Most read article(s)
Research Article | Host-Microbe BiologyGut Microbiota Has a Widespread and Modifiable Effect on Host Gene RegulationThe composition of the gut microbiome has been associated with various aspects of human health, but the mechanism of this interaction is still unclear. We utilized a cellular system to characterize the effect of the microbiome on human gene expression. We showed that some of these changes in expression may be mediated by changes in chromatin accessibility. Furthermore, we validate the role of a specific microbe and show that changes in...
Research Article | Host-Microbe BiologyAmerican Gut: an Open Platform for Citizen Science Microbiome ResearchWe show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the...
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.
Editor's Pick Research Article | Novel Systems Biology TechniquesA Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human MicrobiotaExperimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to...
Research Article | Host-Microbe BiologyInfluence of Feeding Type and Nosema ceranae Infection on the Gut Microbiota of Apis cerana WorkersThe gut microbiota plays an essential role in the health of bees. Scientific evidence suggests that diet and infection can affect the gut microbiota and modulate the health of the gut; however, the interplay between those two factors and the bee gut microbiota is not well known. In this study, we used a high-throughput sequencing method to monitor the changes of gut microbiota associated with both feeding types and...
Editor's Pick Research Article | Applied and Environmental SciencePhylogenetically Novel Uncultured Microbial Cells Dominate Earth MicrobiomesIn the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of...
Research Article | Ecological and Evolutionary ScienceExisting Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil ProkaryotesThere have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the...
Research Article | Clinical Science and EpidemiologyTransmission of Hepatitis B and D Viruses in an African Rural CommunityThis study revealed that the prevalence of HBV and HDV in a rural area of Cameroon is extremely high, underlining the pressing need for the improvement of control strategies. Systematic serological and phylogenetic analyses of HBV sequences turned out to be useful tools to identify networks of virus transmission within and between households. The high HBsAg carriage rate found among children demonstrates that implementation of the HBV...
Editor's Pick Research Article | Ecological and Evolutionary ScienceA Genome-Based Species Taxonomy of the Lactobacillus Genus ComplexThe Lactobacillus genus complex is a group of bacteria that constitutes an important source of strains with medical and food applications. The number of bacterial whole-genome sequences available for this taxon has been increasing rapidly in recent years. Despite this wealth of information, the species within this group are still largely defined by older techniques. Here, we constructed a completely new species-level taxonomy...
Research Article | Applied and Environmental ScienceProteomic Dissection of the Cellulolytic Machineries Used by Soil-Dwelling BacteroidetesCellulose is the most abundant renewable polymer on earth, but its recalcitrance limits highly efficient conversion methods for energy-related and material applications. Though microbial cellulose conversion has been studied for decades, recent advances showcased that large knowledge gaps still exist. Bacteria of the phylum Bacteroidetes are regarded as highly efficient carbohydrate metabolizers, but most species are limited to...