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Applied and Environmental Science

  • Open Access
    Elucidation of Regulatory Modes for Five Two-Component Systems in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Reveals Novel Relationships
    Research Article | Applied and Environmental Science
    Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships

    E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and...

    Kumari Sonal Choudhary, Julia A. Kleinmanns, Katherine Decker, Anand V. Sastry, Ye Gao, Richard Szubin, Yara Seif, Bernhard O. Palsson
  • 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
    Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy
    Editor's Pick Research Article | Applied and Environmental Science
    Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

    The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that...

    Nunzia Picone, Carmen Hogendoorn, Geert Cremers, Lianna Poghosyan, Arjan Pol, Theo A. van Alen, Antonina L. Gagliano, Walter D’Alessandro, Paola Quatrini, Mike S. M. Jetten, Huub J. M. Op den Camp, Tom Berben
  • Open Access
    Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
    Research Article | Applied and Environmental Science
    Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

    This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel...

    Shuilin Liao, Yayu Wang, Huan Liu, Guangyi Fan, Sunil Kumar Sahu, Tao Jin, Jianwei Chen, Pengfan Zhang, Lone Gram, Mikael Lenz Strube, Qiong Shi, Simon Ming Yuen Lee, Xin Liu
  • Open Access
    Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems
    Perspective | Applied and Environmental Science
    Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems

    Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial...

    Sarah M. Allard, Matthew T. Costa, Ashley N. Bulseco, Véronique Helfer, Laetitia G. E. Wilkins, Christiane Hassenrück, Karsten Zengler, Martin Zimmer, Natalia Erazo, Jorge L. Mazza Rodrigues, Norman Duke, Vânia M. M. Melo, Inka Vanwonterghem, Howard Junca, Huxley M. Makonde, Diego Javier Jiménez, Tallita C. L. Tavares, Marco Fusi, Daniele Daffonchio, Carlos M. Duarte, Raquel S. Peixoto, Alexandre S. Rosado, Jack A. Gilbert, Jeff Bowman
  • Open Access
    Long-Term Temporal Stability of the Resistome in Sewage from Copenhagen
    Editor's Pick Research Article | Applied and Environmental Science
    Long-Term Temporal Stability of the Resistome in Sewage from Copenhagen

    The Copenhagen sewage resistome is surprisingly stable in time. The implication is that, at least for cities that are comparable to Copenhagen in terms of sewer infrastructure, few or even single samples provide a robust picture of the resistome within a city.

    Christian Brinch, Pimlapas Leekitcharoenphon, Ana S. R. Duarte, Christina A. Svendsen, Jacob D. Jensen, Frank M. Aarestrup
  • Open Access
    Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle
    Research Article | Applied and Environmental Science
    Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle

    Biological wastewater conversion processes collectively constitute one of the single biggest worldwide applications of microbial communities. There is an obvious requirement, therefore, to study the microbial systems central to the success of such technologies. Methanogenic granules, in particular, are architecturally fascinating biofilms that facilitate highly organized cooperation within the metabolic network of the anaerobic...

    Anna Christine Trego, Sarah O’Sullivan, Christopher Quince, Simon Mills, Umer Zeeshan Ijaz, Gavin Collins
  • Open Access
    Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models
    Research Article | Applied and Environmental Science
    Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models

    Microbiomes are vital to human health, agriculture, and protecting the environment. Predicting behavior of self-assembled or synthetic microbiomes, however, remains a challenge. In this work, we used unicellular and guild-based metabolic models to investigate production of medium-chain fatty acids by a mixed microbial community that is fed multiple organic substrates. Modeling results provided insights into metabolic pathways of three...

    Matthew J. Scarborough, Joshua J. Hamilton, Elizabeth A. Erb, Timothy J. Donohue, Daniel R. Noguera
  • 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
    Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
    Research Article | Applied and Environmental Science
    Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

    Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we...

    Shaoting Li, David Ames Mann, Shaokang Zhang, Yan Qi, Richard J. Meinersmann, Xiangyu Deng

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