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

Marsh AJ, O'Sullivan O, Hill C, Ross RP, Cotter PD - PLoS ONE (2013)

Bottom Line: 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.As a result several genera and species not previously identified in kefir were revealed.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.

View Article: PubMed Central - PubMed

Affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.

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.

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Procrustes imaging of unweighted UniFrac distance matrices highlight the diversity amongst the 16S bacterial component (A) and fungal component (B) of the different kefir samples.The two different sample types are linked with a bar (white represents grain flora; red represents milk flora). The direction of each axis is arbitrary.
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pone-0069371-g002: Procrustes imaging of unweighted UniFrac distance matrices highlight the diversity amongst the 16S bacterial component (A) and fungal component (B) of the different kefir samples.The two different sample types are linked with a bar (white represents grain flora; red represents milk flora). The direction of each axis is arbitrary.

Mentions: Principal Co-ordinate Analysis plots were generated based on the unweighted UniFrac distance matrix (Figure 1AB), the only tree-based metric. From this analysis, it was evident that there was no clustering amongst kefir populations from different countries (Figure 1AB), and correlated with the other distance matrices (data not shown). Procrustes analysis indicated that the ordinations of kefir and kefir grains were not related to each other (M2 = 0.924, p = 0.644, Figure 2A). The similarities between kefir grain communities were not the same as the similarities between kefir communities.


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

Marsh AJ, O'Sullivan O, Hill C, Ross RP, Cotter PD - PLoS ONE (2013)

Procrustes imaging of unweighted UniFrac distance matrices highlight the diversity amongst the 16S bacterial component (A) and fungal component (B) of the different kefir samples.The two different sample types are linked with a bar (white represents grain flora; red represents milk flora). The direction of each axis is arbitrary.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3716650&req=5

pone-0069371-g002: Procrustes imaging of unweighted UniFrac distance matrices highlight the diversity amongst the 16S bacterial component (A) and fungal component (B) of the different kefir samples.The two different sample types are linked with a bar (white represents grain flora; red represents milk flora). The direction of each axis is arbitrary.
Mentions: Principal Co-ordinate Analysis plots were generated based on the unweighted UniFrac distance matrix (Figure 1AB), the only tree-based metric. From this analysis, it was evident that there was no clustering amongst kefir populations from different countries (Figure 1AB), and correlated with the other distance matrices (data not shown). Procrustes analysis indicated that the ordinations of kefir and kefir grains were not related to each other (M2 = 0.924, p = 0.644, Figure 2A). The similarities between kefir grain communities were not the same as the similarities between kefir communities.

Bottom Line: 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.As a result several genera and species not previously identified in kefir were revealed.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.

View Article: PubMed Central - PubMed

Affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Ireland.

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.

Show MeSH