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metabolome

  • Open Access
    Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of <em>Butyricicoccus pullicaecorum</em> to Healthy Volunteers
    Research Article | Host-Microbe Biology
    Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers

    This study is the first to determine the safety and tolerance in humans of a butyrate-producing Clostridium cluster IV next-generation probiotic. Advances in gut microbiota research have triggered interest in developing colon butyrate producers as next-generation probiotics. Butyricicoccus pullicaecorum...

    Leen Boesmans, Mireia Valles-Colomer, Jun Wang, Venessa Eeckhaut, Gwen Falony, Richard Ducatelle, Filip Van Immerseel, Jeroen Raes, Kristin Verbeke
  • Open Access
    Crowdsourcing Our National Gut
    Commentary | Host-Microbe Biology
    Crowdsourcing Our National Gut

    The microbes of the human intestinal tract play a profound role in our health. The complex interactions between our gut microbial communities and the external environment, and the resulting functional consequences, can be difficult to disentangle.

    Laura E. Grieneisen, Ran Blekhman
  • Open Access
    Can Diet Influence Our Health by Altering Intestinal Microbiota-Derived Fecal Metabolites?
    Special Issue Perspective | Host-Microbe Biology
    Can Diet Influence Our Health by Altering Intestinal Microbiota-Derived Fecal Metabolites?

    The human gastrointestinal tract harbors a diverse, highly mutualistic microbial flora which could produce a myriad of specialized metabolites. These specialized metabolites are the chemical cellphones that gut microflora use to communicate with their human host and could potentially be used to cure diseases.

    Qiang Lyu, Cheng-Chih Hsu
  • Open Access
    Role of the Gut Microbiome in Vertebrate Evolution
    Special Issue Perspective | Host-Microbe Biology
    Role of the Gut Microbiome in Vertebrate Evolution

    Darwin referred to life as a struggle. Organisms compete for limited resources in nature, and their traits influence the outcome.

    Thomas J. Sharpton
  • Open Access
    Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics
    Special Issue Perspective | Therapeutics and Prevention
    Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics

    Over the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems.

    Casey M. Theriot
  • Open Access
    Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment
    Editor's Pick Research Article | Host-Microbe Biology
    Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment

    Periodontal disease affects the majority of adults worldwide and has been linked to numerous systemic diseases. Despite decades of research, the reasons for the substantial differences among periodontitis patients in disease incidence, progressivity, and response to treatment remain poorly understood. While deep sequencing of oral bacterial communities has greatly expanded our comprehension of the microbial diversity of periodontal...

    Katy J. Califf, Karen Schwarzberg-Lipson, Neha Garg, Sean M. Gibbons, J. Gregory Caporaso, Jørgen Slots, Chloe Cohen, Pieter C. Dorrestein, Scott T. Kelley
  • Open Access
    Integrated Role of <span class="named-content genus-species" id="named-content-1">Bifidobacterium animalis</span> subsp. <em>lactis</em> Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys
    Editor's Pick Research Article | Host-Microbe Biology
    Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys

    Probiotics are becoming increasingly popular due to their perceived effects on health, despite a lack of mechanistic information on how they impart these benefits. Infant formula and complementary foods are common targets for supplementation with probiotics. However, different probiotic strains have different properties, and there is a lack of data on long-term health effects on the consumer. Given the increasing interest in...

    Xuan He, Carolyn M. Slupsky, James W. Dekker, Neill W. Haggarty, Bo Lönnerdal
  • Open Access
    From Sample to Multi-Omics Conclusions in under 48 Hours
    Research Article | Novel Systems Biology Techniques
    From Sample to Multi-Omics Conclusions in under 48 Hours

    Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial...

    Robert A. Quinn, Jose A. Navas-Molina, Embriette R. Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, Jeremiah J. Minich, Alexey V. Melnik, Jakob Herschend, Jeff DeReus, Austin Durant, Rachel J. Dutton, Mahdieh Khosroheidari, Clifford Green, Ricardo da Silva, Pieter C. Dorrestein, Rob Knight
  • Open Access
    cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
    Methods and Protocols | Novel Systems Biology Techniques
    cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies

    The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis,...

    John H. Chase, Evan Bolyen, Jai Ram Rideout, J. Gregory Caporaso

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