Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources

PLoS One. 2013 Jul 19;8(7):e69371. doi: 10.1371/journal.pone.0069371. Print 2013.

Abstract

Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacteria / classification*
  • Bacteria / genetics*
  • Biodiversity
  • Cultured Milk Products / microbiology*
  • DNA, Intergenic / genetics
  • Fungi / classification*
  • Fungi / genetics*
  • High-Throughput Nucleotide Sequencing
  • Metagenomics
  • Milk / microbiology*
  • Phylogeny

Substances

  • DNA, Intergenic

Grant support

The Alimentary Pharmabiotic Centre is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI CSET grant APC CSET 2 grant 07/CE/B1368. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript