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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/28335474/coccolithoviruses-a-review-of-cross-kingdom-genomic-thievery-and-metabolic-thuggery
#1
Jozef I Nissimov, António Pagarete, Fangrui Ma, Sean Cody, David D Dunigan, Susan A Kimmance, Michael J Allen
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28334833/chip-seq-analysis-of-the-luxr-type-regulator-vjbr-reveals-novel-insights-into-the-brucella-virulence-gene-expression-network
#2
Claudia L Kleinman, Gabriela Sycz, Hernán R Bonomi, Romina M Rodríguez, Angeles Zorreguieta, Rodrigo Sieira
LuxR-type transcription factors control diverse physiological functions necessary for bacterial adaptation to environmental changes. In the intracellular pathogen Brucella, the LuxR homolog VjbR has been shown to regulate the expression of virulence factors acting at early stages of the intracellular infection and, directly or indirectly, hundreds of additional genes. However, the precise determination of VjbR direct targets has so far proved elusive. Here, we performed chromatin immunoprecipitation of VjbR followed by next-generation sequencing (ChIP-seq)...
March 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334154/ethical-issues-of-crispr-technology-and-gene-editing-through-the-lens-of-solidarity
#3
John J Mulvihill, Benjamin Capps, Yann Joly, Tamra Lysaght, Hub A E Zwart, Ruth Chadwick
Background: The avalanche of commentaries on CRISPR-Cas9 technology, a bacterial immune system modified to recognize any short DNA sequence, cut it out, and insert a new one, has rekindled hopes for gene therapy and other applications and raised criticisms of engineering genes in future generations. Sources of data: This discussion draws on articles that emphasize ethics, identified partly through PubMed and Google, 2014-2016. Areas of agreement: CRISPR-Cas9 has taken the pace and prospects for genetic discovery and applications to a high level, stoking anticipation for somatic gene engineering to help patients...
February 23, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#4
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#5
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#6
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28326685/hugonella-massiliensis-gen-nov-sp-nov-genome-sequence-and-description-of-a-new-strictly-anaerobic-bacterium-isolated-from-the-human-gut
#7
Ziena Elsawi, Amadou Hamidou Togo, Mamadou Beye, Grégory Dubourg, Claudia Andrieu, Nicholas Armsrtong, Magali Richez, Fabrizio di Pinto, Fadi Bittar, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Saber Khelaifia
The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8(T) (=CSUR P2118 =  DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8(T) is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities...
March 21, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28326093/the-complete-chloroplast-genome-of-wild-rice-oryza-minuta-and-its-comparison-to-related-species
#8
Sajjad Asaf, Muhammad Waqas, Abdul L Khan, Muhammad A Khan, Sang-Mo Kang, Qari M Imran, Raheem Shahzad, Saqib Bilal, Byung-Wook Yun, In-Jung Lee
Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28323406/affinity-selection-mass-spectrometry-identifies-a-novel-antibacterial-rna-polymerase-inhibitor
#9
Scott S Walker, David Degen, Elliott Nickbarg, Donna Carr, Aileen Soriano, Mihir Baran Mandal, Ronald E Painter, Payal R Sheth, Li Xiao, Xinwei Sher, Nicholas Murgolo, Jing Su, David B Olsen, Richard H Ebright, Katherine Young
The growing prevalence of drug-resistant Gram-negative bacteria is a significant global threat to human health. Rifampicin, an RNA polymerase-targeting agent, is an important part of the antibacterial armamentarium; however the emergence of resistance requires that it be used against only certain infections and usually in combination with another antibiotic. While rifampicin has significant clinical limitations, it does show that bacterial RNA polymerase can be an effective target for antibacterial intervention...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28321010/discovery-and-complete-genome-sequence-of-a-bacteriophage-from-an-obligate-intracellular-symbiont-of-a-cellulolytic-protist-in-the-termite-gut
#10
Ajeng K Pramono, Hirokazu Kuwahara, Takehiko Itoh, Atsushi Toyoda, Akinori Yamada, Yuichi Hongoh
Termites depend nutritionally on their gut microbes, and protistan, bacterial, and archaeal gut communities have been extensively studied. However, limited information is available on viruses in the termite gut. We herein report the complete genome sequence (99,517 bp) of a phage obtained during a genome analysis of "Candidatus Azobacteroides pseudotrichonymphae" phylotype ProJPt-1, which is an obligate intracellular symbiont of the cellulolytic protist Pseudotrichonympha sp. in the gut of the termite Prorhinotermes japonicus...
March 17, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28320301/characterization-of-two-recombinant-3-hexulose-6-phosphate-synthases-from-the-halotolerant-obligate-methanotroph-methylomicrobium-alcaliphilum-20z
#11
O N Rozova, S Y But, V N Khmelenina, A S Reshetnikov, I I Mustakhimov, Y A Trotsenko
Two key enzymes of the ribulose monophosphate (RuMP) cycle for formaldehyde fixation, 3-hexulose-6-phosphate synthase (HPS) and 6-phospho-3-hexulose isomerase (PHI), in the aerobic halotolerant methanotroph Methylomicrobium alcaliphilum 20Z are encoded by the genes hps and phi and the fused gene hps-phi. The recombinant enzymes HPS-His6, PHI-His6, and the two-domain protein HPS-PHI were obtained by heterologous expression in Escherichia coli and purified by affinity chromatography. PHI-His6, HPS-His6 (2 × 20 kDa), and the fused protein HPS-PHI (2 × 40 kDa) catalyzed formation of fructose 6-phosphate from formaldehyde and ribulose-5-phosphate with activities of 172 and 22 U/mg, respectively...
February 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#12
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28316574/alterations-of-urinary-microbiota-in-type-2-diabetes-mellitus-with-hypertension-and-or-hyperlipidemia
#13
Fengping Liu, Zongxin Ling, Yonghong Xiao, Qing Yang, Baohong Wang, Li Zheng, Ping Jiang, Lanjuan Li, Wei Wang
Evidence shows urine specimens from different women have different populations of bacteria. The co-occurrence of hypertension and hyperlipidemia in those with diabetes may alter the composition of urine and the microenviroment of the bladder in which bacteria live. The aim of this study was to characterize the urinary microbiota in women with type 2 diabetes mellitus only and those with diabetes plus hypertension and/or hyperlipidemia, and to explore whether the composition of the urinary microbiota is affected by fasting blood glucose, blood pressure, and blood lipids...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28316324/spatial-organization-of-dna-sequences-directs-the-assembly-of-bacterial-chromatin-by-a-nucleoid-associated-protein
#14
Aleksandre Japarize, Sylvain Renevey, Parick Sobetzko, Liubov Stoliar, William Nasser, Giovanni Dietler, Georgi Muskhelishvili
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS binding sequences in the assembly of long-range nucleoprotein structures remains unknown...
March 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28316093/morphology-heterogeneity-within-a-campylobacter-jejuni-helical-population-the-use-of-calcofluor-white-to-generate-rod-shaped-c-jejuni-81-176-clones-and-the-genetic-determinants-responsible-for-differences-in-morphology-within-11168-strains
#15
Emilisa Frirdich, Jacob Biboy, Steven Huynh, Craig T Parker, Waldemar Vollmer, Erin C Gaynor
Campylobacter jejuni helical shape is important for colonization and host interactions with straight mutants having altered biological properties. Passage on calcofluor white (CFW) resulted in C. jejuni 81-176 isolates with morphology changes: either a straight morphology from frameshift mutations and single nucleotide polymorphisms in peptidoglycan hydrolase genes pgp1 or pgp2 or a reduction in curvature due a frameshift mutation in cjj81176_1105, a putative peptidoglycan endopeptidase. Shape defects were restored by complementation...
March 18, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28314921/comparative-genomics-analysis-of-five-psychrobacter-strains-isolated-from-world-wide-habitats-reveal-high-intra-genus-variations
#16
Shan Zhang, Weizhi Song, Min Yu, Xuezheng Lin
Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96...
March 17, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28314727/transcriptomic-analyses-elucidate-adaptive-differences-of-closely-related-strains-of-p-aeruginosa-in-fuel
#17
Thusitha S Gunasekera, Loryn L Bowen, Carol E Zhou, Susan C Howard-Byerly, William S Foley, Richard C Striebich, Larry C Dugan, Oscar N Ruiz
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28306363/genome-database-mining-for-the-discovery-of-novel-lantibiotics
#18
Stephanie K Sandiford
The effectiveness of lantibiotics against MDR pathogens and the progression of agents MU1140, NAI-107, NVB302 and duramycin into pre-clinical and clinical trials have highlighted their potential in the fight against bacterial resistance. The number of known lantibiotics and knowledge of their biosynthetic pathways has increased in recent years due to higher quality genomic data being delivered by next generation sequencing technologies combined with the development of specific genome mining tools, enabling the prediction of lantibiotic clusters...
March 17, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28303813/molecular-typing-of-chlamydia-trachomatis-an-overview
#19
REVIEW
Jyoti Rawre, Deepak Juyal, Benu Dhawan
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease and its transmission dynamics in sexual networks. Traditionally, strain typing of CT was based on serotyping methods characterising the major outer membrane protein (MOMP). With the advent of polymerase chain reaction and sequencing the era of molecular typing began...
January 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28303404/phylogenetic-analysis-of-proteins-involved-in-the-stringent-response-in-plant-cells
#20
Doshun Ito, Yuta Ihara, Hidenori Nishihara, Shinji Masuda
The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear...
March 16, 2017: Journal of Plant Research
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