Latest Articles
Research Article | Ecological and Evolutionary ScienceComparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical DistributionThe COVID-19 pandemic continues to storm the world, with over 6.5 million cases worldwide. The severity of the disease varies with the territories and is mainly influenced by population density and age factor. In this study, we analyzed the transmission pattern of 95 SARS-CoV-2 genomes isolated from 11 different countries. Our study also revealed several nonsynonymous mutations in ORF1b and S-proteins and the impact on their structural...
Research Article | Host-Microbe BiologyHost Genetic Factors Associated with Vaginal Microbiome Composition in Kenyan WomenGlobally, bacterial vaginosis (BV) is a common condition in women. BV is associated with poorer reproductive health outcomes and HIV risk. Typically, BV represents a shift in the vaginal microbiome from one that is dominated by Lactobacillus to one that is diverse. Despite many women having similar exposures, the prevalence of BV and nonoptimal vaginal microbiome is increased for women of African descent, suggesting a possible...
Research Article | Molecular Biology and PhysiologySystematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by RecombinationMany bacterial species contain DNA methyltransferases that have random on/off switching of expression. These systems, called phasevarions (phase-variable regulons), control the expression of multiple genes by global methylation changes. In every previously characterized phasevarion, genes involved in pathobiology, antibiotic resistance, and potential vaccine candidates are randomly varied in their expression, commensurate with...
Research Article | Applied and Environmental SciencePlant and Soil Development Cooperatively Shaped the Composition of the phoD-Harboring Bacterial Community along the Primary Succession in the Hailuogou Glacier ChronosequencePhosphorus was the key limiting nutrient for soil development during primary succession that occurred in alpine and high-latitude ecosystems with cold and humid climates. The interactions of functional microbiota involved in phosphorus cycling in the rhizosphere under different soil developmental stages along primary succession are still rarely examined. We selected the pioneer species Populus purdomii as a model plant to study...
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 ScienceUntangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic ApproachWe developed a novel method for accurate cataloguing of bacterial communities at (sub)species level involving amplification of the internal transcribed spacer (ITS) region through optimized primers, followed by next-generation sequencing and taxonomic classification of amplicons by means of a comprehensive database of bacterial ITS sequences. Host-associated, food, and environmental matrices were employed to test the performance of the...
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...