Zooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses

Abstract

Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL–1 or g–1, and 2.49 to 7.80 log CFU mL–1 or g–1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples. On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.

Comparison of commercial and traditional kefir microbiota using metagenomic analysis

“…Similarly, in a study conducted by Kazou et al . (2021), the microbiota of homemade and industrial kefir beverages was investigated. While the researchers detected Firmicutes as the dominant phylum in all samples, Proteobacteria were the mainly identified phylum in homemade kefir.…”

“…Kazou et al . (2021) reported that, while Lactobacillus and Lactococcus were dominant in almost all grains and homemade kefir beverages, Streptococcus , Lactobacillus and Lactococcus were found to be dominant in industrial kefir beverages. The researchers also reported that due to the new taxonomy of lactic acid bacteria made by Zheng et al .…”

Lactobacillus kefiranofaciens: From Isolation and Taxonomy to Probiotic Properties and Applications

“…Lately, the microbiota of kefir grains and beverages produced in Greece were examined using a holistic approach combining classical microbiological, molecular and ampliconbased metagenomics analyses [68]. Although L. kefiranofaciens was not isolated using the growth media MRS and Rogosa, the amplification of the V1-V3 hypervariable region of the 16S rRNA gene revealed its occurrence in both kefir grains and beverages (unpublished data).…”

Advantages and disadvantages of non‐starter lactic acid bacteria from traditional fermented foods: Potential use as starters or probiotics

“…Lactic acid bacteria (LAB) are food‐fermentation agents involved in the manufacturing of yogurt, cheese, cultured butter, sour cream, sausages, cucumber pickles, olives, sauerkraut, and cocoa, among many other foods (Ho et al., 2018; Kazou et al., 2021; Mannaa et al., 2019; Nguyen et al., 2015; Todorov et al., 2017; Touret et al., 2018). However, some LAB species may spoil beer, wine, and processed meats (Laranjo et al., 2017; Ray & Joshi, 2015;).…”