Marked variation in the bacterial microbiota of commercially produced Greek kefir products revealed by full-length 16S rRNA gene sequencing
- 1Department of Food Science and Technology, Faculty of Food Sciences, University of West Attica
- 2Department of Chemical Engineering, BioTeC—Chemical and Biochemical Process Technology and Control
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.
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BibTeX
@article{vougiouklaki2026marked,
title = {{Marked variation in the bacterial microbiota of commercially produced Greek kefir products revealed by full-length 16S rRNA gene sequencing}},
author = {Despina Vougiouklaki and Panagiotis Lamprou and Nikos Mouhtouris and Marialena Fonazaki and Anthimia Batrinou and Spyros J. Konteles and Monika Polanska and Jan F. M. Van Impe and Efstathia Tsakali and Dimitra Houhoula},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1951948},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1951948/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Marked variation in the bacterial microbiota of commercially produced Greek kefir products revealed by full-length 16S rRNA gene sequencing
AU - Despina Vougiouklaki
AU - Panagiotis Lamprou
AU - Nikos Mouhtouris
AU - Marialena Fonazaki
AU - Anthimia Batrinou
AU - Spyros J. Konteles
AU - Monika Polanska
AU - Jan F. M. Van Impe
AU - Efstathia Tsakali
AU - Dimitra Houhoula
PY - 2026
DA - 2026/10/07
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1951948
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1951948/full
AB - 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.
SN - 1664-302X
ER -