Archive
Editorials
EditorialAnnouncement 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,...
Perspectives
Perspective | Host-Microbe BiologyThe Current and Future State of Department of Defense (DoD) Microbiome Research: a Summary of the Inaugural DoD Tri-Service Microbiome Consortium Informational MeetingThe 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...
Methods and Protocols
Methods and Protocols | Host-Microbe BiologyBalances: a New Perspective for Microbiome AnalysisWe 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.
Research Articles
Research Article | Applied and Environmental ScienceCoproporphyrin III Produced by the Bacterium Glutamicibacter arilaitensis Binds Zinc and Is Upregulated by Fungi in Cheese RindsBacterium-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...
Research Article | Host-Microbe BiologyHolistic Assessment of Rumen Microbiome Dynamics through Quantitative Metatranscriptomics Reveals Multifunctional Redundancy during Key Steps of Anaerobic Feed DegradationRuminant 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...
Research Article | Therapeutics and PreventionCombinatorial Approaches to Viral AttenuationLive 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...
Editor's Pick Research Article | Host-Microbe BiologyResponses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic DisturbancesResearch 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...
Research Article | Ecological and Evolutionary ScienceGenomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 StrainsBacillus 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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceMicrobial Community Cohesion Mediates Community Turnover in Unperturbed AquifersMany 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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceSelection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome ResearchAncient 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...
Research Article | Ecological and Evolutionary ScienceLimitations of Correlation-Based Inference in Complex Virus-Microbe CommunitiesInferring 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...
Research Article | Molecular Biology and PhysiologyReconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease DigestionTranscription 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...
