The microbial composition of kefir fermented from raw milk

Abstract

Aim: This research aims to elucidate the microbial composition and ratio between myco- and microbiota abundance of two raw milk kefir-style beverages (RMK). Produced by backslopping a traditionally with kefir-grains fermented raw milk kefir or by a commercially available defined starter culture. Additionally, kefir from pasteurized milk (PMK) was analysed to determine specific effects of raw milk on the microbial composition. Methods: DNA extracted from kefir beverages was artificially spiked with a microbial standard containing known concentrations of fungal and bacterial genomic DNA. In order to avoid over or under spiking of the samples, a specific amount of spike-in was added in proportion to the sample bacterial genomic DNA content determined by qPCR, followed by metagenomic amplicon sequencing of the bacterial V3-V4 region of the 16S rRNA gene and the fungal ITS1 region. Results: Backslopping of traditional kefir changed the microbial composition with a decrease of Lactobacilli and an increase of Lactococcus species. Defined culture based RMK contained all the myco-microbiota present in the added starter culture and raw milk specific microbes, such as Galacotomyces, Streptococcus dysgalactiae, Pichia kudriavzevii and Staphylococcus sciuri were detected in end products implicating their contribution in the fermentation process. No differences were observed in bacterial genomic DNA content between PMK or RMK for both style kefir beverages. Higher relative amounts of mycobiotal spike-in were found in both styles of RMK compared to PMK, implicating lower concentrations of fungi in RMK. Conclusion: This study indicates that the majority of microbial species found in RMK and PMK are similar albeit in different proportions. Furthermore there appears to be a higher amount of fungi present in PMK. These findings could have implications regarding the observed beneficial health effect of RMK consumption, but future studies are required to determine the exact molecular immunological mechanism.