Metagenomic analysis of the microbial community in fermented grape marc reveals that Lactobacillus fabifermentans is one of the dominant species: insights into its genome structure

Abstract

Grape marc used for the production of distilled beverages undergoes prolonged storage which allows alcoholic fermentation to occur. Harsh conditions including low pH, limited oxygen and nutrients, temperature fluctuations, and high ethanol concentrations imposed by that environment create a strong selective pressure on microorganisms. A detailed characterization of the bacterial community during two time points of the fermentation process was performed using high-throughput sequencing of the V3-V6 16S rDNA hypervariable regions. The results revealed a marked reduction in the number of bacterial species after 30 days of incubation and made it possible to identify those species that are able to grow in that extreme environment. The genome sequence of Lactobacillus fabifermentans, one of the dominant species identified, was then analyzed using shotgun sequencing and comparative genomics. The results revealed that it is one of the largest genomes among the Lactobacillus sequenced and is characterized by a large number of genes involved in carbohydrate utilization and in the regulation of gene expression. The genome was shaped through a large number of gene duplication events, while lateral gene transfer contributed to a lesser extent with respect to other Lactobacillus species. According to genomic analysis, its carbohydrate utilization pattern and ability to form biofilm are the main genetic traits linked to the adaptation the species underwent permitting it to grow in fermenting grape marc.

Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

“…For instance, Bokulich et al [22] showed that Acetobacter, Gluconobacter, and Gluconoacetobacter are dominant in winemaking processes, whereas Campanaro et al [52] in a grape marc study added that Gluconobacter and Gluconoacetobacter do not survive a prolonged grape marc storage period.…”

Formation of In Vitro Mixed-Species Biofilms by Lactobacillus pentosus and Yeasts Isolated from Spanish-Style Green Table Olive Fermentations

“…Instead, they are composed of mixed species of bacteria and eukaryotes, which are thought to be more stable than monospecies films (3,4). This behavior is also the case with microbial communities in food environments (5)(6)(7)(8)(9)(10). In the particular case of olive table fermentations, the presence of polymicrobial communities composed of yeasts and lactic acid bacteria (LAB) attached to both biotic (skin of the olives) and abiotic (inner fermenter walls) surfaces has been reported (11)(12)(13)(14).…”

Assessment of bacterial communities in skin ulceration in cultured sea cucumber Apostichopus japonicus (Selenka)

“…D. singaporensis, L. fabifermentans, P. dokdonensis, B. argentinensis, L. agarilyticus, and L. algae from the DE group are associated with various metabolic pathways related to skin ulcerations but have not been reported as actual pathogens (Lie et al 1999;Yoon et al 2006;Bercovich et al 2008;De Bruyne et al 2009;Lanzarotti et al 2011;Park et al 2013;Aran et al 2014;Campanaro et al 2014;Treu et al 2014;Yoon et al 2017).…”