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16S rRNA gene

  • Open Access
    Dryland Cropping Systems, Weed Communities, and Disease Status Modulate the Effect of Climate Conditions on Wheat Soil Bacterial Communities
    Research Article | Applied and Environmental Science
    Dryland Cropping Systems, Weed Communities, and Disease Status Modulate the Effect of Climate Conditions on Wheat Soil Bacterial Communities

    Climate change is affecting global moisture and temperature patterns, and its impacts are predicted to worsen over time, posing progressively larger threats to food production. In the Northern Great Plains of the United States, climate change is forecast to increase temperature and decrease precipitation during the summer, and it is expected to negatively affect cereal crop production and pest management. In this study, temperature,...

    Suzanne L. Ishaq, Tim Seipel, Carl Yeoman, Fabian D. Menalled
  • Open Access
    Gut Microbiomes of the Eastern Oyster (<em>Crassostrea virginica</em>) and the Blue Mussel (<em>Mytilus edulis</em>): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities
    Research Article | Host-Microbe Biology
    Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities

    This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited...

    Melissa L. Pierce, J. Evan Ward
  • Open Access
    The Proton Pump Inhibitor Omeprazole Does Not Promote <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Colonization in a Murine Model
    Observation | Host-Microbe Biology
    The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model

    Antibiotics are the primary risk factor for Clostridioides difficile infections (CDIs), but other factors may also increase a person’s risk. In epidemiological studies, proton pump inhibitor (PPI) use has been associated with CDI incidence and recurrence. PPIs have also been associated with alterations in the human intestinal microbiota in observational and...

    Sarah Tomkovich, Nicholas A. Lesniak, Yuan Li, Lucas Bishop, Madison J. Fitzgerald, Patrick D. Schloss
  • Open Access
    The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data
    Research Article | Ecological and Evolutionary Science
    The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

    A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream...

    Marc A. Sze, Patrick D. Schloss
  • Open Access
    Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria
    Research Article | Ecological and Evolutionary Science
    Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

    Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed...

    Holly M. Bik, Alexandra Alexiev, Sabreen K. Aulakh, Lakshmi Bharadwaj, Jennifer Flanagan, John M. Haggerty, Sarah M. Hird, Guillaume Jospin, Jenna M. Lang, Laura A. Sauder, Josh D. Neufeld, Andrew Shaver, Akshay Sethi, Jonathan A. Eisen, David A. Coil
  • Open Access
    TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
    Research Article | Ecological and Evolutionary Science
    TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

    Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or...

    Robin R. Rohwer, Joshua J. Hamilton, Ryan J. Newton, Katherine D. McMahon
  • Open Access
    Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder
    Research Article | Ecological and Evolutionary Science
    Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

    Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects...

    Vincent J. Denef, Hunter J. Carrick, Joann Cavaletto, Edna Chiang, Thomas H. Johengen, Henry A. Vanderploeg
  • Open Access
    OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
    Editor's Pick Research Article | Ecological and Evolutionary Science
    OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

    The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other, irrespective of a database. In this study, we present a new algorithm for the latter approach...

    Sarah L. Westcott, Patrick D. Schloss
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