Santamarina-García Gorka, Yap Min, Crispie Fiona, Amores Gustavo, Lordan Cathy, Virto Mailo, Cotter Paul D
Lactiker Research Group, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, Vitoria-Gasteiz, 01006, Spain.
Bioaraba Health Research Institute-Prevention, Promotion and Health Care, Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de La Universidad 7, Vitoria-Gasteiz, 01006, Spain.
Microbiome. 2024 Dec 20;12(1):262. doi: 10.1186/s40168-024-01980-0.
Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.
The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.
This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.
众多研究强调了细菌群落对生羊乳奶酪质量和安全的影响。尽管已报道不同类型奶酪甚至不同生产商之间微生物群存在差异，但据我们所知，尚无研究全面评估所有潜在微生物来源及其对任何生羊乳奶酪的贡献，而该领域的研究可能具有巨大的潜在益处。在此，以原产地保护认证的伊迪亚扎巴尔奶酪为例，通过鸟枪法宏基因组测序研究了手工乳制品厂的环境和操作（包括牛群饲料、乳头皮肤、乳制品表面和原料）对相关生乳、乳清和衍生奶酪微生物组的影响。
结果揭示了不同样本类型中多样的微生物生态系统，包含超过1300个细菌属和3400个物种。SourceTracker分析表明商业饲料和乳头皮肤是生乳微生物群的主要贡献者（分别为45.6%和33.5%），例如是乳酸乳球菌和泛菌的来源，凝乳酶则对乳清和奶酪的组成有贡献（分别为17.4%和41.0%），包括链球菌、假单胞菌_E或乳酸杆菌_H等分类群。功能分析将微生物生态位与奶酪质量和安全相关的代谢途径联系起来，盐水和食品接触表面最为相关，与短杆菌属、甲基杆菌属或嗜盐单胞菌属等属有关。关于病毒组（与毒力相关的基因谱），除了乳清和奶酪外，商业饲料和草是主要储存库（与例如短短芽孢杆菌_B或CAG - 196有关）。同样，草、乳头皮肤或凝乳酶是抗菌抗性基因的主要贡献者（例如Bact - 11或拟杆菌_B）。在奶酪香气和质地方面，除了奶酪本身的微生物组外，盐水、草和食品接触表面是水解酶编码基因的关键储存库，例如源自乳酸乳球菌、乳酸杆菌、李斯特菌或嗜盐色杆菌。此外，还产生了300多个宏基因组组装基因组（MAG），包括60个高质量MAG，从几个属中产生了28个新的假定物种，例如柠檬酸球菌属、棒状杆菌属或迪茨氏菌属。
本研究强调了手工乳制品厂环境在决定奶酪微生物群以及进而决定奶酪质量和安全方面的作用。视频摘要。
