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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 | Host-Microbe BiologyEcology and Host Identity Outweigh Evolutionary History in Shaping the Bat MicrobiomeThis study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across...
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 | Applied and Environmental ScienceIntegrated Meta-omics Approaches To Understand the Microbiome of Spontaneous Fermentation of Traditional Chinese Pu-erh TeaFermented foods play important roles in diets worldwide and account for approximately one-third of all foods and beverages consumed. To date, traditional fermentation has used spontaneous fermentation. The microbiome in fermentation has direct impacts on the quality and safety of fermented foods and contributes to the preservation of traditional methods. Here, we used an integrated meta-omics approach to study the microbiome in the...
Research Article | Host-Microbe BiologyRacial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European AncestryIn this systemic investigation of racial differences in the oral microbiome using a large data set, we disclosed the significant differences in the oral microbial richness/evenness, as well as in the overall microbial composition, between African-Americans and European-Americans. We also found multiple oral bacterial taxa, including several preidentified oral pathogens, showing a significant different abundance or prevalence between...
Research Article | Host-Microbe BiologyAssociation of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in IndiaThis study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut...
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.
Methods and Protocols | Novel Systems Biology TechniquesEvaluating the Information Content of Shallow Shotgun MetagenomicsA common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S...
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 | Novel Systems Biology TechniquesQuantifying and Understanding Well-to-Well Contamination in Microbiome ResearchMicrobiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...