Latest Articles
Commentary | Applied and Environmental ScienceThe Built Environment Is a Microbial WastelandHumanity’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.
Editor's Pick Research Article | Applied and Environmental ScienceGeography and Location Are the Primary Drivers of Office Microbiome CompositionOur 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...
Research Article | Molecular Biology and PhysiologyComprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence GenesS. 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...
Editor's Pick Perspective | Host-Microbe BiologyGetting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their MicrobiomesGiven 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...
Editor's Pick Research Article | Host-Microbe BiologyLocal Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and BacteriophagesWhile 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...
Research Article | Molecular Biology and PhysiologyCharacterization of the Δ7 Mutant of Cupriavidus metallidurans with Deletions of Seven Secondary Metal Uptake SystemsBacteria, 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...
Research Article | Molecular Biology and PhysiologyA Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia colisRNAs 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...
Research Article | Ecological and Evolutionary ScienceOpen-Source Sequence Clustering Methods Improve the State Of the ArtMassive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate...
Editor's Pick Research Article | Novel Systems Biology TechniquesADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host InteractionsThe quantity and breadth of genome-scale data sets that examine RNA expression in diverse bacterial and eukaryotic species are increasing more rapidly than for curated knowledge. Our ADAGE method integrates such data without requiring gene function, gene pathway, or experiment labeling, making practical its application to any large gene expression compendium. We built a ...
Editor's Pick Research Article | Novel Systems Biology TechniquesMetabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic VariationStudies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on...