In recent years, the fermented milk product kefir has been intensively studied because of its health benefits. Here, we evaluated the microbial consortia of two kefir samples, from Escarcega, Campeche, and Campeche (México). We considered a functional comparison between both samples, including fungal and bacterial inhibition; second, we applied shotgun metagenomics to assess the structure and functional diversity of the communities of microorganisms. These two samples exhibited antagonisms against bacterial and fungal pathogens. Bioactive polyketides and nonribosomal peptides were identified by LC‐HRMS analysis. We also observed a high bacterial diversity and an abundance of Actinobacteria in both kefir samples, and a greater abundance of Saccharomyces species in kefir of Escarcega than in the Campeche kefir. When the prophage compositions were evaluated, the Campeche sample showed a higher diversity of prophage sequences. In Escarcega, we observed a prevalence of prophage families that infect Enterobacteria and Lactobacillus. The sequences associated with secondary metabolites, such as plipastatin, fengycin, and bacillaene, and also bacteriocins like helveticin and zoocin, were also found in different proportions, with greater diversity in the Escarcega sample. The analyses described in this work open the opportunity to understand the microbial diversity in kefir samples from two distant localities.

中文翻译：

---

两种发酵乳开菲尔样品的宏基因组分析和抗菌活性

近年来，发酵乳制品开菲尔因其健康益处而受到深入研究。在这里，我们评估了来自埃斯卡塞加、坎佩切和坎佩切（墨西哥）的两个开菲尔样品的微生物群落。我们考虑了两个样品之间的功能比较，包括真菌和细菌抑制；其次，我们应用鸟枪宏基因组学来评估微生物群落的结构和功能多样性。这两个样品表现出对细菌和真菌病原体的拮抗作用。通过 LC-HRMS 分析鉴定了生物活性聚酮化合物和非核糖体肽。我们还在两个开菲尔样品中观察到了高度的细菌多样性和大量的放线菌，以及更丰富的酵母菌Escarcega 的开菲尔中的种类比坎佩切开菲尔中的种类多。当评估原噬菌体组成时，坎佩切样本显示出更高的原噬菌体序列多样性。在 Escarcega 中，我们观察到感染肠杆菌和乳酸杆菌的原噬菌体家族的流行。与次生代谢产物相关的序列，如 plipastatin、fengycin 和 bacillaene，以及细菌素如 helveticin 和 Zoocin，也以不同的比例被发现，在 Escarcega 样本中具有更大的多样性。这项工作中描述的分析为了解来自两个遥远地区的开菲尔样品中的微生物多样性提供了机会。