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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.

frontiers in microbiology

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