Abstract
BackgroundThe emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate.ResultsTwo hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification. Both the diversity and abundance of these genes were higher in concentrate-fed animals. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals (P < 0.001), while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. A high ratio of Proteobacteria to (Firmicutes + Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis, with eight cases all from concentrate-fed animals. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome.ConclusionsDiet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.
Highlights
The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health
Major factors influencing functional genes in the microbiome Two hundred and four genes associated with resistance, colonisation, communication or pathogenicity functions were identified from 4966 metagenomic genes using KEGG identification
In conclusion, diets with high fibrous forage components would be recommended over those with high grain components to lower the abundance and diversity of AMR genes and to avoid rumen microbiome dysbiosis associated with pathogenic species among ruminal Proteobacteria
Summary
The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. The first is to feed a human population that may soon exceed nine billion people [1]; the second is to deal with increasing medical and veterinary problems arising from the emergence of antimicrobial-resistant (AMR) pathogenic bacteria [2]. Ruminants consume feedstuffs, including forages and by-products that cannot be used by Auffret et al Microbiome (2017) 5:159 composition of the ruminal microbiome [10, 11], we considered that the absence of knowledge about the influence of diet on the ruminal “resistome” (the collection of all identified antibiotic resistance genes) was a deficiency in understanding how AMR develops and spreads in livestock. We analysed metagenomics data from beef cattle which had previously been used to explore links between the host animal, its microbiome/metagenome and methane emissions and feed efficiency
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