ecology
Research Article | Ecological and Evolutionary ScienceStreamlined and Abundant Bacterioplankton Thrive in Functional CohortsThis study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing...
Research Article | Ecological and Evolutionary ScienceAbundant and Diverse RNA Viruses in Insects Revealed by RNA-Seq Analysis: Ecological and Evolutionary ImplicationsInsects comprise the largest proportion of animals on earth and are frequently implicated in the transmission of vector-borne diseases. However, considerable attention has been paid to the phytophagous and hematophagous insects, with results that provide insufficient and biased information about the viruses in insects. Here, we have delivered compelling evidence for the exceptional abundance and genetic diversity of RNA viruses in a...
Research Article | Ecological and Evolutionary ScienceBiofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible BacteriaIn the natural environment, bacteria most often live in communities bound to one another by secreted adhesives. These communities, or biofilms, play a central role in biogeochemical cycling, microbiome functioning, wastewater treatment, and disease. Wherever there are bacteria, there are also viruses that attack them, called phages. Interactions between bacteria and phages are likely to occur ubiquitously in biofilms. We show here,...
Research Article | Novel Systems Biology TechniquesTheoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled GenomesShort-read sequencing with Illumina sequencing technology provides an accurate, high-throughput method for characterizing the metabolic potential of microbial communities. Short-read sequences can be assembled and binned into metagenome-assembled genomes, thus shedding light on the function of microbial ecosystems that are important for health, agriculture, and Earth system processes. The work presented here provides an analytical...
Special Issue Perspective | Ecological and Evolutionary ScienceThe Power of Metabolism for Predicting Microbial Community DynamicsQuantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interactions, evolutionary trajectories, and response to perturbation in simple synthetic consortia.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput ToolsVirus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion.
Special Issue Perspective | Host-Microbe BiologyDefining Microbiome Health through a Host LensWe are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state.
Special Issue Perspective | Ecological and Evolutionary ScienceSynergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research...Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap.
Research Article | Host-Microbe BiologyColonic Butyrate-Producing Communities in Humans: an Overview Using Omics DataStudies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable...
Commentary | Host-Microbe BiologyParasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host InteractionsUnderstanding how microbiomes affect host resistance, parasite virulence, and parasite-associated diseases requires a collaborative effort between parasitologists, microbial ecologists, virologists, and immunologists. We hereby propose the Parasite Microbiome Project to bring together researchers with complementary expertise and to study the role of microbes in host-parasite interactions.