Latest Articles
Research Article | Host-Microbe BiologyA Simple Screening Approach To Prioritize Genes for Functional Analysis Identifies a Role for Interferon Regulatory Factor 7 in the Control of Respiratory Syncytial Virus DiseaseMaking the most of “big data” is one of the core challenges of current biology. There is a large array of heterogeneous data sets of host gene responses to infection, but these data sets do not inform us about gene function and require specialized skill sets and training for their utilization. Here we describe an approach that combines and simplifies these data sets, distilling this information into a single list of genes commonly...
Commentary | Applied and Environmental ScienceAvoiding Pandemic Fears in the Subway and Conquering the PlatypusMetagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and...
Editor's Pick Research Article | Novel Systems Biology TechniquesMoleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil MetagenomesSoil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches,...
Editor's Pick Research Article | Applied and Environmental ScienceUrban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the EnvironmentMass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million...
Editor's Pick Research Article | Host-Microbe BiologyIs the Evolution of Salmonella enterica subsp. enterica Linked to Restriction-Modification Systems?The evolution of bacterial pathogens, their plasticity and ability to rapidly change and adapt to new surroundings are crucial for understanding the epidemiology and public health. With the application of genomics, it became clear that horizontal gene transfer played a key role in evolution. To understand the evolution and diversification of pathogens, we need to understand the processes that drive the horizontal gene transfer....
Research Article | Applied and Environmental ScienceThermus and the Pink Discoloration Defect in CheesePink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In...
Research Article | Novel Systems Biology TechniquesA Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA VirusesThis report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities...
Research Article | Applied and Environmental ScienceMetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain VariationTaxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-...
Research Article | Molecular Biology and PhysiologyTemporal Regulation of the Bacillus subtilis Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall GrowthThe past decade highlighted Nε-lysine acetylation as a prevalent posttranslational modification in bacteria. However, knowledge regarding the physiological importance and temporal regulation of acetylation has remained limited. To uncover potential regulatory roles for acetylation, we analyzed how acetylation patterns and abundances change between growth phases in...
