Evaluation of extended-spectrum Beta-lactamase (ESBL) producing bacteria in feces of shelter dogs as a biomarker for altered gut microbial taxa and functional profiles

Millions of shelter dogs move through the supply chain from their geographical origin to adoptive homes, with possible exposure to pathogens and shifts in their gut microbiota. However, research in this area is limited. This study examined the effects of intestinal colonization by ESBL bacteria on gut taxa abundance, diversity, and functions in 52 shelter dogs of various ages, sexes, and fertility statuses. We isolated fecal DNA, sequenced their 16S rRNA genes, processed the sequences using DADA2, and identified taxa profiles and their abundance as well as microbiome functional profiles in each dog. Our findings indicate that gut colonization by ESBL bacteria impacts beyond their role in antimicrobial resistance, as they are associated with altered gut microbiota and gut microbiome functions through the down- and upregulation of multiple metabolic and biosynthesis pathways.