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Archive

July/August 2018; Volume 3,Issue 4

Editorials

  • Critical Assessment of Metagenome Interpretation Enters the Second Round
    Editorial
    Critical Assessment of Metagenome Interpretation Enters the Second Round
    Andreas Bremges, Alice C. McHardy
    10 Jul 2018
  • Announcement of 2019 Keystone Symposia Conference: “Microbiome: Chemical Mechanisms and Biological Consequences”
    Editorial
    Announcement of 2019 Keystone Symposia Conference: “Microbiome: Chemical Mechanisms and Biological Consequences”

    The Keystone Symposia will be hosting a conference organized by Emily Balskus, Peter Turnbaugh, and Dennis Wolan entitled “Microbiome: Chemical Mechanisms and Biological Consequences” 10 to 14 March 2019 in Montreal, Québec, Canada. Our goal for this meeting is to focus attention on the intersection of chemistry and biology by bringing together scientists in these two disciplines, while also including talks about other hosts,...

    Emily P. Balskus, Peter J. Turnbaugh, Dennis W. Wolan
    24 Jul 2018

Perspectives

  • The Current and Future State of Department of Defense (DoD) Microbiome Research: a Summary of the Inaugural DoD Tri-Service Microbiome Consortium Informational Meeting
    Perspective | Host-Microbe Biology
    The Current and Future State of Department of Defense (DoD) Microbiome Research: a Summary of the Inaugural DoD Tri-Service Microbiome Consortium Informational Meeting

    The Tri-Service Microbiome Consortium (TSMC) was recently established to enhance collaboration, coordination, and communication of microbiome research among Department of Defense (DoD) organizations. The TSMC aims to serve as a forum for sharing information related to DoD microbiome research, policy, and applications, to monitor global advances relevant to human health and performance, to identify priority objectives, and to facilitate...

    Sarah Glaven, Kenneth Racicot, Dagmar H. Leary, J. Philip Karl, Steven Arcidiacono, Blair C. R. Dancy, Linda A. Chrisey, Jason W. Soares
    10 Jul 2018

Methods and Protocols

  • Balances: a New Perspective for Microbiome Analysis
    Methods and Protocols | Host-Microbe Biology
    Balances: a New Perspective for Microbiome Analysis

    We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual’s specific microbiota.

    J. Rivera-Pinto, J. J. Egozcue, V. Pawlowsky-Glahn, R. Paredes, M. Noguera-Julian, M. L. Calle
    17 Jul 2018

Research Articles

  • Coproporphyrin III Produced by the Bacterium <em>Glutamicibacter arilaitensis</em> Binds Zinc and Is Upregulated by Fungi in Cheese Rinds
    Research Article | Applied and Environmental Science
    Coproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese Rinds

    Bacterium-fungus interactions play key roles in the assembly of cheese rind microbial communities, but the molecular mechanisms underlying these interactions are poorly characterized. Moreover, millions of people around the world enjoy eating cheeses and cheese rinds, but our understanding of the diversity of microbial metabolites ingested during cheese consumption is limited. The discovery of zinc coproporphyrin III as the cause of...

    Jessica L. Cleary, Shilpa Kolachina, Benjamin E. Wolfe, Laura M. Sanchez
    21 Aug 2018
  • Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation
    Research Article | Host-Microbe Biology
    Holistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed Degradation

    Ruminant animals, such as cows, live in a tight symbiotic association with microorganisms, allowing them to feed on otherwise indigestible plant biomass as food sources. Methane is produced as an end product of the anaerobic feed degradation in ruminants and is emitted to the atmosphere, making ruminant animals among the major anthropogenic sources of the potent greenhouse gas methane. Using newly developed quantitative...

    Andrea Söllinger, Alexander Tøsdal Tveit, Morten Poulsen, Samantha Joan Noel, Mia Bengtsson, Jörg Bernhardt, Anne Louise Frydendahl Hellwing, Peter Lund, Katharina Riedel, Christa Schleper, Ole Højberg, Tim Urich
    7 Aug 2018
  • Combinatorial Approaches to Viral Attenuation
    Research Article | Therapeutics and Prevention
    Combinatorial Approaches to Viral Attenuation

    Live viral vaccines rely on attenuated viruses that can successfully infect their host but have reduced fitness or virulence. Such attenuated viruses were originally developed through trial and error, typically by adaptation of the wild-type virus to novel conditions. That method was haphazard, with no way of controlling the degree of attenuation or the number of attenuating mutations or preventing evolutionary reversion. Synthetic...

    Matthew L. Paff, Benjamin R. Jack, Bartram L. Smith, James J. Bull, Claus O. Wilke
    31 Jul 2018
  • Responses of the Human Gut <em>Escherichia coli</em> Population to Pathogen and Antibiotic Disturbances
    Editor's Pick Research Article | Host-Microbe Biology
    Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances

    Research on human-associated E. coli tends to focus on pathogens, such as enterotoxigenic E. coli (ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenic...

    Taylor K. S. Richter, Jane M. Michalski, Luke Zanetti, Sharon M. Tennant, Wilbur H. Chen, David A. Rasko
    24 Jul 2018
  • Genomic Characterization and Copy Number Variation of <em>Bacillus anthracis</em> Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains
    Research Article | Ecological and Evolutionary Science
    Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains

    Bacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the...

    Angela Pena-Gonzalez, Luis M. Rodriguez-R, Chung K. Marston, Jay E. Gee, Christopher A. Gulvik, Cari B. Kolton, Elke Saile, Michael Frace, Alex R. Hoffmaster, Konstantinos T. Konstantinidis
    14 Aug 2018
  • Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers

    Many microbial ecology studies have examined community structuring processes in dynamic or perturbed situations, while stable environments have been investigated to a lesser extent. Researchers have predicted that environmental communities never truly reach a steady state but rather exist in states of constant flux due to internal, rather than external, dynamics. The research presented here utilized a combined null model approach to...

    Robert E. Danczak, Michael D. Johnston, Chris Kenah, Michael Slattery, Michael J. Wilkins
    3 Jul 2018
  • Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research

    Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately...

    Irina M. Velsko, Laurent A. F. Frantz, Alexander Herbig, Greger Larson, Christina Warinner
    17 Jul 2018
  • Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities
    Research Article | Ecological and Evolutionary Science
    Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities

    Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite...

    Ashley R. Coenen, Joshua S. Weitz
    28 Aug 2018
  • Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion
    Research Article | Molecular Biology and Physiology
    Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

    Transcription factors play a crucial role in the regulation of gene expression and adaptation to different environments. To better understand the underlying roles of these adaptations, we performed experiments that give us high-resolution binding of transcription factors to their targets. We investigated five transcription factors involved in lipid metabolism in yeast, and we discovered multiple novel targets and condition-specific...

    David Bergenholm, Guodong Liu, Petter Holland, Jens Nielsen
    31 Jul 2018

Erratum

  • Erratum for Grieneisen and Blekhman, “Crowdsourcing Our National Gut”
    Erratum
    Erratum for Grieneisen and Blekhman, “Crowdsourcing Our National Gut”
    Laura E. Grieneisen, Ran Blekhman
    10 Jul 2018
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mSystems: 3 (4)

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volume 3, issue 4
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  • High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County
  • Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
  • 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission
  • Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice
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