Marked variation in the bacterial microbiota of commercially produced Greek kefir products revealed by full-length 16S rRNA gene sequencing

Abstract

Kefir is a fermented dairy beverage characterized by a complex microbial community that contributes to its technological and sensory properties and has been associated in previous studies with potential health-related effects. While the microbiota of kefir grains has been extensively studied, information regarding the bacterial communities of commercially produced Greek kefir remains limited. The aim of the present study was to characterize the bacterial community composition of commercially produced kefir products collected from different regions of Greece using full-length 16S rRNA gene sequencing and to assess variation among the analyzed commercial product groups. A total of 32 kefir samples were collected from eight regions of Greece: Koufalia, Kilkis, Drama, Thrace, Katerini, Larissa, Volos, and Attica. Genomic DNA was extracted and subjected to Oxford Nanopore full-length 16S rRNA gene sequencing. Taxonomic profiling was performed following quality filtering and bioinformatic analysis. The bacterial communities were predominantly composed of members of the phylum Bacillota, representing more than 92% of the total bacterial relative abundance in all samples. At the species level, Streptococcus thermophilus (45.89%) and Lactococcus cremoris (37.72%) were identified as the dominant shared taxa. Bray–Curtis dissimilarities and PERMANOVA supported differentiation among the commercial product groups (pseudo- F = 5.630, R 2 = 0.622, and permutation p = 0.001). Kefir samples from Koufalia were strongly dominated by L. cremoris (88.59%), whereas samples from Attica, Thrace, and Kilkis showed a predominance of S. thermophilus . In contrast, Katerini showed a compositionally heterogeneous bacterial profile with comparatively low dominance of the two core taxa. It also presented relatively higher abundances of Leuconostoc spp., Lacticaseibacillus rhamnosus, Lactobacillus delbrueckii , and Bifidobacterium animalis . These findings demonstrate that commercially produced Greek kefir products share dominant bacterial taxa while exhibiting marked variation among commercial product groups. The observed variation among commercial product groups may be associated with product- and manufacturer-related factors, although the relative contribution of these factors cannot be determined from the present dataset.