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antibiotics

  • Open Access
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic
    Observation | Novel Systems Biology Techniques
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic

    We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a...

    Alison Vrbanac, Kathryn A. Patras, Alan K. Jarmusch, Robert H. Mills, Samuel R. Shing, Robert A. Quinn, Fernando Vargas, David J. Gonzalez, Pieter C. Dorrestein, Rob Knight, Victor Nizet
  • Open Access
    Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity
    Editor's Pick Research Article | Applied and Environmental Science
    Marine Sediments Hold an Untapped Potential for Novel Taxonomic and Bioactive Bacterial Diversity

    Since bacterial resistance to antibiotics is developing worldwide, new antibiotics are needed. Most antibiotics discovered so far have been found in soil-dwelling bacteria, so we instead targeted marine environments as a novel source of bioactive potential. We used amplicon sequencing of bioactive gene clusters in the microbiome of coastal seawater and sandy sediments and found the bioactive potential to be comparable to, but distinct...

    Pernille Kjersgaard Bech, Klaus Lars Lysdal, Lone Gram, Mikkel Bentzon-Tilia, Mikael Lenz Strube
  • Open Access
    Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
    Research Article | Host-Microbe Biology
    Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin

    Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our “Western”-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in...

    Damien J. Cabral, Jenna I. Wurster, Benjamin J. Korry, Swathi Penumutchu, Peter Belenky
  • Open Access
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy
    Research Article | Clinical Science and Epidemiology
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy

    Subjects with cystic fibrosis battle polymicrobial lung infections throughout their lifetime. Although antibiotic therapy is a principal treatment for CF lung disease, we have little understanding of how antibiotics affect the CF lung microbiome and metabolome and how much the community changes on daily timescales. By analyzing 594 longitudinal CF sputum samples from six adult subjects, we show that the sputum microbiome and metabolome...

    Ruma Raghuvanshi, Karla Vasco, Yoshiki Vázquez-Baeza, Lingjing Jiang, James T. Morton, Danxun Li, Antonio Gonzalez, Lindsay DeRight Goldasich, Gregory Humphrey, Gail Ackermann, Austin D. Swafford, Douglas Conrad, Rob Knight, Pieter C. Dorrestein, Robert A. Quinn
  • Open Access
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
    Research Article | Host-Microbe Biology
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

    Metabolome-informed analyses can enhance omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate here the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an...

    Julia M. Gauglitz, James T. Morton, Anupriya Tripathi, Shalisa Hansen, Michele Gaffney, Carolina Carpenter, Kelly C. Weldon, Riya Shah, Amy Parampil, Andrea L. Fidgett, Austin D. Swafford, Rob Knight, Pieter C. Dorrestein
  • Open Access
    Adaptation of <span class="named-content genus-species" id="named-content-1">Lactobacillus plantarum</span> to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis
    Research Article | Ecological and Evolutionary Science
    Adaptation of Lactobacillus plantarum to Ampicillin Involves Mechanisms That Maintain Protein Homeostasis

    Antibiotic resistance acquired by adaptation to certain antibiotics has led to growing public concerns. Here, a long-term evolution experiment was used together with proteomic analysis to identify genes/proteins responsible for the adaptive phenotype. This work has provided novel insights into the biosafety of new probiotics with high tolerance to antibiotics.

    Chenxia Cao, Jicheng Wang, Yangshuo Liu, Lai-Yu Kwok, Heping Zhang, Wenyi Zhang
  • Open Access
    The Power of Metabolism for Predicting Microbial Community Dynamics
    Special Issue Perspective | Ecological and Evolutionary Science
    The Power of Metabolism for Predicting Microbial Community Dynamics

    Quantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.

    Jeremy M. Chacón, William R. Harcombe
  • Open Access
    Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes

    Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the...

    Pablo Tsukayama, Manish Boolchandani, Sanket Patel, Erica C. Pehrsson, Molly K. Gibson, Kenneth L. Chiou, Clifford J. Jolly, Jeffrey Rogers, Jane E. Phillips-Conroy, Gautam Dantas
  • Open Access
    Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish
    Editor's Pick Research Article | Host-Microbe Biology
    Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish

    Prophylactic antibiotics are widespread in the aquaculture industry and are used where vaccination is impossible or overly expensive. If antibiotics impact fish as they do mice and humans, prophylactic administrations in aquaculture and ornamental fish farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. Recent research has suggested that their use exacerbates bacterial...

    Victor Schmidt, Marta Gomez-Chiarri, Chelsea Roy, Katherine Smith, Linda Amaral-Zettler
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