Purpose: The purpose of the study was to elucidate the microbial composition of kefir grains of different origin using a high-throughput, sequence-based approach.
Methods: DNA was extracted from kefir grains originating from Athens (kefir A) and Crete (kefir B) using a commercial kit. Identification of bacteria and fungi was based on amplification and sequencing of the V4 variable region of the 16S rRNA gene and of the Internal Transcribed Spacer region, respectively. Sequencing was performed on an Illumina MiSeq instrument following the manufacturer’s guidelines. Sequence data were processed to remove barcodes and primer sequences, denoised, and clustered at 3% divergence to generate Operational Taxonomic Units (OTUs) followed by removal of chimeric sequences. Final OTUs were taxonomically classified using BLASTn against a curated database derived from GreenGenes, RDPII, and NCBI.
Results: A total of 730,517 raw sequences were generated. Firmicutes and Ascomycota were the predominant phyla for bacteria and fungi, respectively. Lactobacillaceae was the dominant family in both kefirs (ca. 98%) followed by Ruminococcaceae (0.6%), Lachnospiraceae (0.4%), Bacteroidaceae (0.2%) and Syntrophomonadaceae (0.2%). The microbiota of kefir A was more diverse, consisting of 124 different bacterial genera compared to 114 genera in kefir B. Fungal OTUs belonged to the family Dipodascaceae (99.9%) and the predominant genus was Galactomyces.
Significance: The detailed composition of the kefir microbiota from different sources obtained in this study will be valuable in order to screen for beneficial strains from this traditional fermented probiotic dairy product. Also, this study provides novel data on the microbial ecology of Greek kefir.