PDF(Pubmed)
Abstract：
In this pilot study, we compared the metagenomic profiles of different types of artisanal fermented meat products collected in Italy, Greece, Portugal, and Morocco to investigate their taxonomic profile, also in relation to the presence of foodborne pathogens and antimicrobial resistance genes. In addition, technical replicates of the same biological sample were tested to estimate the reproducibility of shotgun metagenomics. The taxonomic analysis showed a high level of variability between different fermented meat products at both the phylum and genus levels. Staphylococcus aureus was identified with the highest abundance in Italian fermented meat; Escherichia coli in fermented meat from Morocco; Salmonella enterica in fermented meat from Greece; Klebsiella pneumoniae and Yersinia enterocolitica in fermented meat from Portugal. The fungi Aspergillus, Neosartoria, Emericella, Penicillum and Debaryomyces showed a negative correlation with Lactococcus, Enterococcus, Streptococcus, Leuconostoc and Lactobacillus. The resistome analysis indicated that genes conferring resistance to aminoglycoside, macrolide, and tetracycline were widely spread in all samples. Our results showed that the reproducibility between technical replicates tested by shotgun metagenomic was very high under the same conditions of analysis (either DNA extraction, library preparation, sequencing analysis, and bioinformatic analysis), considering both the degree of overlapping and the pairwise correlation.
摘要：
在这项试点研究中，我们比较了在意大利收集的不同类型的手工发酵肉制品的宏基因组概况，希腊,葡萄牙,和摩洛哥来调查他们的分类概况，还与食源性病原体和抗菌素抗性基因的存在有关。此外,对同一生物样品的技术重复进行了测试,以估计鸟枪宏基因组学的可重复性.分类学分析表明，在门和属水平上，不同发酵肉制品之间的变异性很高。金黄色葡萄球菌在意大利发酵肉中的丰度最高；摩洛哥发酵肉中的大肠杆菌；希腊发酵肉中的沙门氏菌；葡萄牙发酵肉中的肺炎克雷伯菌和小肠结肠炎耶尔森氏菌。曲霉菌,Neosartoria,Emericella,青霉和去细菌与乳球菌呈负相关，肠球菌,链球菌,明串珠菌和乳杆菌。抗性组分析表明，赋予氨基糖苷抗性的基因，大环内酯,四环素在所有样本中广泛存在。我们的结果表明，在相同的分析条件下（无论是DNA提取，图书馆准备,测序分析,和生物信息学分析)，同时考虑重叠程度和成对相关性。
