microbial ecology
Research Article | Ecological and Evolutionary ScienceExperimental Evidence for Adaptation to Species-Specific Gut Microbiota in House MiceThe communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased...
Commentary | Applied and Environmental SciencemSphere of Influence: Engineering MicrobesPatrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L.
Research Article | Ecological and Evolutionary ScienceThe Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence DataA steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream...
Research Article | Ecological and Evolutionary ScienceGene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic ConditionsBy combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this...
Research Article | Host-Microbe BiologyThe Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection StatusWaterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual’s microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed...
Perspective | Host-Microbe BiologyBats Are an Untapped System for Understanding Microbiome Evolution in MammalsMammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals.
Research Article | Ecological and Evolutionary ScienceTaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic ResolutionMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or...
Observation | Ecological and Evolutionary ScienceBroadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic UnitsMicrobial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive...
Research Article | Host-Microbe BiologyClostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained ColonizationClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with...
Opinion/Hypothesis | Ecological and Evolutionary ScienceModel Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater BacteriaGenome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations.