microbiome
Perspective | Applied and Environmental ScienceCurrent State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019...Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses.
Research Article | Host-Microbe BiologyMolecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic FibrosisMicrobial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same...
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...
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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceStrategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME WorkshopHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A weeklong workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional...
Research Article | Host-Microbe BiologyThe Oral Mouse Microbiome Promotes Tumorigenesis in Oral Squamous Cell CarcinomaThere is growing evidence that changes in the microbiome are associated with carcinogenesis. To date, no consistent oral microbiome composition associated with OSCC has been identified. Longitudinal and functional studies like the study presented here should yield a better understanding of the role that the oral microbiome plays in OSCC. Our findings, obtained using a germ-free mouse model, indicate that the presence of different oral...
Research Article | Applied and Environmental ScienceLongitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City SewageUrban sewage or wastewater is a diverse source of bacterial growth, as well as a hot spot for the development of environmental antibiotic resistance, which can in turn influence the health of the residents of the city. As part of a larger study to characterize the urban New York City microbial metagenome, we collected raw sewage samples representing three seasonal time points spanning the five boroughs of NYC and went on to characterize...
Perspective | Ecological and Evolutionary ScienceExperimental Microbiomes: Models Not to ScaleLow-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static “screenshots” derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems.
Research Article | Novel Systems Biology TechniquesSpecies Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut MicrobesGut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability...
Observation | Novel Systems Biology Techniquesredbiom: a Rapid Sample Discovery and Feature Characterization SystemAlthough analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify...