Charting the post-antibiotic trajectory of the microbiome and resistome and elucidating the role of pet ownership

ABSTRACT The gut microbiome plays a crucial role in health, and its disruption by antibiotics can lead to decreased microbial diversity, loss of essential metabolic functions, and increased susceptibility to infections with pathogens such as Clostridioides difficile. The mechanisms and factors influencing the recovery of the microbiome from antibiotics remain inadequately understood. Notably, the potential impact of companion animals on the human microbiome is often overlooked, even though recent evidence suggests that pets can modulate the human microbiome and protect against colonization and recurrence of infection with C. difficile. To investigate these dynamics, the REMBRANDT study (REcovery of the MicroBiome fRom ANtibiotics for Dental implanTs) was initiated as a longitudinal cohort study examining microbiome disruption and recovery in pet owners and non-pet owners receiving antibiotic prophylaxis for dental surgeries. Stool and saliva samples are collected from participants, and if applicable, their pets, before, during, and after the antibiotic regimen, alongside extensive meta-data. Currently, metagenomic 16S rRNA sequencing is performed on all samples, which provides genus-level taxonomic data. Preliminary analyses appear to confirm that pet ownership can influence the post-antibiotic trajectory of the microbiome. Here, we propose to sequence REMBRANDT samples more deeply using shotgun metagenomic sequencing (SMS) to achieve higher-resolution taxonomic profiling of the microbiome and its associated gene families and metabolic pathways. This enhanced sequencing approach will allow for a comprehensive characterization of the taxonomic and functional disruption and recovery of the microbiome and a more sensitive detection of patient and household-level characteristics that affect recovery. Additionally, this approach will provide insight into the post-antibiotic collection of antimicrobial resistance genes in the gut (the resistome) and the factors that govern the acquisition and persistence of antimicrobial resistance genes within the host and their potential dissemination to pets. Findings from this research will be used to inform public health strategies and interventions aimed at enhancing microbiome recovery and limiting the spread of antimicrobial resistance.