Latest Articles
Research Article | Molecular Biology and PhysiologyPivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial EcosystemLactate is formed by many species of colonic bacteria, and can accumulate to high levels in the colons of inflammatory bowel disease subjects. Conversely, in healthy colons lactate is metabolized by lactate-utilizing species to the short-chain fatty acids butyrate and propionate, which are beneficial for the host. Here, we investigated the impact of continuous lactate infusions (up to 20 mM) at two pH values (6.5 and 5.5) on human...
Research Article | Applied and Environmental ScienceMicrobiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast MicrobiomesChicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey, we...
Research Article | Molecular Biology and PhysiologyA Decrease in Transcription Capacity Limits Growth Rate upon Translation InhibitionExposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that...
Research Article | Host-Microbe BiologyDietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life UndernutritionNonalcoholic fatty liver disease (NAFLD) remains a global epidemic, but it is often studied in the context of obesity and aging. Nutritional deficits, however, also trigger hepatic steatosis, influencing health trajectories in undernourished pediatric populations. Here, we report that exposure to specific gut microbes impacts fatty liver pathology in mice fed a protein/fat-deficient diet. We utilize a multiomics approach to (i)...
Research Article | Novel Systems Biology TechniquesIntegrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coliMost studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single...
Editor's Pick Research Article | Host-Microbe BiologyRespiratory Bacteria Stabilize and Promote Airborne Transmission of Influenza A VirusInfection with influenza A virus (IAV), especially when complicated with a secondary bacterial infection, is a leading cause of global mortality and morbidity. Gaining a greater understanding of the transmission dynamics of IAV is important during seasonal IAV epidemics and in the event of a pandemic. Direct bacterium-virus interactions are a recently appreciated aspect of infectious disease biology. Direct interactions between IAV and...
Research Article | Host-Microbe BiologyLow Baseline Pulmonary Levels of Cytotoxic Lymphocytes as a Predisposing Risk Factor for Severe COVID-19COVID-19 is caused by the highly contagious coronavirus SARS-CoV-2 and currently has detrimental human health, community, and economic impacts around the world. It is unclear why some SARS-CoV-2-positive individuals develop severe COVID-19 symptoms, which can be fatal, while others only develop mild symptoms. In the absence of an effective and widely available vaccine, it is of paramount importance that we identify risk factors for...
Research Article | Molecular Biology and PhysiologyNegative Interplay between Biofilm Formation and Competence in the Environmental Strains of Bacillus subtilisThe soil bacterium Bacillus subtilis can form robust biofilms, which are important for its survival in the environment. B. subtilis also exhibits natural competence. By investigating competence development in B. subtilis in...
Research Article | Novel Systems Biology TechniquesRRE-Finder: a Genome-Mining Tool for Class-Independent RiPP DiscoveryBioinformatics-powered discovery of novel ribosomal natural products (RiPPs) has historically been hindered by the lack of a common genetic feature across RiPP classes. Herein, we introduce RRE-Finder, a method for identifying RRE domains, which are present in a majority of prokaryotic RiPP biosynthetic gene clusters (BGCs). RRE-Finder identifies RRE domains 3,000 times faster than current methods, which rely on time-consuming secondary...
Research Article | Novel Systems Biology TechniquesMetabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicronBacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron (B. theta) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s)...