microbiota
Resource Report | Host-Microbe BiologyNew Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive TractThe eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD...
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...
Research Article | Therapeutics and PreventionBacteriophages Synergize with the Gut Microbial Community To Combat SalmonellaAntibiotic-resistant bacteria are a global threat. Therefore, alternative approaches for combatting bacteria, especially antibiotic-resistant bacteria, are urgently needed. Using a human gut microbiota model, we demonstrate that bacteriophages (phages) are able to substantially decrease pathogenic Salmonella without perturbing the microbiota. Conversely, antibiotic treatment leads to the eradication of close to all commensal...
Special Issue Perspective | Therapeutics and PreventionBeyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized TherapeuticsOver the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems.
Methods and Protocols | Novel Systems Biology TechniquesDirect PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut MicrobiomesThe microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA...
Editor's Pick Research Article | Host-Microbe BiologyMulti-omics Comparative Analysis Reveals Multiple Layers of Host Signaling Pathway Regulation by the Gut MicrobiotaMultiple host pathways were affected by its adaptation to the microbiota. We have found significant transcriptome-proteome discordance caused by the microbiota. This discovery leads to the definite conclusion that transcript-level analysis is not sufficient to predict protein levels and their influence on the function of many specific cellular pathways, so only analysis of combinations of the quantitative data determined at different...
Research Article | Host-Microbe BiologyDifferences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their DietsThe human gastrointestinal microbiota functions as an important mediator of diet for host metabolism. To evaluate how consumed diets influence the gut environment, we carried out simultaneous interrogations of distal gut microbiota and metabolites in samples from healthy children in Egypt and the United States. While Egyptian children consumed a Mediterranean diet rich in plant foods, U.S. children consumed a Western diet high in animal...
Research Article | Applied and Environmental ScienceMicrobial Succession and Flavor Production in the Fermented Dairy Beverage KefirTraditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that...
Research Article | Applied and Environmental ScienceThermus and the Pink Discoloration Defect in CheesePink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In...