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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/29156585/pan-cellulosomics-of-mesophilic-clostridia-variations-on-a-theme
#1
Bareket Dassa, Ilya Borovok, Vincent Lombard, Bernard Henrissat, Raphael Lamed, Edward A Bayer, Sarah Moraïs
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature...
November 18, 2017: Microorganisms
https://www.readbyqxmd.com/read/29155033/the-gut-virome-of-the-protochordate-model-organism-ciona-intestinalis-subtype-a
#2
Brittany A Leigh, Anni Djurhuus, Mya Breitbart, Larry J Dishaw
The identification of host-specific bacterial and viral communities associated with diverse animals has led to the concept of the metaorganism, which defines the animal and all of its associated microbes as a single unit. Here we sequence the viruses found in the gut (i.e., the gut virome) of the marine invertebrate model system, Ciona intestinalis subtype A, in samples collected one year apart. We present evidence for a host-associated virome that is distinct from the surrounding seawater and contains some temporally-stable members...
November 15, 2017: Virus Research
https://www.readbyqxmd.com/read/29155030/transcriptome-analysis-and-discovery-of-genes-involved-in-immune-pathways-from-coelomocytes-of-onchidium-struma-after-bacterial-challenge
#3
Mingming Zhang, Guo Qiao, Qiang Li, De-Hai Xu, Zhitao Qi, Aiming Wang, Mengyao Xu, Jintian Huang
Onchidium struma widely distributes in subtidal and low-tidal zones, which is considered to be an economical species with rich nutrition, a valuable biomonitor for heavy metal pollution and a representative species for evolution from ocean to land. However, there is limited genetic information available for O. struma development. This study compared transcriptomic profiles of coelomocytes from normal and bacteria infected O. struma by Illumina-based paired-end sequencing to explore the molecular immune mechanism of O...
November 15, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29153620/targeted-dna-enrichment-and-whole-genome-sequencing-of-neisseria-meningitidis-directly-from-clinical-specimens
#4
Stephen A Clark, Ronan Doyle, Jay Lucidarme, Ray Borrow, Judith Breuer
In England and Wales, approximately one half of all laboratory-confirmed meningococcal disease cases fail to yield a viable invasive isolate, primarily due to the use of antibiotics. Characterisation of non-culture meningococci has been restricted to the detection or sequencing of specific gene targets within clinical specimens. In this study we investigated the ability of the Agilent SureSelectXT kit to facilitate DNA enrichment and genome sequencing of meningococcal DNA within a small panel of blood and CSF specimens...
November 13, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29153320/novel-microbial-diversity-and-functional-potential-in-the-marine-mammal-oral-microbiome
#5
Natasha K Dudek, Christine L Sun, David Burstein, Rose S Kantor, Daniela S Aliaga Goltsman, Elisabeth M Bik, Brian C Thomas, Jillian F Banfield, David A Relman
The vast majority of bacterial diversity lies within phylum-level lineages called "candidate phyla," which lack isolated representatives and are poorly understood. These bacteria are surprisingly abundant in the oral cavity of marine mammals. We employed a genome-resolved metagenomic approach to recover and characterize genomes and functional potential from microbes in the oral gingival sulcus of two bottlenose dolphins (Tursiops truncatus). We detected organisms from 24 known bacterial phyla and one archaeal phylum...
November 8, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29152584/large-scale-bioinformatics-analysis-of-bacillus-genomes-uncovers-conserved-roles-of-natural-products-in-bacterial-physiology
#6
Kirk J Grubbs, Rachel M Bleich, Kevin C Santa Maria, Scott E Allen, Sherif Farag, Elizabeth A Shank, Albert A Bowers
Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs...
November 2017: MSystems
https://www.readbyqxmd.com/read/29152409/long-adapter-single-strand-oligonucleotide-probes-for-the-massively-multiplexed-cloning-of-kilobase-genome-regions
#7
Lorenzo Tosi, Viswanadham Sridhara, Yunlong Yang, Dongli Guan, Polina Shpilker, Nicola Segata, H Benjamin Larman, Biju Parekkadan
As the catalogue of sequenced genomes and metagenomes continues to grow, massively parallel approaches for the comprehensive and functional analysis of gene products and regulatory elements are becoming increasingly valuable. Current strategies to synthesize or clone complex libraries of DNA sequences are limited by the length of the DNA targets, throughput and cost. Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA fragments in a single reaction...
2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/29152310/genome-resequencing-and-transcriptome-profiling-reveal-structural-diversity-and-expression-patterns-of-constitutive-disease-resistance-genes-in-huanglongbing-tolerant-poncirus-trifoliata-and-its-hybrids
#8
Nidhi Rawat, Brajendra Kumar, Ute Albrecht, Dongliang Du, Ming Huang, Qibin Yu, Yi Zhang, Yong-Ping Duan, Kim D Bowman, Fred G Gmitter, Zhanao Deng
Huanglongbing (HLB) is the most destructive bacterial disease of citrus worldwide. While most citrus varieties are susceptible to HLB, Poncirus trifoliata, a close relative of Citrus, and some of its hybrids with Citrus are tolerant to HLB. No specific HLB tolerance genes have been identified in P. trifoliata but recent studies have shown that constitutive disease resistance (CDR) genes were expressed at much higher levels in HLB-tolerant Poncirus hybrids and the expression of CDR genes was modulated by Candidatus Liberibacter asiaticus (CLas), the pathogen of HLB...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29148362/pseudomonas-floridensis-sp-nov-a-bacterial-pathogen-isolated-from-tomato
#9
Sujan Timilsina, Gerald V Minsavage, James Preston, Eric A Newberry, Matthews L Paret, Erica M Goss, Jeffrey B Jones, Gary E Vallad
An unusual fluorescent pseudomonad was isolated from tomato exhibiting leaf spot symptoms similar to bacterial speck. Strains were fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco and produced a soft rot on potato slices. However, the strains produced an unusual yellow, mucoid growth on media containing 5 % sucrose that is not typical of levan. Based on multilocus sequence analysis using 16S rRNA, gap1, gltA, gyrB and rpoD, these strains formed a distinct phylogenetic group in the genus Pseudomonas and were most closely related to Pseudomonas viridiflava within the Pseudomonassyringae complex...
November 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29147991/the-role-of-the-gut-microbiome-in-multiple-sclerosis-risk-and-progression-towards-characterization-of-the-ms-microbiome
#10
REVIEW
Anne-Katrin Pröbstel, Sergio E Baranzini
Multiple sclerosis (MS) is the prototypic complex disease, in which both genes and the environment contribute to its pathogenesis. To date, > 200 independent loci across the genome have been associated with MS risk. However, these only explain a fraction of the total phenotypic variance, suggesting the possible presence of additional genetic factors, and, most likely, also environmental factors. New DNA sequencing technologies have enabled the sequencing of all kinds of microorganisms, including those living in and around humans (i...
November 16, 2017: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29146856/complete-genome-sequence-of-xanthomonas-campestris-pv-viticola-strain-ccrmxcv-80-from-brazil
#11
Nelson B Lima, Marco A S Gama, Rosa L R Mariano, Wilson J Silva, Antônio R G Farias, Raul M Falcão, Lucas C Sousa-Paula, Ana M Benko-Iseppon, Sérgio S L Paiva, Valdir Q Balbino, Elineide B Souza
Here, we report the complete 5.3-Mb genome sequence of Xanthomonas campestris pv. viticola (CCRMXCV 80), which causes grapevine (Vitis vinifera L.) bacterial canker. Genome data will improve our understanding of the strain's comparative genomics and epidemiology, and help to further define plant protection and quarantine procedures.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146837/draft-genome-sequence-of-the-naturally-competent-bacillus-simplex-strain-wy10
#12
Eric C Keen, Valery V Bliskovsky, Sankar L Adhya, Gautam Dantas
We sequenced a naturally competent bacterial isolate, WY10, cultured from a Wyoming soil sample. Sequence analysis revealed that WY10 is a novel strain of Bacillus simplex To our knowledge, WY10 is the first B. simplex strain to be characterized as naturally competent for DNA uptake by transformation.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146152/improved-antifungal-activity-of-barley-derived-chitinase-i-gene-that-overexpress-a-32kda-recombinant-chitinase-in-escherichia-coli-host
#13
Nida Toufiq, Bushra Tabassum, Muhammad Umar Bhatti, Anwar Khan, Muhammad Tariq, Naila Shahid, Idrees Ahmad Nasir, Tayyab Husnain
Agricultural crops suffer many diseases, including fungal and bacterial infections, causing significant yield losses. The identification and characterisation of pathogenesis-related protein genes, such as chitinases, can lead to reduction in pathogen growth, thereby increasing tolerance against fungal pathogens. In the present study, the chitinase I gene was isolated from the genomic DNA of Barley (Hordeum vulgare L.) cultivar, Haider-93. The isolated DNA was used as template for the amplification of the ∼935bp full-length chitinase I gene...
October 31, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29145643/the-merops-database-of-proteolytic-enzymes-their-substrates-and-inhibitors-in-2017-and-a-comparison-with-peptidases-in-the-panther-database
#14
Neil D Rawlings, Alan J Barrett, Paul D Thomas, Xiaosong Huang, Alex Bateman, Robert D Finn
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145635/trex-a-web-portal-for-exploration-of-trna-derived-fragments-in-arabidopsis-thaliana
#15
Agnieszka Thompson, Andrzej Zielezinski, Patrycja Plewka, Maciej Szymanski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Wojciech M Karlowski
tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio...
November 14, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29145627/bacterial-communities-associated-with-the-ectoparasitic-mites-varroa-destructor-and-tropilaelaps-mercedesae-of-honey-bees-apis-mellifera
#16
Chonthicha Pakwan, Martin Kaltenpoth, Benjamin Weiss, Panuwan Chantawannakul, Guo Jun, Terd Disayathanoowat
Varroa and Tropilaelaps mites have been reported as serious ectoparasites of honey bees (Apis mellifera). In this study, bacterial communities associated with Varroa destructor and Tropilaelaps mercedesae from Northern Thailand were determined, using both culture-dependent and culture-independent approaches. Adult female mites were collected from apiaries in Chiang Mai and Lampang provinces. Culturable bacteria were isolated from individual mites. On average, we observed approximately 1340 and 1140 CFU/mite in Varroa and Tropilaelaps, respectively...
November 14, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#17
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29143556/datalbase-a-database-for-genomic-and-transcriptomic-data-related-to-tal-effectors
#18
Alvaro L Pérez-Quintero, Léo Lamy, Carlos A Zarate, Sébastien Cunnac, Erin L Doyle, Adam J Bogdanove, Boris Szurek, Alexis Derepeer
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility S genes, triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs' amino acid sequence. New candidate susceptibility genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements (EBEs)...
November 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29142289/comprehensive-genomic-analysis-of-a-plant-growth-promoting-rhizobacterium-pantoea-agglomerans-strain-p5
#19
Vahid Shariati J, Mohammad Ali Malboobi, Zeinab Tabrizi, Elahe Tavakol, Parviz Owilia, Maryam Safari
In this study, we provide a comparative genomic analysis of Pantoea agglomerans strain P5 and 10 closely related strains based on phylogenetic analyses. A next-generation shotgun strategy was implemented using the Illumina HiSeq 2500 technology followed by core- and pan-genome analysis. The genome of P. agglomerans strain P5 contains an assembly size of 5082485 bp with 55.4% G + C content. P. agglomerans consists of 2981 core and 3159 accessory genes for Coding DNA Sequences (CDSs) based on the pan-genome analysis...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142049/the-occurrence-and-nature-of-double-alleles-in-vntr-patterns-of-more-than-8-000-mycobacterium-tuberculosis-complex-isolates-in-the-netherlands
#20
Rana Jajou, Miranda Kamst, Rianne van Hunen, Carolina Catherina de Zwaan, Arnout Mulder, Philip Supply, Richard Anthony, Wim van der Hoek, Dick van Soolingen
Background: Since 2004, variable number of tandem repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern.Methods/results: In the period 2004 -- 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, of which 186 (2...
November 15, 2017: Journal of Clinical Microbiology
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