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microbiome

  • Open Access
    Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level
    Resource Report | Novel Systems Biology Techniques
    Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level

    A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile.

    ...
    Gongchao Jing, Lu Liu, Zengbin Wang, Yufeng Zhang, Li Qian, Chunxiao Gao, Meng Zhang, Min Li, Zhenkun Zhang, Xiaohan Liu, Jian Xu, Xiaoquan Su
  • Open Access
    Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition

    Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers.

    Vojtěch Tláskal, Vendula Brabcová, Tomáš Větrovský, Mayuko Jomura, Rubén López-Mondéjar, Lummy Maria Oliveira Monteiro, João Pedro Saraiva, Zander Rainier Human, Tomáš Cajthaml, Ulisses Nunes da Rocha, Petr Baldrian
  • Open Access
    Different Arbuscular Mycorrhizal Fungi Cocolonizing on a Single Plant Root System Recruit Distinct Microbiomes
    Research Article | Host-Microbe Biology
    Different Arbuscular Mycorrhizal Fungi Cocolonizing on a Single Plant Root System Recruit Distinct Microbiomes

    Arbuscular mycorrhizal (AM) fungi form tight symbiotic relationships with the majority of terrestrial plants and play critical roles in plant P acquisition, adding a further dimension of complexity. The plant-AM fungus-bacterium system is considered a continuum, with the bacteria colonizing not only the plant roots, but also the associated mycorrhizal hyphal network, known as the hyphosphere microbiome. Plant roots are usually colonized...

    Jiachao Zhou, Xiaofen Chai, Lin Zhang, Timothy S. George, Fei Wang, Gu Feng
  • Open Access
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways
    Minireview | Host-Microbe Biology
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways

    Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical...

    Rutvij A. Khanolkar, Shawn T. Clark, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman
  • 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
    An Expanded Genetic Code Enables Trimethylamine Metabolism in Human Gut Bacteria
    Research Article | Molecular Biology and Physiology
    An Expanded Genetic Code Enables Trimethylamine Metabolism in Human Gut Bacteria

    Links between trimethylamine-N-oxide (TMAO) and cardiovascular disease (CVD) have focused attention on mechanisms by which animal-based diets have negative health consequences. In a meta-analysis of data from foundational gut microbiome studies, we found evidence that specialized bacteria have and express a metabolic pathway that circumvents TMAO production and is often misannotated because it relies on genetic code expansion....

    Veronika Kivenson, Stephen J. Giovannoni
  • 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
    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
    Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2<sup>−/−</sup> Mice
    Research Article | Host-Microbe Biology
    Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2−/− Mice

    Perturbation in the gut microbial ecosystem has been associated with various diseases, including inflammatory bowel disease. Habitual physical activity, through its ability to modulate the gut microbiome, has recently been shown to prophylactically protect against chemically induced models of murine colitis. Here, we (i) confirm previous reports that physical activity has limited but significant effects on the gut microbiome of mice and...

    Mehrbod Estaki, Douglas W. Morck, Sanjoy Ghosh, Candice Quin, Jason Pither, Jacqueline A. Barnett, Sandeep K. Gill, Deanna L. Gibson

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