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diet

  • Open Access
    Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism
    Editor's Pick Research Article | Host-Microbe Biology
    Investigating the Role of Diet and Exercise in Gut Microbe-Host Cometabolism

    Improved control of dietary confounders, through the use of an objective dietary assessment score, has uncovered further insights into the complex, multifactorial relationship between diet, exercise, the gut microbiome, and metabolism. Each of the models pertaining to diet healthiness, physical exercise, or a combination of both, displayed a distinct metabolic and functional microbial signature.

    N. Penney, W. Barton, J. M. Posma, A. Darzi, G. Frost, P. D. Cotter, E. Holmes, F. Shanahan, O. O’Sullivan, I. Garcia-Perez
  • 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
    Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture
    Editor's Pick Research Article | Novel Systems Biology Techniques
    Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

    Bacterial culture and assay are components of basic microbiological research, drug development, and diagnostic screening. However, community diversity can make it challenging to comprehensively perform experiments involving individual microbiota members. Here, we present a new microfluidic culture platform that makes it feasible to measure the growth and function of microbiota constituents in a single set of experiments. As a proof of...

    Max M. Villa, Rachael J. Bloom, Justin D. Silverman, Heather K. Durand, Sharon Jiang, Anchi Wu, Eric P. Dallow, Shuqiang Huang, Lingchong You, Lawrence A. David
  • Open Access
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens
    Research Article | Novel Systems Biology Techniques
    High-Throughput Stool Metaproteomics: Method and Application to Human Specimens

    Widely available technologies based on DNA sequencing have been used to describe the kinds of microbes that might correlate with health and disease. However, mechanistic insights might be best achieved through careful study of the dynamic proteins at the interface between the foods we eat, our microbes, and ourselves. Mass spectrometry-based proteomics has the potential to revolutionize our understanding of this complex system, but its...

    Carlos G. Gonzalez, Hannah C. Wastyk, Madeline Topf, Christopher D. Gardner, Justin L. Sonnenburg, Joshua E. Elias
  • Open Access
    Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma
    Research Article | Host-Microbe Biology
    Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma

    Development of hepatocellular carcinoma in patients with cirrhosis is associated with alterations in intestinal microbiota, including an escalation of dysbiosis and reduced bacterial richness. This study demonstrates that reduced bacterial richness and dysbiosis escalate with the progression of cirrhosis from compensated to decompensated cirrhosis and to HCC-associated cirrhosis (HCC-cirrhosis). Moreover, we report for the first time...

    Yelena Lapidot, Amnon Amir, Rita Nosenko, Atara Uzan-Yulzari, Ella Veitsman, Oranit Cohen-Ezra, Yana Davidov, Peretz Weiss, Tanya Bradichevski, Shlomo Segev, Omry Koren, Michal Safran, Ziv Ben-Ari
  • Open Access
    Molecular Reconstruction of the Diet in Human Stool Samples
    Commentary | Host-Microbe Biology
    Molecular Reconstruction of the Diet in Human Stool Samples

    Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition....

    Frank Maixner
  • Open Access
    Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets
    Research Article | Host-Microbe Biology
    Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets

    The human gastrointestinal microbiota functions as an important mediator of diet for host metabolism. To evaluate how consumed diets influence the gut environment, we carried out simultaneous interrogations of distal gut microbiota and metabolites in samples from healthy children in Egypt and the United States. While Egyptian children consumed a Mediterranean diet rich in plant foods, U.S. children consumed a Western diet high in animal...

    V. Shankar, M. Gouda, J. Moncivaiz, A. Gordon, N. V. Reo, L. Hussein, O. Paliy
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