摘要
Background
The 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.Results
Two 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.Conclusions
Diet has important effects on the complement of AMR genes in the rumen microbial community, with potential implications for human and animal health.
摘要译文
背景抗菌素耐药性的出现和传播是当前对人类和动物健康最迫切的威胁。微生物抗性基因和与动物肠道中微生物定植和致病性相关的基因将在减少动物生产对该问题的贡献方面起主要作用。在这里，从50个无抗生素的肉牛采集的瘤胃消化物样本中评估了饮食对瘤胃抗性组织和致病性基因丰度的影响，[包括四个牛品种接受两种含有不同比例精矿的饮食。结果与抗菌素耐药性（AMR），定植相关的二百四十个基因，]使用KEGG鉴定从4966个宏基因组基因中鉴定了通信或致病性功能。在浓缩饲养的动物中，这些基因的多样性和丰度都较高。氯肥和小菌素抗性基因在饲料喂养的动物样品中占主导地位（P 0.001），而浓缩饲喂的动物中氨基糖苷和链霉素抗性丰富。基于浓缩物的饮食也增加了Proteobacteria的相对丰度，Proteobacteria包括许多动物和人畜共患病原体。Proteobacteria与（Firmicutes + Bacteroidetes）的高比率被证实是瘤胃失调的良好指标，其中8例均来自浓缩饲养的动物。最后，网络分析表明，抗性/致病性基因可能作为瘤胃微生物组健康风险评估的生物标志物。结论饮食对瘤胃微生物群落AMR基因的补体有重要影响，对人类和动物健康具有潜在影响。
Marc D. Auffret[1]]Richard J. Dewhurst[1]]Carol-Anne Duthie[1]]John A. Rooke[1]]R. John Wallace[2]]Tom C. Freeman[3]]Robert Stewart[4]]Mick Watson[3][4]]Rainer Roehe[1]]. The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle[J]. Microbiome, 2017,5(1)