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Methods and Protocols | Novel Systems Biology TechniquesImpact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota ProfilingLarge-scale human microbiota studies require specimens collected from multiple sites and/or time points to maximize detection of the small effects in microbe-host interactions. However, batch biases caused by experimental protocols, such as sample collection, massively parallel sequencing, and bioinformatics analyses, remain critical and should be minimized. This work evaluated the effects of preservation solutions and bacterial 16S...
Editor's Pick Minireview | Applied and Environmental Science2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce TransmissionWith the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for...
Resource Report | Novel Systems Biology TechniquesMicrobiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level...A search-based strategy is useful for large-scale mining of microbiome data sets, such as a bird’s-eye view of the microbiome data space and disease diagnosis via microbiome big data. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes against the existing microbiome data sets on the basis of their similarity in taxonomic structure or functional profile.
Research Article | Ecological and Evolutionary ScienceFungal Communities Are Important Determinants of Bacterial Community Composition in DeadwoodUnderstanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions.
Research Article | Applied and Environmental SciencePhylogenetic Distribution of Plastic-Degrading MicroorganismsWe have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved.
Editor's Pick Research Article | Ecological and Evolutionary ScienceComplementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood DecompositionWood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers.
Research Article | Host-Microbe BiologyHeritable Gut Microbiome Associated with Salmonella enterica Serovar Pullorum Infection in ChickensThe present study investigated the association among the host genome, the gut microbiome, and S. Pullorum infection in chickens. The results suggested that the gut microbial structure is altered in S. Pullorum-infected chickens.
Editor's Pick Research Article | Applied and Environmental ScienceSARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed CasesWastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of...
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...
Minireview | Applied and Environmental ScienceComputational Analysis of Microbial Flow Cytometry DataFlow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.