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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.

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Acknowledgments

Genome sequence and 16S rDNA sequencing were performed at the UNSW Ramaciotti Centre for Gene Function Analysis (UNSW, Sydney, AU); the authors gratefully acknowledge the assistance of the staff in processing our samples. Sample preparation for scanning electron microscopy and sample visualization were performed respectively at the electron microscope facility of the Department of Biology (SME) (http://dept.bio.unipd.it/servizioME/) (University of Padova, Padua, Italy) and at the university center for scientific instruments (CUGAS) (http://www.unipd.it/cugas/) (University of Padova, Padua, Italy). Optical microscopy visualization was performed at the graphics, optical, and confocal microscopy service of the Department of Biology (University of Padova, Padua, Italy) (http://www.biologia.unipd.it/dipartimento/organizzazione/sezione-tecnico-scientifica/servizio-di-grafica-e-microscopia-ottica-e-confocale/). We express thanks to Riccardo Rosselli of the Department of Biology (University of Padua) for suggestions on metagenomic sample preparation. This study was supported, in part, by POR Veneto “Fondo Europeo di Sviluppo Regionale” 2007–2013—Asse 1, Azione 1.1.2 and by “Ricerca Scientifica fondi quota EX 60 % 2013” code 60A06-0375/13.

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Correspondence to Stefano Campanaro.

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Stefano Campanaro and Laura Treu contributed equally to the work.

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Campanaro, S., Treu, L., Vendramin, V. et al. 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. Appl Microbiol Biotechnol 98, 6015–6037 (2014). https://doi.org/10.1007/s00253-014-5795-3

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  • DOI: https://doi.org/10.1007/s00253-014-5795-3

Keywords

  • Lactobacillus fabifermentans
  • Lactobacillus
  • Metagenomics
  • 16S rRNA
  • Grape marc
  • Genome sequencing
  • Carbohydrates utilization
  • Comparative genomics
  • Biofilm