Shotgun metagenomic analysis of traditional kefir from Caucasus
Kefir is a fermented milk thought to have originated from the Caucasus. It is a complex beverage traditionally produced using kefir grains, yet the extent to which regional inheritance and microbial strain dynamics shape kefir microbiomes remain poorly understood. Here, we applied a shotgun metagenomic sequencing-based approach to characterize traditional kefir grains and milk kefirs collected from the Kabardino-Balkaria and Karachay-Cherkessia Republics of the Caucasus. Using taxonomic profiling and community-level functional analysis, combined with metagenome-assembled genomes (MAGs) and strain-resolved approaches, we investigated microbial composition, functional potential, and microbial transmission patterns between grains and milk. As expected, the kefir grains and milk kefirs displayed distinct microbial compositions. While grains were dominated by Lactobacillus kefiranofaciens and Lentilactobacillus kefiri, milk kefirs exhibited strong regional differentiation, characterized by dominance of Enterococcus durans in Kabardino-Balkaria samples and Lactococcus lactis in Karachay-Cherkessia samples, respectively. MAG analysis recovered 42 high-quality metagenome-assembled genomes encoding repertoire of extensive carbohydrate active enzymes (CAZymes) and fermentation-related metabolic pathways. Strain-level analyses revealed species-specific transmission patterns, including strong grain-to-milk sharing for E. durans and L. kefiri, closely related grain-associated strains for L. kefiranofaciens, and marked regional differences in strain diversity for Lacticaseibacillus paracasei, with low divergence in Kabardino-Balkaria samples and higher heterogeneity in Karachay-Cherkessia. Across 291 milk kefir samples, global comparison using the curated Food Metagenomic Data (cFMD) resource revealed that taxonomic composition differed significantly by country of origin or study location, whereas functional differences were weaker and exhibited no significant difference in dispersion, indicating that functional profiles vary less across milk kefirs than their taxonomic composition. Together, these findings highlight how regional grain composition and microbial inheritance shape kefir microbiomes, while the overall functional potential remains relatively stable within the context of milk fermentation.
Kefir is a fermented milk thought to have originated from the Caucasus. It is a complex beverage traditionally produced using kefir grains, yet the extent to which regional inheritance and microbial strain dynamics shape kefir microbiomes remain poorly understood. Here, we applied a shotgun metagenomic sequencing-based approach to characterize traditional kefir grains and milk kefirs collected from the Kabardino-Balkaria and Karachay-Cherkessia Republics of the Caucasus. Using taxonomic profiling and community-level functional analysis, combined with metagenome-assembled genomes (MAGs) and strain-resolved approaches, we investigated microbial composition, functional potential, and microbial transmission patterns between grains and milk. As expected, the kefir grains and milk kefirs displayed distinct microbial compositions. While grains were dominated by Lactobacillus kefiranofaciens and Lentilactobacillus kefiri, milk kefirs exhibited strong regional differentiation, characterized by dominance of Enterococcus durans in Kabardino-Balkaria samples and Lactococcus lactis in Karachay-Cherkessia samples, respectively. MAG analysis recovered 42 high-quality metagenome-assembled genomes encoding repertoire of extensive carbohydrate active enzymes (CAZymes) and fermentation-related metabolic pathways. Strain-level analyses revealed species-specific transmission patterns, including strong grain-to-milk sharing for E. durans and L. kefiri, closely related grain-associated strains for L. kefiranofaciens, and marked regional differences in strain diversity for Lacticaseibacillus paracasei, with low divergence in Kabardino-Balkaria samples and higher heterogeneity in Karachay-Cherkessia. Across 291 milk kefir samples, global comparison using the curated Food Metagenomic Data (cFMD) resource revealed that taxonomic composition differed significantly by country of origin or study location, whereas functional differences were weaker and exhibited no significant difference in dispersion, indicating that functional profiles vary less across milk kefirs than their taxonomic composition. Together, these findings highlight how regional grain composition and microbial inheritance shape kefir microbiomes, while the overall functional potential remains relatively stable within the context of milk fermentation.
Teagasc Food Research Centre