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    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
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microbial ecology

  • Open Access
    The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence <span class="named-content genus-species" id="named-content-1">Clostridioides difficile</span> Clearance in Mice
    Research Article | Host-Microbe Biology
    The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice

    Clostridioides difficile is a leading nosocomial infection. Although perturbation to the gut microbiota is an established risk, there is variation in who becomes asymptomatically colonized, develops an infection, or has adverse infection outcomes. Mouse models of C. difficile infection (CDI) are...

    Sarah Tomkovich, Joshua M. A. Stough, Lucas Bishop, Patrick D. Schloss
  • Open Access
    Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, <span class="named-content genus-species" id="named-content-1">Scomber japonicus</span>
    Research Article | Ecological and Evolutionary Science
    Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

    Pacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may...

    Jeremiah J. Minich, Semar Petrus, Julius D. Michael, Todd P. Michael, Rob Knight, Eric E. Allen
  • Open Access
    Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
    Research Article | Applied and Environmental Science
    Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities

    Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment...

    Ryan B. Ghannam, Laura G. Schaerer, Timothy M. Butler, Stephen M. Techtmann
  • Open Access
    Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates <em>Clostridioides difficile</em> Colonization
    Research Article | Host-Microbe Biology
    Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization

    A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C....

    Matthew K. Schnizlein, Kimberly C. Vendrov, Summer J. Edwards, Eric C. Martens, Vincent B. Young
  • 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
    Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<em>Candidatus</em> Liberibacter asiaticus”
    Research Article | Applied and Environmental Science
    Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”

    Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to...

    Marian Dominguez-Mirazo, Rong Jin, Joshua S. Weitz
  • Open Access
    Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice
    Research Article | Ecological and Evolutionary Science
    Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice

    The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased...

    Andrew H. Moeller, João C. Gomes-Neto, Sara Mantz, Hatem Kittana, Rafael R. Segura Munoz, Robert J. Schmaltz, Amanda E. Ramer-Tait, Michael W. Nachman
  • Open Access
    mSphere of Influence: Engineering Microbes
    Commentary | Applied and Environmental Science
    mSphere of Influence: Engineering Microbes

    Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L.

    Patrick J. McNamara
  • 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
    Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions
    Research Article | Ecological and Evolutionary Science
    Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions

    By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this...

    Ruben Props, Pieter Monsieurs, Peter Vandamme, Natalie Leys, Vincent J. Denef, Nico Boon

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