Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceIs Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis...
Editor's Pick Research Article | Ecological and Evolutionary ScienceBlack Queen Evolution and Trophic Interactions Determine Plasmid Survival after the Disruption of the Conjugation NetworkBacterial antibiotic resistance is often a part of mobile genetic elements that move from one bacterium to another. By interfering with the horizontal movement and the maintenance of these elements, it is possible to remove the resistance from the population. Here, we show that a so-called plasmid-dependent bacteriophage causes the initially resistant bacterial population to become susceptible to antibiotics. However, this effect is...
Research Article | Ecological and Evolutionary ScienceLimitations of Correlation-Based Inference in Complex Virus-Microbe CommunitiesInferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems—particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference—using correlations to predict interactions—is widespread. However, it is well-known that “correlation does not imply causation.” Despite...
Research Article | Ecological and Evolutionary ScienceGenomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 StrainsBacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B. anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the...
Editor's Pick Research Article | Ecological and Evolutionary ScienceSelection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome ResearchAncient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately...
Editor's Pick Research Article | Ecological and Evolutionary ScienceMicrobial Community Cohesion Mediates Community Turnover in Unperturbed AquifersMany microbial ecology studies have examined community structuring processes in dynamic or perturbed situations, while stable environments have been investigated to a lesser extent. Researchers have predicted that environmental communities never truly reach a steady state but rather exist in states of constant flux due to internal, rather than external, dynamics. The research presented here utilized a combined null model approach to...
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 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...
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;...
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.