Latest Articles
Research Article | Applied and Environmental ScienceMicrobiome and Metagenome Analyses of a Closed Habitat during Human OccupationThis study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely...
Research Article | Novel Systems Biology TechniquesSelective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarumOur findings demonstrate conclusively that low abundance and upregulated transcripts are preferentially translated, potentially by environment-specific translation systems with distinct ribosomal protein composition. We show that a complex interplay of transcriptional and posttranscriptional regulation underlies the conditional and modular regulatory programs that generate ribosomes of distinct protein composition. The modular...
Research Article | Host-Microbe BiologyConsumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to CiprofloxacinDue to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our “Western”-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in...
Research Article | Applied and Environmental ScienceImpact of Glyphosate on the Honey Bee Gut Microbiota: Effects of Intensity, Duration, and Timing of ExposureAs is true of many animal species, honey bees depend on their gut microbiota for health. The bee gut microbiota has been shown to regulate the host immune system and to protect against pathogenic diseases, and disruption of the normal microbiota leads to increased mortality. Understanding these effects can give broad insights into vulnerabilities of gut communities, and, in the case of honey bees, could provide information useful for...
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 | Applied and Environmental ScienceTemperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation SystemWe used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it...
Editor's Pick Research Article | Ecological and Evolutionary ScienceSoil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic ResolutionIt is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is...
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 | Applied and Environmental ScienceSystem Performance Corresponding to Bacterial Community Succession after a Disturbance in an Autotrophic Nitrogen Removal BioreactorDynamics of microbial communities are believed to be associated with system functional processes in bioreactors. However, few studies have provided quantitative evidence. The difficulty of evaluating direct microbe-system relationships arises from the fact that system performance is affected by convolved effects of microbiota and bioreactor operational parameters (i.e., deterministic external physicochemical forcing). Here, using fine-...
Research Article | Molecular Biology and PhysiologyGenome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and PromotersEfforts to rationally engineer synthetic pathways in Zymomonas mobilis are impeded by a lack of knowledge and tools for predictable and quantitative programming of gene regulation at the transcriptional, posttranscriptional, and posttranslational levels. With the detailed functional characterization of the...