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genomics

  • Open Access
    Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Clones, PA14 and ST235
    Research Article | Host-Microbe Biology
    Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235

    The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus...

    Sebastian Fischer, Sarah Dethlefsen, Jens Klockgether, Burkhard Tümmler
  • Open Access
    Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective
    Research Article | Clinical Science and Epidemiology
    Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective

    Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, ...

    John Osei Sekyere, Melese Abate Reta
  • Open Access
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in <span class="named-content genus-species" id="named-content-1">Mycobacterium abscessus</span>
    Research Article | Novel Systems Biology Techniques
    A Simplified and Efficient Method for Himar-1 Transposon Sequencing in Bacteria, Demonstrated by Creation and Analysis of a Saturated Transposon-Mutant Library in Mycobacterium abscessus

    Transposon insertion sequencing is a powerful tool, but many researchers are discouraged by the apparent technical complexity of preparing the genomic library for deep sequencing and by the complicated computational analysis needed for insertion site identification. Our proposed method makes the preparation of the library easy and straightforward, relying on well-known molecular biology techniques. In addition, the results obtained from...

    Mark Foreman, Moran Gershoni, Daniel Barkan
  • Open Access
    Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
    Research Article | Applied and Environmental Science
    Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

    Accurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the ...

    Elizabeth A. McDaniel, Benjamin D. Peterson, Sarah L. R. Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon
  • Open Access
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
    Research Article | Host-Microbe Biology
    Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

    It is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization of multiple open source software tools. We present Bactopia, a pipeline for bacterial genome analysis, as an option for processing bacterial genome data. Bactopia also automates downloading of data from multiple public sources and species-specific customization. Because the pipeline...

    Robert A. Petit, Timothy D. Read
  • Open Access
    Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
    Research Article | Ecological and Evolutionary Science
    Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

    Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities...

    Brittany A. Niccum, Erik K. Kastman, Nicole Kfoury, Albert Robbat, Benjamin E. Wolfe
  • Open Access
    Comparative Genomics and Metabolomics in the Genus <em>Nocardia</em>
    Research Article | Applied and Environmental Science
    Comparative Genomics and Metabolomics in the Genus Nocardia

    Our work emphasizes that Nocardia represent a prolific source for natural products rivaling better-characterized genera such as Streptomyces or Amycolatopsis. Furthermore, we showed that large-scale analysis of biosynthetic gene clusters using similarity networks with high stringency allows the distinction and prediction of natural product structural variations. This will facilitate future genomics-driven drug...

    Daniel Männle, Shaun M. K. McKinnie, Shrikant S. Mantri, Katharina Steinke, Zeyin Lu, Bradley S. Moore, Nadine Ziemert, Leonard Kaysser
  • Open Access
    Overexpression of the Small RNA PA0805.1 in <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
    Research Article | Molecular Biology and Physiology
    Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance

    P. aeruginosa is an opportunistic pathogen of humans. With roughly 10% of its genes encoding transcriptional regulators, and hundreds of small noncoding RNAs (sRNAs) interspersed throughout the genome, P. aeruginosa is able to fine-tune its response to adapt and survive in the host and resist...

    Shannon R. Coleman, Maren L. Smith, Victor Spicer, Ying Lao, Neeloffer Mookherjee, Robert E. W. Hancock
  • Open Access
    Prophage-Mediated Disruption of Genetic Competence in <span class="named-content genus-species" id="named-content-1">Staphylococcus pseudintermedius</span>
    Research Article | Ecological and Evolutionary Science
    Prophage-Mediated Disruption of Genetic Competence in Staphylococcus pseudintermedius

    Staphylococcus pseudintermedius is a bacterium responsible for clinically important infections in dogs and can infect humans. In this study, we performed genomic analysis of 371 S. pseudintermedius isolates to understand the evolution of antibiotic resistance and virulence in this organism. The...

    Michael R. Brooks, Lyan Padilla-Vélez, Tarannum A. Khan, Azaan A. Qureshi, Jason B. Pieper, Carol W. Maddox, Md Tauqeer Alam
  • Open Access
    Conserved Patterns of Symmetric Inversion in the Genome Evolution of <em>Bordetella</em> Respiratory Pathogens
    Research Article | Ecological and Evolutionary Science
    Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens

    Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable...

    Michael R. Weigand, Yanhui Peng, Dhwani Batra, Mark Burroughs, Jamie K. Davis, Kristen Knipe, Vladimir N. Loparev, Taccara Johnson, Phalasy Juieng, Lori A. Rowe, Mili Sheth, Kevin Tang, Yvette Unoarumhi, Margaret M. Williams, M. Lucia Tondella

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