Phylogenetic identification of bacteria within kefir by both culture-dependent and culture-independent methods

Abstract

A combination of culture-dependent and independent methods was used in an attempt to identify the bacteria present in kefir grains and kefir liquid. Culture-independent methods involved direct extraction of DNA by mechanical means from either grains or liquid, followed by PCR amplification and sequencing of 16S rRNA genes. Culture-dependent methods were performed by inoculating samples from both the kefir grains and the kefir liquid to solid media followed by incubation under either aerobic or anerobic conditions in order to selectively enrich aerobic and anaerobic bacteria. Pure cultures were isolated from enriched bacteria and their DNA was extracted for the amplification and sequencing of 16S rRNA genes. Results indicate that kefir grains had a different bacterial composition compared to the kefir liquid. While Lactobacillus kefiranofaciens, Lactobacillus kefiri, Enterococcus faecium and Acetobacter syzygii were found only in the kefir grains, Lactobacillus helveticus was found only in the kefir liquid. On the other hand, Lactococcus lactis subsp. lactis, Leuconostoc mesenteroides and Acetobacter lovaniensis were found to be present in both the grains and the liquid. To the best of our knowledge, this work is the first to report the presence of A.lovaniensis, A. syzygii and Enterococcus faecium in kefir.

Biotecnología del kéfir: una revisión sobre las aplicaciones y sus perspectivas futuras

“…Conocer la biología evolutiva de los microrganismos presentes en el kéfir facilita el estudio de las relaciones entre la microbiota presente, y así identificar los microorganismos que proporcionan los beneficios a la bebida (Burcu & Alper, 2013). La principal herramienta empleada para este fin es la construcción de árboles filogenéticos basados en las secuencias del gen 16S rRNA (Burcu & Alper, 2013;Gondaliya et al, 2021;Mogheth & El Gendy, 2017).…”