Metagenomic analysis and antimicrobial activity of two fermented milk kefir samples

Abstract

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.

Unveiling the Brazilian Kefir Microbiome: Discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties

“…The bacteria present in Ke r are responsible for the fermentative process that produces biomolecules with healthy bene ces. Studies have shown the effects of ke r against pathogenic bacteria, oxidative stress, in ammation, obesity, diabetes, osteoporosis, cardiovascular disease, and neurodegeneration [34]- [39]. Our previous works show that our sample of Brazilian ke r may contain metabolites and peptides with anti-Alzheimer's effects.…”

Metagenomic analysis and antibacterial activity of kefir microorganisms

“…For example, Tenorio‐Salgado et al. (2021) reported that bacteria species of two Mexican milk kefirs consisted of Acetobacter okinawensis (10.9%), L. kefiranofaciens (7.8%), and L. helveticus (2.8%) among others.…”

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

“…In the current study, a metagenomic approach was carried out to observe prophage signatures in bacterial metagenomes throughout the cider fermentation process. A total of 1174 putative prophage contigs were identified in silico in the bacterial metagenomes using VIBRANT software, such as has been done in cheese [44] and kefir [45]. Among them, two complete prophages were found, NODE_55 and NODE_129, matching with phages isolated from human gut metagenomic data.…”