metagenomics
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...
Editor's Pick Research Article | Applied and Environmental ScienceValidating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal VentsIron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron...
Research Article | Therapeutics and PreventionIdentification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community AssemblyAntibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C...
Research Article | Molecular Biology and PhysiologyRegulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial CommunityMicroorganisms in the natural world are found in communities, communicating and interacting with each other; therefore, it is essential that microbial regulatory mechanisms, such as gene regulation affected by small RNAs (sRNAs), be investigated at the community level. This work demonstrates that metatranscriptomic field experiments can link environmental variation with changes in RNA pools and have the potential to provide new insights...
Research Article | Ecological and Evolutionary ScienceConsistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species BoundariesThere is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is...
Observation | Novel Systems Biology TechniquesNetwork-Based Prediction of Novel CRISPR-Associated Genes in MetagenomesEvery branch on the tree of life, including microbial life, faces the threat of viral pathogens. Over the course of billions of years of coevolution, prokaryotes have evolved a great diversity of strategies to defend against viral infections. One of these is the CRISPR adaptive immune system, which allows microbes to “remember” past infections in order to better fight them in the future. There has been much interest among molecular...
Research Article | Applied and Environmental ScienceUncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland SoilsUnderstanding the sources and controls on microbial methane production from wetland soils is critical to global methane emission predictions, particularly in light of changing climatic conditions. Current biogeochemical models of methanogenesis consider only acetoclastic and hydrogenotrophic sources and exclude methylotrophic methanogenesis, potentially underestimating microbial contributions to methane flux. Our multi-omic results...
Research Article | Ecological and Evolutionary ScienceTrends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the MediterraneanViruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance, few studies have addressed trends of mutation accumulation in marine viral communities across depth gradients. By investigating these trends, we show that mutation frequencies differ among viral genes according to their molecular functions, with the highest microdiversity occurring...
Research Article | Host-Microbe BiologyOral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic ActivitiesDental caries is a highly prevalent oral disease that can lead to severe dental damage and may greatly compromise the quality of life of the affected individuals. Previous studies, including those based on 16S rRNA gene, have revealed that the oral microbiota plays a prominent role in development of the disease. But the approach of those studies was limited in analyzing several key microbiome traits, including species- or strain-level...
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.