Ecological and Evolutionary Science
Editor's Pick Research Article | Ecological and Evolutionary ScienceCharacterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic ResistomesAntibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the...
Research Article | Ecological and Evolutionary ScienceQuantifying the Evolutionary Conservation of Genes Encoding Multidrug Efflux Pumps in the ESKAPE Pathogens To Identify Antimicrobial Drug TargetsIncreasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogen group represents the leading cause of these infections, and upregulation of efflux pump expression is a significant mechanism of resistance in these pathogens. This has resulted in substantial interest in the development of efflux pump inhibitors to combat antibiotic-resistant infections;...
Research Article | Ecological and Evolutionary SciencePhylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical InformationThe move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits...
Special Issue Perspective | Ecological and Evolutionary ScienceAt the Nexus of History, Ecology, and Hydrobiogeochemistry: Improved Predictions across Scales through IntegrationTo improve predictions of ecosystem function in future environments, we need to integrate the ecological and environmental histories experienced by microbial communities with hydrobiogeochemistry across scales. A key issue is whether we can derive generalizable scaling relationships that describe this multiscale integration.
Special Issue Perspective | Ecological and Evolutionary ScienceIn Search of Model Ecological Systems for Understanding Specialized MetabolismMicrobes occupy diverse habitats, forming interconnected, dynamic communities. Elucidating the principles of microbial community function is a grand challenge for microbiology, and it will entail experiments that engage microbiomes across multiple levels of complexity.
Special Issue Perspective | Ecological and Evolutionary ScienceUsing Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path AheadAs troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge.
Research Article | Ecological and Evolutionary ScienceluxR Homolog-Linked Biosynthetic Gene Clusters in ProteobacteriaBacteria biosynthesize specialized metabolites with a variety of ecological functions, including defense against other microbes. Genes that code for specialized metabolite biosynthetic enzymes are frequently clustered together. These BGCs are often regulated by a transcription factor encoded within the cluster itself. These pathway-specific regulators respond to a signal or indirectly through other means of environmental sensing. Many...
Special Issue Perspective | Ecological and Evolutionary ScienceUnderstanding Microbiome Stability in a Changing WorldMicrobiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon and nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change.
Special Issue Perspective | Ecological and Evolutionary ScienceSeven Billion Microcosms: Evolution within Human MicrobiomesRational microbiome-based therapies may one day treat a wide range of diseases and promote wellness. Yet, we are still limited in our abilities to employ such therapies and to predict which bacterial strains have the potential to stably colonize a person.
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.