Latest Articles
Research Article | Host-Microbe BiologyConsumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and MetabolomePublic interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented...
Research Article | Applied and Environmental ScienceFORENSIC: an Online Platform for Fecal Source IdentificationFORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk...
Research Article | Ecological and Evolutionary ScienceHorizontal Plasmid Transfer Promotes the Dissemination of Asian Acute Hepatopancreatic Necrosis Disease and Provides a Novel Mechanism for Genetic Exchange and Environmental AdaptationGlobal outbreaks of shrimp acute hepatopancreatic necrosis disease (AHPND) caused by V. parahaemolyticus represent an urgent issue for the shrimp industry. This study revealed that the transmission mode of AHPND consists of two steps, the transregional dissemination of V. parahaemolyticus and the...
Research Article | Molecular Biology and PhysiologyIn Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H TracersThermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as...
Research Article | Host-Microbe BiologyThe Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin DegradationThe gut microbiome may play an important role in insect-plant interactions mediated by plant secondary metabolites, but the microbial communities and functions of toxic plant feeders are still poorly characterized. In the present study, we provide the first metagenome of gut bacterial communities associated with a specialist weevil feeding on saponin-rich and saponin-low camellia seeds, and the results reveal the correlation between...
Research Article | Ecological and Evolutionary ScienceGenomic and Transcriptomic Evidence Supports Methane Metabolism in ArchaeoglobiCurrent understanding of the diversity, biology, and ecology of Archaea is very limited, especially considering how few of the known phyla have been cultured or genomically explored. The reconstruction of “Ca. Methanomixophus” MAGs not only expands the known range of metabolic versatility of the members of Archaeoglobi but also suggests that the phylogenetic distribution of MCR and MTR complexes is even wider...
Research Article | Novel Systems Biology TechniquesMultiple-Disease Detection and Classification across Cohorts via Microbiome SearchHere, we present a search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares them to databases of samples from patients. This approach enables the identification of microbiome states associated with disease even in the presence of different cohorts, multiple sequencing platforms, or significant...
Research Article | Ecological and Evolutionary ScienceEcological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale EcosystemsInteractions between viral communities and their microbial hosts have been the subject of many recent studies in a wide range of ecosystems. The degree of coordination between ecological assembly processes influencing viral and microbial communities, however, has been explored to a much lesser degree. By using a combined null modeling approach, this study investigated the ecological assembly processes influencing both viral and...
Research Article | Molecular Biology and PhysiologyRedox-Regulated Adaptation of Streptococcus oligofermentans to Hydrogen Peroxide StressThe catalase-negative streptococci produce as well as tolerate high levels of H2O2. This work reports the molecular mechanisms of low-H2O2-concentration-induced adaptation to higher H2O2 stress in a Streptococcus species, in which the peroxide-responsive repressor PerR and its redox regulons play the major role. Distinct from the...
Author Reply | Host-Microbe BiologyReply to Kenyon, “Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?”