost,&nbsp;Lucia Castro-Garcia,&nbsp;Olivier Imbaud,&nbsp;Danis Abrouk,&nbsp;Pascale Fournier,&nbsp;Jérôme Briolay,&nbsp;Agnès Nguyen,&nbsp;Philippe Normand,&nbsp;Maria P Fernandez,&nbsp;Céline Brochier-Armanet,&nbsp;Aude Herrera-Belaroussi","doi":"10.7150/jgen.35875","DOIUrl":"https://doi.org/10.7150/jgen.35875","url":null,"abstract":"<p><p>Actinobacteria from genus <i>Frankia</i> are able to form symbiotic associations with actinorhizal plants including alders. Among them, Sp+ strains are characterized by their ability to differentiate numerous sporangia inside host plant cells (unlike \"Sp-\" strains unable of <i>in-planta</i> sporulation). Here, we report the first genome sequences of three unisolated Sp+ strains: AgTrS, AiOr and AvVan obtained from <i>Alnus glutinosa</i>, <i>A. incana</i> and <i>A. alnobetula</i> (previously known as <i>viridis</i>), respectively (with genome completeness estimated at more than 98%). They represent new <i>Frankia</i> species based on Average Nucleotide Identity (ANI) calculations, and the smallest <i>Alnus</i>-infective <i>Frankia</i> genomes so far sequenced (~5 Mbp), with 5,178, 6,192 and 5,751 candidate protein-encoding genes for AgTrS, AiOr and AvVan, respectively.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"50-55"},"PeriodicalIF":0.0,"publicationDate":"2019-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.35875","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41202983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Sequence of <i>Kordia</i> sp. Strain SMS9 Identified in a Non-Axenic Culture of the Diatom <i>Skeletonema marinoi</i>.","authors":"Matthew I M Pinder, Oskar N Johansson, Alvar Almstedt, Olga Kourtchenko, Adrian K Clarke, Anna Godhe, Mats Töpel","doi":"10.7150/jgen.35061","DOIUrl":"10.7150/jgen.35061","url":null,"abstract":"<p><p>Initial efforts to sequence the genome of the marine diatom <i>Skeletonema marinoi</i> were hampered by the presence of genetic material from bacteria, and there was sufficient material from some of these bacteria to enable the assembly of full chromosomes. Here, we report the genome of strain SMS9, one such bacterial species identified in a non-axenic culture of <i>S. marinoi</i> strain ST54. Its 5,482,391 bp circular chromosome contains 4,641 CDSs, and has a G+C content of 35.6%. Based on 16S rRNA comparison, phylotaxonomic analysis, and the genome similarity metrics dDDH and OrthoANI, we place this strain in the genus <i>Kordia</i>, and to the best of our knowledge, this is the first <i>Kordia</i> species to be initially described from European waters. As attempts to culture this strain have failed, however, the specifics of its relationship with <i>S. marinoi</i> are still uncertain.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"46-49"},"PeriodicalIF":0.0,"publicationDate":"2019-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/36/1e/jgenv07p0046.PMC6536808.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37310036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metadata Analysis Approaches for Understanding and Improving the Functional Involvement of Rumen Microbial Consortium in Digestion and Metabolism of Plant Biomass.","authors":"Ayyappa Kumar Sista Kameshwar,&nbsp;Luiz Pereira Ramos,&nbsp;Wensheng Qin","doi":"10.7150/jgen.32164","DOIUrl":"10.7150/jgen.32164","url":null,"abstract":"<p><p>Rumen is one of the most complex gastro-intestinal system in ruminating animals. With bountiful of microorganisms supporting in breakdown and consumption of minerals and nutrients from the complex plant biomass. It is predicted that a table spoon of ruminal fluid can reside up to 150 billion microorganisms including various species of bacteria, fungi and protozoa. Several studies in the past have extensively explained about the structural and functional physiology of the rumen. Studies based on rumen and its microbiota has increased significantly in the last decade to understand and reveal applications of the rumen microbiota in food processing, pharmaceutical, biofuel and biorefining industries. Recent high-throughput meta-genomic and proteomic studies have revealed humongous information on rumen microbial diversity. In this study, we have extensively reviewed and reported present-day's progress in understanding the rumen microbial diversity. As of today, NCBI resides about 821,870 records based on rumen with approximately 889 genome sequencing studies. We have retrieved all the rumen-based records from NCBI and extensively catalogued the rumen microbial diversity and the corresponding genomic and proteomic studies respectively. Also, we have provided a brief inventory of metadata analysis software packages and reviewed the metadata analysis approaches for understanding the functional involvement of these microorganisms. Knowing and understanding the present progress on rumen microbiota and performing metadata analysis studies will significantly benefit the researchers in identifying the molecular mechanisms involved in plant biomass degradation. These studies are also necessary for developing highly efficient microorganisms and enzyme mixtures for enhancing the benefits of cattle-feedstock and biofuel industries.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"31-45"},"PeriodicalIF":0.0,"publicationDate":"2019-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.32164","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37342278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SELfies and CELLfies: Whole Genome Sequencing and Annotation of Five Antibiotic Resistant Bacteria Isolated from the Surfaces of Smartphones, An Inquiry Based Laboratory Exercise in a Genomics Undergraduate Course at the Rochester Institute of Technology.","authors":"Anutthaman Parthasarathy,&nbsp;Narayan H Wong,&nbsp;Amanda N Weiss,&nbsp;Susan Tian,&nbsp;Sara E Ali,&nbsp;Nicole T Cavanaugh,&nbsp;Tyler M Chinsky,&nbsp;Chelsea E Cramer,&nbsp;Aditya Gupta,&nbsp;Rakshanda Jha,&nbsp;Loryn K Johnson,&nbsp;Elizabeth D Tuason,&nbsp;Lauren M Klafehn,&nbsp;Varada Krishnadas,&nbsp;Ryan J Musich,&nbsp;Jennifer M Pfaff,&nbsp;Spencer C Richman,&nbsp;Alexandria J Shumway,&nbsp;André O Hudson","doi":"10.7150/jgen.31911","DOIUrl":"https://doi.org/10.7150/jgen.31911","url":null,"abstract":"<p><p>Are touchscreen devices a public health risk for the transmission of pathogenic bacteria, especially those that are resistant to antibiotics? To investigate this, we embarked on a project aimed at isolating and identifying bacteria that are resistant to antibiotics from the screens of smartphones. Touchscreen devices have become ubiquitous in society, and it is important to evaluate the potential risks they pose towards public health, especially as it pertains to the harboring and transmission of pathogenic bacteria that are resistant to antibiotics. Sixteen bacteria were initially isolated of which five were unique (four <i>Staphylococcus</i> species and one <i>Micrococcus</i> species). The genomes of the five unique isolates were subsequently sequenced and annotated. The genomes were analyzed using <i>in silico</i> tools to predict the synthesis of antibiotics and secondary metabolites using the <b>anti</b>biotics and <b>S</b>econdary <b>M</b>etabolite <b>A</b>nalysis <b>SH</b>ell (antiSMASH) tool in addition to the presence of gene clusters that denote resistance to antibiotics using the <b>R</b>esistance <b>G</b>ene <b>I</b>dentifier (RGI) tool. <i>In vivo</i> analysis was also done to assess resistance/susceptibility to four antibiotics that are commonly used in a research laboratory setting. The data presented in this manuscript is the result of a semester-long inquiry based laboratory exercise in the genomics course (BIOL340) in the Thomas H. Gosnell School of Life Sciences/College of Science at the Rochester Institute of Technology.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"26-30"},"PeriodicalIF":0.0,"publicationDate":"2019-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.31911","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37012381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete Genome Sequence of <i>Arthrobacter sp</i>. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert.","authors":"Konosuke Mark Ii,&nbsp;Nobuaki Kono,&nbsp;Ivan Glaucio Paulino-Lima,&nbsp;Masaru Tomita,&nbsp;Lynn Justine Rothschild,&nbsp;Kazuharu Arakawa","doi":"10.7150/jgen.32194","DOIUrl":"https://doi.org/10.7150/jgen.32194","url":null,"abstract":"<p><p><i>Arthrobacter sp.</i> strain MN05-02 is a UV-resistant bacterium isolated from a manganese deposit in the Sonoran Desert, Arizona, USA. The LD₁₀ of this strain is 123 Jm^-2, which is twice that of <i>Escherichia coli</i>, and therefore can be a useful resource for comparative study of UV resistance and the role of manganese on this phenotype. Its complete genome is comprised of a chromosome of 3,488,433 bp and a plasmid of 154,991 bp. The chromosome contains 3,430 putative genes, including 3,366 protein coding genes, 52 tRNA and 12 rRNA genes. Carotenoid biosynthesis operon structure coded within the genome mirrors the characteristic orange-red pigment this bacterium produces, which presumably partly contribute to its UV resistance.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"18-25"},"PeriodicalIF":0.0,"publicationDate":"2019-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.32194","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37011892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Draft Genome Sequence of the Oleaginous Yeast <i>Apiotrichum porosum</i> (syn. <i>Trichosporon porosum</i>) DSM 27194.","authors":"Olga Gorte,&nbsp;Habibu Aliyu,&nbsp;Anke Neumann,&nbsp;Katrin Ochsenreither","doi":"10.7150/jgen.32210","DOIUrl":"https://doi.org/10.7150/jgen.32210","url":null,"abstract":"<p><p>Here, we present the draft genome sequence of <i>Apiotrichum porosum</i> DSM 27194 generated on PacBio platform. Characterization of this oleaginous yeast originally collected from the grassland in Karlsruhe Germany, revealed potential for its utilization as a source of single cell oil (SCO) and gluconic acid (GA). The availability of the genome sequence provides a valuable resource for the elucidation of the genetic processes determining SCO and GA biosynthesis.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"11-13"},"PeriodicalIF":0.0,"publicationDate":"2019-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.32210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37011890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Sequencing and Annotation of <i>Bacillus subtilis</i> UBBS-14 to Ensure Probiotic Safety.","authors":"Ayesha Sulthana,&nbsp;Suvarna G Lakshmi,&nbsp;Ratna Sudha Madempudi","doi":"10.7150/jgen.31170","DOIUrl":"https://doi.org/10.7150/jgen.31170","url":null,"abstract":"<p><p><i>Bacillus subtilis</i> is a rod shaped, gram positive, spore producing bacterium. They are the normal flora of gastrointestinal tract of humans and it is the best characterized model organism for endospore formation. It has the ability to withstand environmental stress, and synthesize beneficial compounds, therefore, it is recognized as a high-quality probiotic supplement. To ensure the probiotic safety and the efficiency, we report the whole genome sequence (WGS) of <i>Bacillus subtilis</i> UBBS-14 strain. The draft genome sequence of <i>Bacillus subtilis</i> UBBS-14 consists of 4,048,984 bp and 4,017 genes, respectively. <i>Bacillus subtilis</i> UBBS-14 does not carry any antibiotic resistant genes containing plasmid, nor it contains any harmful putative virulence factors coding genes, therefore, it confirms the probiotic safety of the respective strain at genome level.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"14-17"},"PeriodicalIF":0.0,"publicationDate":"2019-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.7150/jgen.31170","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37011891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete Genome Sequence of Novel <i>Sulfitobacter pseudonitzschiae</i> Strain SMR1, Isolated from a Culture of the Marine Diatom <i>Skeletonema marinoi</i>.","authors":"Mats Töpel, Matthew I M Pinder, Oskar N Johansson, Olga Kourtchenko, Adrian K Clarke, Anna Godhe","doi":"10.7150/jgen.30559","DOIUrl":"10.7150/jgen.30559","url":null,"abstract":"<p><p>When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of <i>Skeletonema marinoi</i> strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp. After phylotaxonomic analysis and 16S rRNA sequence comparison, we place this strain in the taxon <i>Sulfitobacter pseudonitzschiae</i> on account of similarity to the type strain. The annotated genome suggests similar interactions between strain SMR1 and its host diatom as have been shown previously in diatom-associated <i>Sulfitobacter</i>, for example bacterial production of growth hormone for its host, and breakdown of diatom-derived DMSP by <i>Sulfitobacter</i> for use as a sulfur source.</p>","PeriodicalId":15834,"journal":{"name":"Journal of Genomics","volume":"7 ","pages":"7-10"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d7/8a/jgenv07p0007.PMC6328299.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36880959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}