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    • Latest Articles
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    • COVID-19 Special Collection
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    • Special Series: Sponsored Minireviews and Video Abstracts
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  • Topics
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Most read article(s)

  • Open Access
    Phylogenetic Distribution of Secondary Metabolites in the <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span> Species Complex
    Observation
    Phylogenetic Distribution of Secondary Metabolites in the Bacillus subtilis Species Complex

    Members of the B. subtilis species complex are commonly recognized producers of secondary metabolites, among those, the production of antifungals, which makes them promising biocontrol strains. While there are studies examining the distribution of well-known secondary metabolites in Bacilli, intraspecies clade-specific distribution has not been systematically...

    Kat Steinke, Omkar S. Mohite, Tilmann Weber, Ákos T. Kovács
  • Open Access
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
    Research Article | Novel Systems Biology Techniques
    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

    The bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions...

    Christian Diener, Sean M. Gibbons, Osbaldo Resendis-Antonio
  • Open Access
    Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants
    Research Article | Applied and Environmental Science
    Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants

    Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-...

    John Leech, Raul Cabrera-Rubio, Aaron M. Walsh, Guerrino Macori, Calum J. Walsh, Wiley Barton, Laura Finnegan, Fiona Crispie, Orla O’Sullivan, Marcus J. Claesson, Paul D. Cotter
  • Open Access
    Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation
    Research Article | Host-Microbe Biology
    Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation

    Recent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent.

    Oliver Aasmets, Kreete Lüll, Jennifer M. Lang, Calvin Pan, Johanna Kuusisto, Krista Fischer, Markku Laakso, Aldons J. Lusis, Elin Org
  • Open Access
    Genomic and Chemical Diversity of <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span> Secondary Metabolites against Plant Pathogenic Fungi
    Research Article | Ecological and Evolutionary Science
    Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi

    Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity.

    Heiko T. Kiesewalter, Carlos N. Lozano-Andrade, Mario Wibowo, Mikael L. Strube, Gergely Maróti, Dan Snyder, Tue Sparholt Jørgensen, Thomas O. Larsen, Vaughn S. Cooper, Tilmann Weber, Ákos T. Kovács
  • Open Access
    Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages
    Research Article | Host-Microbe Biology
    Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages

    T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology, from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories.

    Dinesh Subedi, Jeremy J. Barr
  • Open Access
    Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <em>Zetaproteobacteria</em> Iron Mats at Marine Hydrothermal Vents
    Editor's Pick Research Article | Applied and Environmental Science
    Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents

    Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron...

    Sean M. McAllister, Shawn W. Polson, David A. Butterfield, Brian T. Glazer, Jason B. Sylvan, Clara S. Chan
  • Open Access
    Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities
    Perspective | Applied and Environmental Science
    Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

    Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical.

    Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh
  • Open Access
    Phylogenetic Distribution of Plastic-Degrading Microorganisms
    Research Article | Applied and Environmental Science
    Phylogenetic Distribution of Plastic-Degrading Microorganisms

    We have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved.

    Victor Gambarini, Olga Pantos, Joanne M. Kingsbury, Louise Weaver, Kim M. Handley, Gavin Lear
  • Open Access
    Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics
    Research Article
    Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics

    As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry.

    Aeriel D. Belk, Toni Duarte, Casey Quinn, David A. Coil, Keith E. Belk, Jonathan A. Eisen, Jason C. Quinn, Jennifer N. Martin, Xiang Yang, Jessica L. Metcalf

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