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Bacterial genomics

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https://www.readbyqxmd.com/read/28938018/genome-wide-identification-of-bacterial-plant-colonization-genes
#1
Benjamin J Cole, Meghan E Feltcher, Robert J Waters, Kelly M Wetmore, Tatiana S Mucyn, Elizabeth M Ryan, Gaoyan Wang, Sabah Ul-Hasan, Meredith McDonald, Yasuo Yoshikuni, Rex R Malmstrom, Adam M Deutschbauer, Jeffery L Dangl, Axel Visel
Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28937735/whole-genome-shotgun-sequencing-and-comparison-of-two-%C3%AE-proteobacterial-species-in-search-of-the-bulgecin-biosynthetic-cluster
#2
Mark E Horsman, Daniel R Marous, Rongfeng Li, Ryan A Oliver, Byungjin Byun, Scott J Emrich, Bill Boggess, Craig A Townsend, Shahriar Mobashery
We have produced draft whole-genome sequences for two bacterial strains reported to produce the bulgecins as well as NRPS-derived monobactam β-lactam antibiotics. We propose reclassification of ATCC 31363 from the original Pseudomonas genus to Paraburkholderia acidophila. We further reaffirm that ATCC 31433 (Burkholderia mesoacidophila) is a taxonomically distinct producer of bulgecins with notable gene regions shared with Paraburkholderia acidophila. We use RAST multiple gene comparison and MASH distancing with published genomes to order the draft contigs and identify unique gene regions for characterization...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28936944/bacterial-endosymbionts-master-modulators-of-fungal-phenotypes
#3
Sarah J Araldi-Brondolo, Joseph Spraker, Justin P Shaffer, Emma H Woytenko, David A Baltrus, Rachel E Gallery, A Elizabeth Arnold
The ecological modes of fungi are shaped not only by their intrinsic features and the environment in which they occur, but also by their interactions with diverse microbes. Here we explore the ecological and genomic features of diverse bacterial endosymbionts-endohyphal bacteria-that together are emerging as major determinants of fungal phenotypes and plant-fungi interactions. We first provide a historical perspective on the study of endohyphal bacteria. We then propose a functional classification of three main groups, providing an overview of their genomic, phylogenetic, and ecological traits...
September 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28936425/gut-dysbiosis-in-animals-due-to-environmental-chemical-exposures
#4
REVIEW
Cheryl S Rosenfeld
The gut microbiome consists of over 10(3)-10(4) microorganism inhabitants that together possess 150 times more genes that the human genome and thus should be considered an "organ" in of itself. Such communities of bacteria are in dynamic flux and susceptible to changes in host environment and body condition. In turn, gut microbiome disturbances can affect health status of the host. Gut dysbiosis might result in obesity, diabetes, gastrointestinal, immunological, and neurobehavioral disorders. Such host diseases can originate due to shifts in microbiota favoring more pathogenic species that produce various virulence factors, such as lipopolysaccharide...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28935751/genome-sequence-of-bacillus-safensis-strain-ingolstadt-isolated-from-the-pectoralis-pouch-of-a-patient-with-defibrillator-related-surgery
#5
Flavia Dematheis, Markus H Antwerpen, Gregor Grass, Mathias C Walter, Stefan Borgmann
We report the draft genome sequence of clindamycin-resistant Bacillus safensis strain Ingolstadt isolated from a patient with bacterial colonization after heart surgery. The draft genome comprises 3.75 Mbp and harbors 3,793 predicted protein-encoding genes and a small plasmid.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935749/complete-genome-sequence-of-actinobacillus-pleuropneumoniae-strain-kl-16-serotype-1
#6
Byung-Sun Park, Jemin Han, Dong-Ju Shin, Young-Ju Jeong, Nakhyung Lee
Actinobacillus pleuropneumoniae is a bacterial pathogen causing highly contagious porcine pleuropneumonia. Due to limited information on this species, it is difficult to study the biology of A. pleuropneumoniae at the genome level. Here, we report the fully annotated genome sequence of A. pleuropneumoniae strain KL 16.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935737/draft-genome-sequence-of-listeria-monocytogenes-strain-atcc-7644
#7
Marc-Olivier Duceppe, Catherine Carrillo, Hongsheng Huang
Listeria monocytogenes is a Gram-positive, rod-shaped, non-spore-forming bacterium which is an important foodborne bacterial pathogen for humans worldwide with high mortality rates. Here, we report a 2,964,284-bp draft genome sequence of Listeria monocytogenes strain ATCC 7644 (American Type Culture Collection).
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935481/stalking-a-lethal-superbug-by-whole-genome-sequencing-and-phylogenetics-influence-on-unraveling-a-major-hospital-outbreak-of-carbapenem-resistant-klebsiella-pneumoniae
#8
Thorsten Kaiser, Knut Finstermeier, Madlen Häntzsch, Sarah Faucheux, Martin Kaase, Tim Eckmanns, Sven Bercker, Udo X Kaisers, Norman Lippmann, Arne C Rodloff, Joachim Thiery, Christoph Lübbert
BACKGROUND: From July 2010-April 2013, Leipzig University Hospital experienced the largest outbreak of a Klebsiella pneumoniae carbapenemase 2 (KPC-2)-producing Klebsiella pneumoniae (KPC-2-Kp) strain observed in Germany to date. After termination of the outbreak, we aimed to reconstruct transmission pathways by phylogenetics based on whole-genome sequencing (WGS). METHODS: One hundred seventeen KPC-2-Kp isolates from 89 outbreak patients, 5 environmental KPC-2-Kp isolates, and 24 K pneumoniae strains not linked to the outbreak underwent WGS...
September 18, 2017: American Journal of Infection Control
https://www.readbyqxmd.com/read/28934627/in-it-for-the-long-haul-evolutionary-consequences-of-persistent-endosymbiosis
#9
REVIEW
Jennifer J Wernegreen
Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination...
September 18, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28934168/role-of-the-genes-of-type-vi-secretion-system-in-virulence-of-rice-bacterial-brown-stripe-pathogen-acidovorax-avenae-subsp-avenae-strain-rs-2
#10
Md Mahidul Islam Masum, Yingzi Yang, Bin Li, Ogunyemi Solabomi Olaitan, Jie Chen, Yang Zhang, Yushi Fang, Wen Qiu, Yanli Wang, Guochang Sun
The Type VI secretion system (T6SS) is a class of macromolecular machine that is required for the virulence of gram-negative bacteria. However, it is still not clear what the role of T6SS in the virulence of rice bacterial brown stripe pathogen Acidovorax avenae subsp. avenae (Aaa) is. The aim of the current study was to investigate the contribution of T6SS in Aaa strain RS2 virulence using insertional deletion mutation and complementation approaches. This strain produced weak virulence but contains a complete T6SS gene cluster based on a genome-wide analysis...
September 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28933324/photobacterium-toruni-sp-nov-a-bacterium-isolated-from-diseased-farmed-fish
#11
Alejandro M Labella, David R Arahal, Teresa Lucena, Manuel Manchado, Dolores Castro, Juan J Borrego
Three bacterial strains were isolated from liver and spleen of diseased farmed redbanded seabream (Pagrus auriga) in south-west Spain. Their partial 16S rRNA gene sequences clustered within those of the genus Photobacterium, showing high similarity (98.6-99.3 %) to the type strains of Photobacterium iliopiscarium, P. piscicola, P. kishitanii, P. aquimaris and P. phosphoreum. Multilocus sequence analysis using six housekeeping genes (gapA, topA, mreB, ftsZ, gyrB and 16S rRNA) confirmed the new strains as forming an independent branch with a bootstrap value of 100, likely to represent a novel species...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28933317/elstera-cyanobacteriorum-sp-nov-a-novel-bacterium-isolated-from-cyanobacterial-aggregates-in-a-eutrophic-lake
#12
Haiyuan Cai, Yonghui Zeng, Yanan Wang, Helong Jiang
A bacterial strain, TH019T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Cells were observed to be slightly curved rod-shaped and stained Gram-negative. Optimal growth was obtained at pH 7.0 (range, 5.0-9.0) and 28 °C (range, 20-37 °C) in R2A broth. The cells were found to be positive for oxidase and catalase activities, nitrate reduction and denitrification. The major respiratory quinone was ubiquinone Q-10. The major fatty acids were identified as C18 : 1 ω6c/C18 : 1 ω7c and C18 : 1 2OH...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28932201/the-placental-microbiota-is-altered-among-subjects-with-gestational-diabetes-mellitus-a-pilot-study
#13
Jia Zheng, Xinhua Xiao, Qian Zhang, Lili Mao, Miao Yu, Jianping Xu, Tong Wang
Gestational diabetes mellitus (GDM) has significant implications for the future health of the mother and child. However, the associations between human placental microbiota and GDM are poorly understood. We aimed to profile the placental microbiota of GDM and further define whether or not certain placental microbiota taxon correlates with specific clinical characteristics. Placenta were collected from GDM women and women with normal pregnancies (n = 10, in each group) consecutively recruited at Peking Union Medical College Hospital...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28931093/synthesis-of-udp-apiose-in-bacteria-the-marine-phototroph-geminicoccus-roseus-and-the-plant-pathogen-xanthomonas-pisi
#14
James Amor Smith, Maor Bar-Peled
The branched-chain sugar apiose was widely assumed to be synthesized only by plant species. In plants, apiose-containing polysaccharides are found in vascularized plant cell walls as the pectic polymers rhamnogalacturonan II and apiogalacturonan. Apiosylated secondary metabolites are also common in many plant species including ancestral avascular bryophytes and green algae. Apiosyl-residues have not been documented in bacteria. In a screen for new bacterial glycan structures, we detected small amounts of apiose in methanolic extracts of the aerobic phototroph Geminicoccus roseus and the pathogenic soil-dwelling bacteria Xanthomonas pisi...
2017: PloS One
https://www.readbyqxmd.com/read/28930567/molecular-mechanisms-of-chlamydia-trachomatis-resistance-to-antimicrobial-drugs
#15
Tomislav Mestrovic, Suncanica Ljubin-Sternak
Chlamydia trachomatis (C. trachomatis) is a leading cause of bacterial sexually transmitted infections in developed and undeveloped countries, and therefore a global public health issue. In an era of increasing bacterial resistance to antibiotics, resistance has been an exceedingly rare phenomenon in C. trachomatis; however, clinical treatment failures attributed to multidrug-resistant C. trachomatis strains have been described on several occasions. Cell culture systems using McCoy cells and subsequent immunofluorescent staining are still the most common methodology used for antimicrobial susceptibility testing, but the presence of resistance markers should be appraised by further genetic analysis...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28929383/evaluation-of-the-impact-of-six-different-dna-extraction-methods-for-the-representation-of-the-microbial-community-associated-with-human-chronic-wound-infections-using-a-gel-based-dna-profiling-method
#16
Ayomi Dilhari, Asanga Sampath, Chinthika Gunasekara, Neluka Fernando, Deepaka Weerasekara, Chris Sissons, Andrew McBain, Manjula Weerasekera
Infected chronic wounds are polymicrobial in nature which include a diverse group of aerobic and anaerobic microorganisms. Majority of these communal microorganisms are difficult to grow in vitro. DNA fingerprinting methods such as polymerase chain reaction-denaturation gradient gel electrophoresis (PCR-DGGE) facilitate the microbial profiling of complex ecosystems including infected chronic wounds. Six different DNA extraction methods were compared for profiling of the microbial community associated with chronic wound infections using PCR-DGGE...
September 19, 2017: AMB Express
https://www.readbyqxmd.com/read/28928442/genome-wide-association-and-hla-region-fine-mapping-studies-identify-susceptibility-loci-for-multiple-common-infections
#17
Chao Tian, Bethann S Hromatka, Amy K Kiefer, Nicholas Eriksson, Suzanne M Noble, Joyce Y Tung, David A Hinds
Infectious diseases have a profound impact on our health and many studies suggest that host genetics play a major role in the pathogenesis of most of them. We perform 23 genome-wide association studies for common infections and infection-associated procedures, including chickenpox, shingles, cold sores, mononucleosis, mumps, hepatitis B, plantar warts, positive tuberculosis test results, strep throat, scarlet fever, pneumonia, bacterial meningitis, yeast infections, urinary tract infections, tonsillectomy, childhood ear infections, myringotomy, measles, hepatitis A, rheumatic fever, common colds, rubella and chronic sinus infection, in over 200,000 individuals of European ancestry...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928212/population-and-whole-genome-sequence-based-characterization-of-invasive-group-a-streptococci-recovered-in-the-united-states-during-2015
#18
Sopio Chochua, Ben J Metcalf, Zhongya Li, Joy Rivers, Saundra Mathis, Delois Jackson, Robert E Gertz, Velusamy Srinivasan, Ruth Lynfield, Chris Van Beneden, Lesley McGee, Bernard Beall
Group A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing. Predictions were made for genotype, GAS carbohydrate, antimicrobial resistance, surface proteins (M family, fibronectin binding, T, R28), secreted virulence proteins (Sda1, Sic, exotoxins), hyaluronate capsule, and an upregulated nga operon (encodes NADase and streptolysin O) promoter (Pnga3)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#19
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28928209/combining-comprehensive-analysis-of-off-site-lambda-phage-integration-with-a-crispr-based-means-of-characterizing-downstream-physiology
#20
Yu Tanouchi, Markus W Covert
During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance...
September 19, 2017: MBio
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