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next-generation sequencing

  • Open Access
    The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change
    Research Article
    The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change

    Autism spectrum disorder (ASD) is a brain developmental disorder with varying behavioral symptom severity both across individuals and within individuals over time. There have been promising but also inconsistent literature results regarding how the gut microbiota (microbiome) may be involved.

    Jennifer Fouquier, Nancy Moreno Huizar, Jody Donnelly, Cody Glickman, Dae-Wook Kang, Juan Maldonado, Rachel A. Jones, Kimberly Johnson, James B. Adams, Rosa Krajmalnik-Brown, Catherine Lozupone
  • Open Access
    Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
    Research Article | Host-Microbe Biology
    Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification

    Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes.

    Kochi Toyomane, Ryo Yokota, Ken Watanabe, Tomoko Akutsu, Ai Asahi, Satoshi Kubota
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Cutibacterium acnes</span> (<span class="named-content genus-species" id="named-content-2">Propionibacterium acnes</span>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
    Research Article | Host-Microbe Biology
    Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

    Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples...

    Jiayue Yang, Tomoya Tsukimi, Mia Yoshikawa, Kenta Suzuki, Tomoki Takeda, Masaru Tomita, Shinji Fukuda
  • Open Access
    A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults
    Research Article | Host-Microbe Biology
    A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

    The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are...

    Owen Cronin, Wiley Barton, Peter Skuse, Nicholas C. Penney, Isabel Garcia-Perez, Eileen F. Murphy, Trevor Woods, Helena Nugent, Aine Fanning, Silvia Melgar, Eanna C. Falvey, Elaine Holmes, Paul D. Cotter, Orla O’Sullivan, Michael G. Molloy, Fergus Shanahan
  • Open Access
    Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective
    Special Issue Perspective | Clinical Science and Epidemiology
    Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective

    Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic...

    Georgios D. Kitsios
  • Open Access
    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
    Research Article | Applied and Environmental Science
    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

    Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial worlds associated with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an...

    Berith E. Knudsen, Lasse Bergmark, Patrick Munk, Oksana Lukjancenko, Anders Priemé, Frank M. Aarestrup, Sünje J. Pamp
  • Open Access
    16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
    Research Article | Clinical Science and Epidemiology
    16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
    Maxime Galan, Maria Razzauti, Emilie Bard, Maria Bernard, Carine Brouat, Nathalie Charbonnel, Alexandre Dehne-Garcia, Anne Loiseau, Caroline Tatard, Lucie Tamisier, Muriel Vayssier-Taussat, Helene Vignes, Jean-François Cosson
  • Open Access
    Is the Evolution of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span> subsp. <em>enterica</em> Linked to Restriction-Modification Systems?
    Editor's Pick Research Article | Host-Microbe Biology
    Is the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?

    The evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer....

    Louise Roer, Rene S. Hendriksen, Pimlapas Leekitcharoenphon, Oksana Lukjancenko, Rolf Sommer Kaas, Henrik Hasman, Frank M. Aarestrup
  • Open Access
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses
    Research Article | Novel Systems Biology Techniques
    A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses

    This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities...

    Lindsey A. Moser, Lisbeth Ramirez-Carvajal, Vinita Puri, Steven J. Pauszek, Krystal Matthews, Kari A. Dilley, Clancy Mullan, Jennifer McGraw, Michael Khayat, Karen Beeri, Anthony Yee, Vivien Dugan, Mark T. Heise, Matthew B. Frieman, Luis L. Rodriguez, Kristen A. Bernard, David E. Wentworth, Timothy B. Stockwell, Reed S. Shabman
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