Evaluation of the Gut Resistome and Microbiome on Healthy Adults Receiving Antibiotic and a Multi‐Strain Probiotic
Authors: MacPherson Chad , Mathieu Olivier , Richard Valérie , Nantel Andre , Tompkins Thomas , Girard Stéphanie‐Anne , Burguière Pierre 
Published: November 2023

Introduction

A recent randomized, double‐blind and placebo‐controlled clinical trial evaluated the effect of Lacidofil® STRONG (Lactobacillus rhamnosus R0011 and Lactobacillus helveticus R0052) in healthy adults on Antibiotic‐Associated Diarrhea (AAD) following administration of amoxicillin‐clavulanic acid. It is has been well established that the use of antibiotics can provoke profile changes in the gut microbiome, both in composition and abundance, and metagenomic investigations have reported on the reservoir of antibiotic resistance (ABR) genes present in the gut termed the gut resistome. Little is known about the impact of probiotics on the gut resistome. The aim of this study was to 1) use an in‐house custom‐designed ABR microarray to evaluate the gut resistome and 2) evaluate the impact of antibiotic and multi‐strain probiotic treatment (Tx) on the gut microbiome obtained from clinical fecal samples.

Methods

DNA microarray, containing 354 ABR gene specific probes, was used to screen 280 fecal DNA samples from a subset of 70 participants. Each participant provided 4 stool samples corresponding to baseline, after antibiotic + probiotic/placebo Tx, probiotic/placebo only and wash out. Quantile and median normalizations were performed for each ABR gene. Microbiome diversity was assessed by sequencing the V4 hypervariable region of the 16S rRNA gene. Reads were QCed, paired‐end assembled and clustered at 97% similarity. Resulting operational taxonomic units (OTUs) were assigned a taxonomic lineage using the RDP classifier with a Greengenes (v13_5) training set. Taxonomic, beta/alpha‐diversities were computed using Qiime and downstream analyses were done with in‐house Perl and R scripts from National Research Council of Canada.

Results

ABR microarray analysis detected and quantified changes in the resistome of fecal samples. The results showed a significant increase (p<0.001) in the total number of ABR genes during antibiotic Tx compared to baseline in both groups. A significant decrease of ABR genes during probiotic/placebo only was observed, suggesting that after antibiotic Tx the resistome reverted back to its earlier baseline status in both groups. The antibiotic Tx resulted in a selective increase of ABR gene classes responsible for the resistance to Aminoglycosides, Beta‐lactams and Tetracycline. No discernible impact of probiotic on gut resistome was observed. Microbiome analysis revealed profile changes in composition and abundance for both groups during antibiotic. Cessation of antibiotic resulted in the microbiome profile reverting back to similar baseline levels.

Conclusions

Profile changes in the gut resistome and microbiome were observed in fecal samples when an antibiotic is used. Utilizing complementary molecular biology tools of ABR microarray and 16S rRNA microbiome sequencing could be used to maximize evidence and further understand the outcomes of clinical studies.