Latest Articles
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...
EditorialmSystems: Learning To Love SystemsWe want this journal to be a forum for publication of research, tools, and data sets that are advancing our understanding of, or ability to investigate or interpret, microbiology systems. For example, I hope that mSystems will be a venue for research that elucidates the metabolic and cell-cell signaling mechanisms that underpin observed successional dynamics in microbial ecosystems.
Methods and Protocols | Novel Systems Biology Techniquescual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics StudiesThe adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis,...
Methods and Protocols | Novel Systems Biology TechniquesImproved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community SurveysWe continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is...
Research Article | Ecological and Evolutionary ScienceClades of Photosynthetic Bacteria Belonging to the Genus Rhodopseudomonas Show Marked Diversity in Light-Harvesting Antenna Complex Gene Composition and ExpressionRhodopseudomonas palustris is a phototrophic purple nonsulfur bacterium that adapts its photosystem to allow growth at a range of light intensities. It does this by adjusting the amount and composition of peripheral light-harvesting (LH) antenna complexes that it synthesizes. Rhodopseudomonas strains are notable for containing numerous sets of light-...