microbial ecology
Research Article | Ecological and Evolutionary ScienceTemporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicusPacific chub mackerel, Scomber japonicus, are one of the largest and most economically important fisheries in the world. The fish is harvested for both human consumption and fish meal. Changing ocean conditions driven by anthropogenic stressors like climate change may negatively impact fisheries. One mechanism for this is through disease. As waters warm and chemistry changes, the microbial communities associated with fish may...
Research Article | Applied and Environmental ScienceBiogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial CommunitiesMicrobes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment...
Research Article | Host-Microbe BiologyDietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile ColonizationA healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C....
Observation | Host-Microbe BiologyThe Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine ModelAntibiotics are the primary risk factor for Clostridioides difficile infections (CDIs), but other factors may also increase a person’s risk. In epidemiological studies, proton pump inhibitor (PPI) use has been associated with CDI incidence and recurrence. PPIs have also been associated with alterations in the human intestinal microbiota in observational and...
Research Article | Applied and Environmental ScienceFunctional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to...
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...