Latest Articles
Resource Report | Novel Systems Biology TechniquesComprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RFThe robust ability of Enterococcus faecalis to survive outside the host and to spread via oral-fecal transmission and its high degree of intrinsic and acquired antimicrobial resistance all complicate the treatment of hospital-acquired enterococcal infections. The conserved E. faecalis core genome...
Research Article | Molecular Biology and PhysiologyCoordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary PhaseDuring the growth transition of E. coli from exponential phase to stationary, the genome expression pattern is altered markedly. For this alteration, the transcription apparatus is altered by binding of anti-sigma factor Rsd to the RpoD sigma factor for sigma factor replacement, while the translation machinery is modulated by binding of RMF to 70S ribosome to form...
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 | 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 | 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...
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 | 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...
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...
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,...
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...