Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

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.

The Relationship between Serum Oxalic Acid, Central Hemodynamic Parameters and Colonization by <b><i>Oxalobacter formigenes </i></b>in Hemodialysis Patients

“…The organisms in kefir produce many known antimicrobials, including lactic acid, acetic acid, carbon dioxide, hydrogen peroxide, ethanol and diacetyl, as well as antimicrobial peptides such as bacteriocins [27]. In addition, kefir may prove useful in the probiotic area as a delivery system for viable health-promoting organisms to the gut [29]. In this regard, probiotics might rearrange the colonic flora via increasing the numbers of anaerobic microorganisms such as O. formigenes .…”

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

“…The use of 16S metagenetic analysis has resulted in a novel description of bacterial consortia associated with cheeses, in which several new bacterial genera, like Prevotella and Arthrobacter, were reported for the first time (Quigley et al, 2012). Metagenomic analyses of various fermented foods like sourdough , kefir (Marsh et al, 2013;Nalbantoglu et al, 2014), fermented mung beans , Mexican Cotija cheese (Escobar-Zepeda et al, 2016), and kimchi (Park et al, 2011) have been performed. A recently published review provides detailed information on the application of high-throughput 16S rRNA sequencing to a variety of fermented foods to elucidate microbiota (Kergourlay et al, 2015).…”

Metagenomic insights into the dynamics of microbial communities in food

“…Otherwise, the kefir milk fermentate was rather dominated by Streptococcaceae and primarily the genera Lactococcus (Dobson et al, 2011). Considering yeasts, the genera Kazachstania, Kluyveromyces, and Saccharomyces dominated this community (Leite et al, 2012;Marsh et al, 2013b). Regarding the water kefir community, it was found to be quite different since Zymomonas was the dominant bacterial genera ahead of Lactobacillus, whereas Dekkera, Hanseniaspora, and Saccharomyces dominated the yeast community (Marsh et al, 2013a).…”