Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources
Open Access
- 19 July 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (7), e69371
- https://doi.org/10.1371/journal.pone.0069371
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.This publication has 72 references indexed in Scilit:
- High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal CheesesApplied and Environmental Microbiology, 2012
- Effect of a New Probiotic Saccharomyces cerevisiae Strain on Survival of Escherichia coli O157:H7 in a Dynamic Gastrointestinal ModelApplied and Environmental Microbiology, 2011
- Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regionsNucleic Acids Research, 2010
- QIIME allows analysis of high-throughput community sequencing dataNature Methods, 2010
- Denaturing Gradient Gel Electrophoresis Analysis of Lactic Acid Bacteria and Yeasts in Traditional Mongolian Fermented MilkFood Science and Technology Research, 2010
- KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization programProtein Science, 2009
- Pyrosequencing of Tagged 16S rRNA Gene Amplicons for Rapid Deciphering of the Microbiomes of Fermented Foods Such as Pearl Millet SlurriesApplied and Environmental Microbiology, 2009
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysisNucleic Acids Research, 2008
- SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARBNucleic Acids Research, 2007
- MEGAN analysis of metagenomic dataGenome Research, 2007