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Latest Articles

  • 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
    26 Apr 2016
  • Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods
    Commentary | Applied and Environmental Science
    Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods

    Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database.

    Patrick D. Schloss
    26 Apr 2016
  • Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton
    Editor's Pick Research Article | Applied and Environmental Science
    Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

    An estimated 50 gigatons of carbon is annually fixed within marine systems, of which heterotrophic microbial populations process nearly half. These communities vary in composition and activity across spatial and temporal scales, so understanding how these changes affect global processes requires the delineation of functional roles for individual members. In a step toward ascertaining these roles, we applied proteomic stable isotope...

    Samuel Bryson, Zhou Li, Jennifer Pett-Ridge, Robert L. Hettich, Xavier Mayali, Chongle Pan, Ryan S. Mueller
    26 Apr 2016
  • The Built Environment Is a Microbial Wasteland
    Commentary | Applied and Environmental Science
    The Built Environment Is a Microbial Wasteland

    Humanity’s transition from the outdoor environment to the built environment (BE) has reduced our exposure to microbial diversity. The relative importance of factors that contribute to the composition of human-dominated BE microbial communities remains largely unknown.

    Sean M. Gibbons
    19 Apr 2016
  • Geography and Location Are the Primary Drivers of Office Microbiome Composition
    Editor's Pick Research Article | Applied and Environmental Science
    Geography and Location Are the Primary Drivers of Office Microbiome Composition

    Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that...

    John Chase, Jennifer Fouquier, Mahnaz Zare, Derek L. Sonderegger, Rob Knight, Scott T. Kelley, Jeffrey Siegel, J. Gregory Caporaso
    19 Apr 2016
  • Comprehensive Transcriptome Profiles of <span class="named-content genus-species" id="named-content-1">Streptococcus mutans</span> UA159 Map Core Streptococcal Competence Genes
    Research Article | Molecular Biology and Physiology
    Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes

    S. mutans has the hard surfaces of the oral cavity as its natural habitat, where it depends on its ability to form biofilms in order to survive. The comprehensive identification of S. mutans regulons activated in response to peptide pheromones provides an important basis for understanding how...

    R. Khan, H. V. Rukke, H. Høvik, H. A. Åmdal, T. Chen, D. A. Morrison, F. C. Petersen
    12 Apr 2016
  • Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes
    Editor's Pick Perspective | Host-Microbe Biology
    Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

    Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area...

    Kevin R. Theis, Nolwenn M. Dheilly, Jonathan L. Klassen, Robert M. Brucker, John F. Baines, Thomas C. G. Bosch, John F. Cryan, Scott F. Gilbert, Charles J. Goodnight, Elisabeth A. Lloyd, Jan Sapp, Philippe Vandenkoornhuyse, Ilana Zilber-Rosenberg, Eugene Rosenberg, Seth R. Bordenstein
    29 Mar 2016
  • Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages
    Editor's Pick Research Article | Host-Microbe Biology
    Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages

    While host-virus interaction interfaces have been previously investigated, relatively little is known about the indirect interactions of pathogen and host proteins required for viral infection and host cell function. Therefore, we investigated the topological relationships of human and bacterial viruses and how they interact with their hosts. We focused on those host proteins that are directly targeted by viruses, those that are...

    Rachelle Mariano, Sawsan Khuri, Peter Uetz, Stefan Wuchty
    8 Mar 2016
  • Characterization of the Δ7 Mutant of <span class="named-content genus-species" id="named-content-1">Cupriavidus metallidurans</span> with Deletions of Seven Secondary Metal Uptake Systems
    Research Article | Molecular Biology and Physiology
    Characterization of the Δ7 Mutant of Cupriavidus metallidurans with Deletions of Seven Secondary Metal Uptake Systems

    Bacteria, including pathogenic strains, need to make use of the metal composition and speciation of their environment to fulfill the requirement of the cytoplasmic metal content and composition. This task is performed by the bacterial metal transportome, composed of uptake and efflux systems. Seven interacting secondary metal uptake systems are at the core of the metal transportome in C. metallidurans. This publication verifies...

    Cornelia Große, Martin Herzberg, Marcel Schüttau, Nicole Wiesemann, Gerd Hause, Dietrich H. Nies
    25 Feb 2016
  • A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in <span class="named-content genus-species" id="named-content-1">Escherichia coli</span>
    Research Article | Molecular Biology and Physiology
    A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli

    sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a...

    Divya Balasubramanian, Preethi T. Ragunathan, Jingyi Fei, Carin K. Vanderpool
    9 Feb 2016

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