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Wine fermentation microbiome: a landscape from different Portuguese wine appellations.

Pinto C, Pinho D, Cardoso R, Custódio V, Fernandes J, Sousa S, Pinheiro M, Egas C, Gomes AC - Front Microbiol (2015)

Bottom Line: The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms.Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF.Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected.

View Article: PubMed Central - PubMed

Affiliation: Genomics Unit, Biocant - Biotechnology Innovation Center, Cantanhede Portugal.

ABSTRACT
Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

No MeSH data available.


Eukaryotic (A) and prokaryotic (B) community distribution over IM, SF, and EF from Portuguese appellations at the class level. Relative abundance of the eukaryotic (A) and prokaryotic (B) community through the class analysis. The members of rare population phyla were placed in an artificial group designed as “Others.”
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Figure 3: Eukaryotic (A) and prokaryotic (B) community distribution over IM, SF, and EF from Portuguese appellations at the class level. Relative abundance of the eukaryotic (A) and prokaryotic (B) community through the class analysis. The members of rare population phyla were placed in an artificial group designed as “Others.”

Mentions: In all samples, the dynamics of microbial populations at phylum level were very similar. Nevertheless, the relative abundances varied along the fermentation and across Portuguese appellations (Figure 2A). Microorganisms belonging to Basidiomycota phylum decreased during the fermentation process. To better understand such population dynamics, the relative abundance at class level was analyzed. The entire microbial community was mostly characterized by Saccharomycetes (22.9%), Dothideomycetes (16.2%), Leotiomycetes (12.9%), Microbotryomycetes (9.6%), and Schizosaccharomycetes (7.7%; Figure 3A).


Wine fermentation microbiome: a landscape from different Portuguese wine appellations.

Pinto C, Pinho D, Cardoso R, Custódio V, Fernandes J, Sousa S, Pinheiro M, Egas C, Gomes AC - Front Microbiol (2015)

Eukaryotic (A) and prokaryotic (B) community distribution over IM, SF, and EF from Portuguese appellations at the class level. Relative abundance of the eukaryotic (A) and prokaryotic (B) community through the class analysis. The members of rare population phyla were placed in an artificial group designed as “Others.”
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555975&req=5

Figure 3: Eukaryotic (A) and prokaryotic (B) community distribution over IM, SF, and EF from Portuguese appellations at the class level. Relative abundance of the eukaryotic (A) and prokaryotic (B) community through the class analysis. The members of rare population phyla were placed in an artificial group designed as “Others.”
Mentions: In all samples, the dynamics of microbial populations at phylum level were very similar. Nevertheless, the relative abundances varied along the fermentation and across Portuguese appellations (Figure 2A). Microorganisms belonging to Basidiomycota phylum decreased during the fermentation process. To better understand such population dynamics, the relative abundance at class level was analyzed. The entire microbial community was mostly characterized by Saccharomycetes (22.9%), Dothideomycetes (16.2%), Leotiomycetes (12.9%), Microbotryomycetes (9.6%), and Schizosaccharomycetes (7.7%; Figure 3A).

Bottom Line: The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms.Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF.Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected.

View Article: PubMed Central - PubMed

Affiliation: Genomics Unit, Biocant - Biotechnology Innovation Center, Cantanhede Portugal.

ABSTRACT
Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

No MeSH data available.