Comparison of bacterial and fungal biodiversity of Turkish kefir grains with high-throughput metagenomic analysis

Kefir is a health-promoting fermented drink having complex microbiota. This complex microbiota consists of bacteria and yeast association that is bound together with a polysaccharide called kefiran. To date, the complex microbiota of fermented foods was enlightened with culture-depended methods, however, recently, metagenomic studies have been started to use to reveal microbial diversity of fermented foods such as kefir. In this present study, we investigated the microbiome of two artisanal Turkish kefir grains (namely, A and G) by high throughput sequencing at the species level. Additionally, physicochemical analyses were carried out besides enumerations of lactobacilli, lactococci, total aerobic, and bifidobacteria in fermented milk kefirs. In these two kefir grains, different bacterial and fungal populations were revealed. In kefir grain A, Bifidobacterium longum was the dominant species while in kefir grain G, Lactobacillus kefiranofaciens was dominant. Concerning fungal diversity, in kefir grain A, Naumovozyma dairensis was the dominant yeast, while in kefir grain G, Zygosaccharomyces rouxii was dominant. High-throughput sequencing studies have revealed that kefir grains were typically dominated by lactobacilli. But, in this study, Bifidobacterium longum was found as a dominant bacterium in kefir for the first time.

Automated summary

Kefir is a health-promoting fermented drink with complex microbiota consisting of bacteria and yeast. Different artisanal Turkish kefir grains have varying dominant bacterial and fungal populations. This study discovered Bifidobacterium longum as a dominant bacterium in kefir for the first time.