High-throughput, sequence-based analysis of the microbiota of Greek kefir grains from two geographic regions

Abstract

Research background. Kefir is a natural probiotic drink traditionally produced by milk fermentation using kefir grains. Kefir grains are composed of a complex population of bacteria and yeasts embedded in a polysaccharide-protein matrix. The geographic origin of kefir grains may largely influence their microbial composition and the associated kefir drink properties. Although the detailed bacterial composition of kefir grains form several geographic regions has been reported, to date, analogous data are lacking regarding the microbiome of Greek kefir. Hence, the aim of this study was to investigate the structure and the diversity of the bacterial community of Greek kefir grains. Experimental approach. The bacterial community structure and diversity of two different kefir grains from distant geographic regions in Greece were examined via high-throughput sequencing analysis, a culture-independent metagenomic approach, targeting the 16S rRNA V4 variable region, in order to gain a deeper understanding of their bacterial population diversities. Results and conclusions. Firmicutes (a phylum that includes lactic acid bacteria) was strikingly dominant amongst the bacterial phyla identified, with over 99 % of the sequences classified to this phylum for both kefir grains. At the family level, Lactobacillaceae sequences accounted for more than 98 % of the Operational Taxonomic Units (OTUs), followed by Ruminococcaceae, Lahnospiraceae, Bacteroidaceae and other bacterial families of lesser abundance. Α relatively small number of bacterial genera dominated, with Lactobacillus kefiranofaciens being the most abundant in both kefir grains (95.0 % of OTUs in Kefir A and 96.3 % of OTUs in kefir B). However, a quite variable sub-dominant population was also present in both grains, including bacterial genera that have been previously associated with the gastrointestinal tract of humans and animals, some of which are believed to possess probiotic properties (Faecalibacterium spp., Bacteroides spp., Blautia spp.). Differences among the bacterial profiles of the two grains were very small indicating a high homogeneity despite the distant geographic origin. Novelty and scientific contribution. This is the first study to deeply explore and report on the bacterial diversity and species richness of Greek kefir.