The microbiota has profound influence on the host through interactions with the immune system early in host development. These interactions are crucial in understanding complex autoimmune diseases, such as Inflammatory Bowel Disease (IBD). Here, we examined how specific groups of microbes in dysbiotic mice impacted outcomes of colitis, host immune response, gene expression, and microbial functional changes. Vertically transmitted dysbiotic pups received fecal microbiota transplantation (FMT) from control mice, at 2, 3, and 8 weeks after birth. After 23 weeks, remaining mice were supplemented with 2.5% dextran sulfate sodium to induce colitis. Colon histology revealed mice receiving FMT displayed less colon inflammation than mice with no gavage. We assembled 190 non-redundant Metagenome-Assembled Genomes (MAGs) from pup fecal content and highlighted microbial community differences in FMT mice compared to dysbiotic groups. Enterococcus sp. and Enterobacteriaceae members were highly detected in dysbiotic mice only. These MAGs shared a large number of antimicrobial resistance genes as well as several virulence factors including a T6SS along with multiple inflammation inducing metabolic pathways. The Enterobacteriaceae sp. displayed the ability to uptake and utilize cysteine and taurine for sulfur metabolism, in addition to utilizing the host immune response production of nitrate and nitrite as energy sources. Here, we find that potentially pathogenic microbes in the dysbiotic gut have the metabolic capability to compete with the host for sulfur-containing amino acids as well as host derived nitrate and nitrite to further inflame the gut, and worsening IBD symptoms.
Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict the response of species to the environmental change. We used reciprocal gardens planted with dry, mesic and wet regional ecotypes of Andropogon gerardii to characterize the rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of the rhizosphere microbial communities, the significant ecotypic effect highlighted active plant microbial recruitment driven by genetic variations. We also showed that ecotypes do better in the recruitment of microbes when planted at homesite, supporting the <home field advantage> hypothesis. At homesites, ecotypes were more successful at recruiting rhizosphere community members unique to the locations - microbial specialists that were potentially linked to the plant stress response functions. In addition, we showed the support for ecotypic variations in the recruitment of bacterial variants from the same genera, highlighting the effect of the plant ecotypes on the rhizosphere microbiome recruitment. The results of this study should facilitate expanded studies on understanding the complexity of relationships between plant host interactions with local soil microbes and identification of functional potential of recruited microbes. Our study has the potential for further predicting ecosystem responses to climate change and the impact of management on restoration practices.
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