Characterization of antimicrobial resistance profiles in the microbiomes of vegetarian and omnivore diets

Salwa Elsaadawy

Mentor: Drs. Jason Kralj and Stephanie Servetas, National Institute of Standards and Technology.

Date/Time: April 30th, 2024 at 12pm.

Abstract: Antimicrobial resistance (AMR) has impacted the microbial ecology in practically all facets of our lives, including our gut microbiome. There are several questions regarding the correlations between diet choice and prevalence of AMR genes. Specifically, this work seeks to identify those correlations in two samples, omnivore, and vegetarian diets.

This research investigates the variances in AMR within vegetarian versus omnivorous dietary microbiomes, centering on the prevalence, diversity, and distribution of AMR genes in response to dietary impacts. The two samples were sequenced, and microbial genomes were assembled generating 564 genomes from omnivores and 364 genomes from vegetarian diets. For data analysis, we processed each assembled genome generating a list of resistant bacteria and classes of AMR using RESFINDER to query AMR markers. Then we used R Studio for data filtration and visualization.

The relative abundances of organisms of each diet were quantified, showing a higher relative abundance of AMR gene-containing organisms in the omnivore sample. Additionally, we examined each sample by individual organism for common antibiotic classes identifying widespread tetracycline resistances in both samples. Moreover, we found the common and unique AMR microbes attributable to each diet. In summary, we developed a landscape of the gut microbiome of dietary choices with the AMR.

This research highlights the complex interplay between diet, the microbiome, and AMR, showing the potential of dietary interventions as a strategic component in managing gut antimicrobial resistance. As the battle against AMR intensifies, understanding the role of diet could become increasingly crucial in developing holistic approaches to curb the spread of AMR genes.