背景:手工干酪通常含有高度多样化的微生物群落,这可以显着影响其质量和安全性。这里,我们描述了一项详细的纵向研究,评估了三个天然洞穴中成熟对三个不同Cabrales蓝脉奶酪生产者的微生物组和抗性组演替的影响。
结果:奶酪成熟的生产者和洞穴都显着影响奶酪微生物组。乳球菌和前乳杆菌属,在其他类群中,在成熟的初始阶段显示出丰富的奶酪,要么来自原材料,使用发酵剂培养,和/或加工厂的环境。随着奶酪在洞穴中成熟,这些类群被其他细菌取代,比如四球菌,棒状杆菌,短杆菌,亚尼埃拉,和葡萄球菌,主要来自洞穴环境(主要是食物接触表面),正如来源追踪分析所证明的那样,读取级别的应变分析,以及613个宏基因组组装基因组的表征。先前在奶酪宏基因组中未发现在奶酪中检测到的高丰度的朝鲜四球菌和嗜盐四球菌。此外,四球菌与奶酪微生物组的其他成员显示出高水平的水平基因转移,主要是乳球菌和葡萄球菌,涉及与碳水化合物代谢功能相关的基因。耐药性分析显示,原料奶和相关的加工环境是抗生素耐药性决定因素的丰富储库,主要与氨基糖苷类耐药有关,四环素,和β-内酰胺类抗生素,并由高相关性的需氧革兰阴性菌从安全的角度来看,如大肠杆菌,肠沙门氏菌,不动杆菌,和肺炎克雷伯菌,成熟过程中,大多数与原料奶相关的类群被与洞穴相关的类群取代,导致ARGs的负荷显著下降,因此,更安全的最终产品。
结论:总体而言,洞穴环境代表了非起始微生物的重要来源,这些微生物可能在最终产品的质量和安全性中起着相关作用。其中,我们已经确定了新的分类群和分类群,这些分类群以前不被认为是奶酪微生物组的主要成分(Tetragenococusspp。),为这种受保护的原产地手工奶酪的认证提供非常有价值的信息。视频摘要。
BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.
RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.
CONCLUSIONS: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.