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Bacterial genome sequencing

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https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#1
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820099/hymenobacter-pallidus-sp-nov-isolated-from-a-freshwater-fish-culture-pond
#2
Shih-Yi Sheu, Yi-Shu Li, Chiu-Chung Young, Wen-Ming Chen
A bacterial strain designated LYH-12T was isolated from a freshwater fish culture pond in Taiwan, ROC and characterized by taking a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LYH-12T belonged to the genus Hymenobacter and was most closely related to Hymenobacter xinjiangensis X2-1gT and Hymenobacter rigui WPCB131T with a sequence similarity of 96.6 % and less than 96.5 % with other members of the genus. Cells of strain LYH-12T were Gram-stain-negative, aerobic, non-motile rods that were covered by large capsules and formed light pink-coloured colonies...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28820086/stenotrophomonas-bentonitica-sp-nov-isolated-from-bentonite-formations
#3
Iván Sánchez-Castro, Miguel Angel Ruiz-Fresneda, Mohammed Bakkali, Peter Kämpfer, Stefanie P Glaeser, Hans Jürgen Busse, Margarita López-Fernández, Pablo Martínez-Rodríguez, Mohamed Larbi Merroun
A Gram-stain negative, rod-shaped, aerobic bacterial strain, BII-R7T, was isolated during a study targeting the culture-dependent microbial diversity occurring in bentonite formations from southern Spain. Comparative 16S rRNA gene sequence analysis showed that BII-R7T represented a member of the genus Stenotrophomonas (class Gammaproteobacteria), and was related most closely to Stenotrophomonas rhizophila e-p10T (99.2 % sequence similarity), followed by Stenotrophomonas pavanii ICB 89T (98.5 %), Stenotrophomonas maltophilia IAM 12423T, Stenotrophomonas chelatiphaga LPM-5T and Stenotrophomonas tumulicola T5916-2-1bT (all 98...
August 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28819111/community-outbreaks-of-group-a-streptococcus-revealed-by-genome-sequencing
#4
Claire E Turner, Luke Bedford, Nicholas M Brown, Kim Judge, M Estée Török, Julian Parkhill, Sharon J Peacock
The frequent occurrence of disease outbreaks in humans caused by group A Streptococcus (GAS) is an on-going public health threat. Conventional bacterial typing methods lack the discriminatory power to confidently confirm or refute outbreaks in hospital and community settings. Microbial whole genome sequencing (WGS) provides a potential solution to this, but, there has been limited population-based surveillance with accompanying sequence data. We performed retrospective genomic surveillance of 93 clinical GAS isolates from individuals in a defined geographic region...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818616/molecular-insights-of-two-stat1-variants-from-rock-bream-oplegnathus-fasciatus-and-their-transcriptional-regulation-in-response-to-pathogenic-stress-interleukin-10-and-tissue-injury
#5
S D N K Bathige, Navaneethaiyer Umasuthan, G I Godahewa, William Shanthakumar Thulasitha, J D H E Jayasinghe, Qiang Wan, Jehee Lee
Signal transducers and activators of transcription 1 (STAT1) is critically involved in mediating cytokine-driven signaling, and triggers the transcription of target genes to activate cellular functions. Although the structural and functional aspects of STAT members have been well described in mammals, only limited information is available for the STAT genes in teleost fishes. In the present study, two variants of STAT1 genes (RbSTAT1 and RbSTAT1L) were identified from rock bream and characterized at the cDNA and genomic sequence levels...
August 14, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28814272/identification-of-new-protein-coding-genes-with-a-potential-role-in-the-virulence-of-the-plant-pathogen-xanthomonas-euvesicatoria
#6
Ulrike Abendroth, Norman Adlung, Andreas Otto, Benjamin Grüneisen, Dörte Becher, Ulla Bonas
BACKGROUND: Bacteria of the genus Xanthomonas are economically important plant pathogens. Pathogenicity of Xanthomonas spp. depends on the type III-secretion system and additional virulence determinants. The number of sequenced Xanthomonas genomes increases rapidly, however, accurate annotation of these genomes is difficult, because it relies on gene prediction programs. In this study, we used a mass-spectrometry (MS)-based approach to identify the proteome of Xanthomonas euvesicatoria (Xe) strain 85-10 also known as X...
August 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28813779/dna-profiling-of-leuconostoc-citreum-strains-in-fermented-foods-by-repetitive-element-polymerase-chain-reaction
#7
Jasmine Kaur, Anshul Sharma, Sulhee Lee, Young-Seo Park
To identify and discriminate the bacterial species at the sub-specific level, rep-PCR method is a reliable genomic fingerprinting tool. Fourteen strains of bacteria were isolated from different food sources, identified as Leuconostoc citreum using 16S rRNA gene sequencing and amplified using rep-primers (REP, ERIC, and (GTG)5). Fingerprinting patterns generated band range in between 300-6000 bp with REP, 150-6000bp with ERIC and 200-1700 bp with (GTG)5 primers respectively. In UPGMA dendrogram analysis, 14 strains were clustered into three clades (I, II and III) with all the primers, thus differentiating them at the molecular level...
August 17, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#8
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811342/bacteriophages-of-gordonia-spp-display-a-spectrum-of-diversity-and-genetic-relationships
#9
Welkin H Pope, Travis N Mavrich, Rebecca A Garlena, Carlos A Guerrero-Bustamante, Deborah Jacobs-Sera, Matthew T Montgomery, Daniel A Russell, Marcie H Warner, Graham F Hatfull
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are "singletons" with no closely related genomes...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28810827/validation-of-%C3%AE-lactam-minimum-inhibitory-concentration-predictions-for-pneumococcal-isolates-with-newly-encountered-penicillin-binding-protein-pbp-sequences
#10
Yuan Li, Benjamin J Metcalf, Sopio Chochua, Zhongya Li, Robert E Gertz, Hollis Walker, Paulina A Hawkins, Theresa Tran, Lesley McGee, Bernard W Beall
BACKGROUND: Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type)...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28809151/the-pentameric-complex-of-human-cytomegalovirus-cell-tropism-virus-dissemination-immune-response-and-vaccine-development
#11
Giuseppe Gerna, Maria Grazia Revello, Fausto Baldanti, Elena Percivalle, Daniele Lilleri
Between the 1980s and 1990s, three assays were developed for diagnosis of human cytomegalovirus (HCMV) infections: leuko (L)-antigenemia, l-viremia and l-DNAemia, detecting viral protein pp65, infectious virus and viral DNA, respectively, in circulating leukocytes Repeated initial attempts to reproduce the three assays in vitro using laboratory-adapted strains and infected cell cultures were consistently unsuccessful. Results were totally reversed when wild-type HCMV strains were used to infect either fibroblasts or endothelial cells...
August 15, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28809148/flaviaesturariibacter-terrae-sp-nov-isolated-from-mountain-soil
#12
Joseph Okiria, Jae-Jin Lee, Su-Jin Park, Yeon-Hee Lee, Seung-Yeol Lee, Sangkyu Park, Byung-Oh Kim, Leonid N Ten, Hee-Young Jung
A Gram-stain-negative, aerobic, rod-shaped, non-motile and pale yellow-pigmented bacterial strain, designated as HY03T, was isolated from mountain soil. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HY03T belonged to the family Chitinophagaceae in the phylum Bacteroidetes and was most closely related to Flaviaesturariibacter amylovorans GCR0105T at a similarity of 95.4 %. The genomic DNA G+C content of strain HY03T was 43.2 mol%. The major fatty acids of the isolate were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH...
August 15, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28807759/development-of-a-highly-resolved-loop-mediated-isothermal-amplification-method-to-detect-the-n526k-ftsi-mutation-of-%C3%AE-lactamase-negative-ampicillin-resistant-haemophilus-influenzae
#13
Shinsuke Tamura, Takuya Maeda, Kazuhisa Misawa, Morichika Osa, Takaaki Hamamoto, Atsushi Yuki, Kazuo Imai, Kei Mikita, Kyoko Morichika, Akihiko Kawana, Hiroshi Matsumoto, Shigeaki Nonoyama
Rapid and easy detection of sequence polymorphisms, including nucleotide point mutations of bacterial pathogens responsible for amino acid substitutions linked to drug resistance, is essential for the proper use of antimicrobial agents. Here, a detection method using loop-mediated amplification (LAMP) combined with amplification refractory mutation system (ARMS) to accurately distinguish a different single nucleotide in the target sequence was established, named ARMS-SNP LAMP. This procedure is capable of species-specific detection of a nucleotide (1578T) in the ftsI gene on Haemophilus influenzae without amplifying the sequence carrying the point mutations (T1578G/A) in β-lactamase-negative ampicillin resistant (BLNAR) strains...
August 11, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#14
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28802023/the-agrobacterium-vire2-effector-interacts-with-multiple-members-of-the-arabidopsis-vip1-protein-family
#15
Luyao Wang, Benoît Lacroix, Jianhua Guo, Vitaly Citovsky
T-DNA transfer from Agrobacterium to its host plant genome relies on multiple interactions between plant proteins and bacterial effectors. One of such plant proteins is the Arabidopsis VirE2 interacting protein (AtVIP1), a transcription factor that binds A. tumefaciens C58 VirE2, potentially acting as an adaptor between VirE2 and several other host factors. It remains unknown, however, whether the same VirE2 protein has evolved to interact with multiple VIP1 homologs in the same host, and whether VirE2 homologs encoded by different bacterial strains/species recognize AtVIP1 or its homologs...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28800583/the-nucleoid-protein-dps-binds-genomic-dna-of-escherichia-coli-in-a-non-random-manner
#16
S S Antipov, M N Tutukina, E V Preobrazhenskaya, F A Kondrashov, M V Patrushev, S V Toshchakov, I Dominova, U S Shvyreva, V V Vrublevskaya, O S Morenkov, N A Sukharicheva, V V Panyukov, O N Ozoline
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity...
2017: PloS One
https://www.readbyqxmd.com/read/28799224/genomic-insights-into-the-pathogenicity-and-environmental-adaptability-of-enterococcus-hirae-r17-isolated-from-pork-offered-for-retail-sale
#17
Zixin Peng, Menghan Li, Wei Wang, Hongtao Liu, Séamus Fanning, Yujie Hu, Jianzhong Zhang, Fengqin Li
Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin-resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC(™) 9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E...
August 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28798165/complete-genome-sequences-of-three-isolates-of-xanthomonas-fragariae-the-bacterium-responsible-for-angular-leaf-spots-on-strawberry-plants
#18
Michael Gétaz, Jan M van der Wolf, Jochen Blom, Joël F Pothier
Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf spots, thus reducing the yield of production for strawberry fruits. Three isolates with various geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genome sequences of virulent strains and observe the variability in their contents.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28797211/disulfide-bonds-a-key-modification-in-bacterial-extracytoplasmic-proteins
#19
S F Lee, L Davey
Disulfide bonds are a common posttranslational modification that contributes to the folding and stability of extracytoplasmic proteins. Almost all organisms, from eukaryotes to prokaryotes, have evolved enzymes to make and break these bonds. Accurate and efficient disulfide bond formation can be vital for protein function; therefore, the enzymes that catalyze disulfide bond formation are involved in multiple biological processes. Recent advances clearly show that oral bacteria also have the ability to from disulfide bonds, and this ability has an effect on a range of dental plaque-related phenotypes...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28797043/next-generation-sequencing-reveals-the-antibiotic-resistant-variants-in-the-genome-of-pseudomonas-aeruginosa
#20
Babu Ramanathan, Hassan Mahmood Jindal, Cheng Foh Le, Ranganath Gudimella, Arif Anwar, Rozaimi Razali, Johan Poole-Johnson, Rishya Manikam, Shamala Devi Sekaran
Rapid progress in next generation sequencing and allied computational tools have aided in identification of single nucleotide variants in genomes of several organisms. In the present study, we have investigated single nucleotide polymorphism (SNP) in ten multi-antibiotic resistant Pseudomonas aeruginosa clinical isolates. All the draft genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) web server and the predicted protein sequences were used for comparison. Non-synonymous single nucleotide polymorphism (nsSNP) found in the clinical isolates compared to the reference genome (PAO1), and the comparison of nsSNPs between antibiotic resistant and susceptible clinical isolates revealed insights into the genome variation...
2017: PloS One
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