Microbiome and resistome of the gastrointestinal tract of broiler chickens

Abstract

Antibiotics are used extensively in agriculture as therapeutics, and in some countries, for prophylaxis and as growth promotors. Alarmingly, there is a potential resistance transmission pathway from animals to humans through food. We analysed the microbiome and resistome of sixteen broiler chickens, which are raised for meat production. DNA was extracted from caecal samples taken at days 27 and 34 posthatch from broilers, half of which had their diets supplemented with a mannan rich fraction. Paired end sequencing was performed using an Illumina HiSeq 4000. The data was analysed by MGnify to generate taxonomic read files. The microbiome was analysed using Calypso software and the antibiotic resistance genes (ARGs) identified using the ARGs-OAP pipeline. The main phyla detected in all samples was Firmicutes and Bacteroidetes. Clostridia was the main class detected and Clostridiales the main order. Faecalibacterium, Lactobacillus and Bacteroides were the main genus detected, which are common in the broiler caecal microbiome. There was an increase in Bifidobacterium in the treated group. Principle component analysis showed that both time points cluster together. Rarefaction analysis confirms that a sufficient sequencing depth was obtained. Tetracycline resistance comprised the greatest proportions of ARGs present, followed by the aminoglycoside, macrolide, vancomycin, beta-lactam and bacitracin classes. Further analysis of the sequences will allow for full characterisation of the resistome between treatment groups. The antibiotic resistance residues in food animals may have the potential to disseminate antibiotic resistance to the human community via the food chain.