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Editor's Pick Minireview | Applied and Environmental Science2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce TransmissionWith the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for...
Research Article | Host-Microbe BiologyBactopia: a Flexible Pipeline for Complete Analysis of Bacterial GenomesIt is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization of multiple open source software tools. We present Bactopia, a pipeline for bacterial genome analysis, as an option for processing bacterial genome data. Bactopia also automates downloading of data from multiple public sources and species-specific customization. Because the pipeline...
Editor's Pick Research Article | Applied and Environmental ScienceSARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed CasesWastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of...
Research Article | Molecular Biology and PhysiologySystematic Reconstruction of the Complete Two-Component Sensorial Network in Staphylococcus aureusBacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by...
Perspective | Host-Microbe BiologyCOVID-19 and the Gut Microbiome: More than a Gut FeelingDue to its fundamental role in the induction, training, and function of the immune system, it is critical to include characterizations of the gut microbiome in clinical trials and studies that aim to broaden our understanding of coronavirus disease 2019 (COVID-19). Understanding the “gut-lung axes,” where gut microbiome composition influences the lung’s susceptibility to viral infections and viral infections of the lung alter gut...
Research Article | Therapeutics and PreventionA Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in ChildrenMiSH, which is based on the skin microbiome, can quantitatively assess pediatric skin health across cohorts from distinct countries over large geographic distances. Moreover, the index can identify a risk-prone skin state and compare treatment effect in children, suggesting applications in diagnosis and patient stratification.
Research Article | Host-Microbe BiologyDistinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosisUnderstanding how Mycobacterium tuberculosis survives during antibiotic treatment is necessary to rationally devise more effective tuberculosis (TB) chemotherapy regimens. Using genome-wide mutant fitness profiling and the mouse model of TB, we identified genes that alter antibiotic efficacy specifically in the infection environment and associated several of these...
Research Article | Applied and Environmental ScienceExpanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating MicroorganismsAccurately assessing the production of bioaccumulative neurotoxic methylmercury by characterizing the phylogenetic diversity, metabolic functions, and activity of methylators in the environment is crucial for understanding constraints on the mercury cycle. Much of our understanding of methylmercury production is based on cultured anaerobic microorganisms within the ...
Research Article | Molecular Biology and PhysiologyProteomic Study of the Survival and Resuscitation Mechanisms of Filamentous Persisters in an Evolved Escherichia coli Population from Cyclic Ampicillin TreatmentPersisters are a subpopulation of cells with enhanced survival toward antibiotic treatment and have the ability to resume normal growth when the antibiotic stress is lifted. Although proteomics is the most suitable tool to study them from a system-level perspective, the number of persisters that present naturally is too few for proteomics analysis, and thus the complex mechanisms through which they are able to survive antibiotic...
Research Article | Ecological and Evolutionary SciencePrivatization of Biofilm Matrix in Structurally Heterogeneous BiofilmsBiofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of nonproducing individuals on biofilm development raise questions about the dynamics between community members, especially when isogenic nonproducers exist within wild-type populations. We asked ourselves whether phenotypic nonproducers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression...