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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...
Observation | Host-Microbe BiologyHuman Skin, Oral, and Gut Microbiomes Predict Chronological AgeConsiderable evidence suggests that the gut microbiome changes with age or even accelerates aging in adults. Whether the age-related changes in the gut microbiome are more or less prominent than those for other body sites and whether predictions can be made about a person’s age from a microbiome sample remain unknown. We therefore combined several large studies from different countries to determine which body site’s microbiome could...
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.
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...
Editor's Pick Research Article | Novel Systems Biology TechniquesSystematic Localization of Escherichia coli Membrane ProteinsCurrent knowledge of protein localization, particularly outer membrane proteins, is highly dependent on bioinformatic predictions. To date, no systematic experimental studies have directly compared protein localization spanning the inner and outer membranes of E. coli. By combining sucrose density gradient fractionation of inner membrane (IM) and outer membrane (OM)...
Research Article | Ecological and Evolutionary ScienceComplementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest SoilMicrobial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of...
Research Article | Host-Microbe BiologyCorrelations between the Composition of the Bovine Microbiota and Vitamin B12 AbundanceIn this paper, we examined the microbiome of the bovine rumen, feces, and milk and attempted to understand how the bacterial communities at each site affected the production and movement of vitamin B12 around the animal’s body. It was determined that the composition of the bovine rumen microbiome correlates well with vitamin B12 concentration, indicating that the rumen microbiota may be a good target for...
Special Issue Perspective | Host-Microbe BiologyNew Approaches to Microbiome-Based TherapiesOver the last decade, our understanding of the composition and functions of the gut microbiota has greatly increased. To a large extent, this has been due to the development of high-throughput genomic analyses of microbial communities, which have identified the critical contributions of the microbiome to human health.
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...