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DNA Res. 2017 Feb 1;24(1):11-24. doi: 10.1093/dnares/dsw043.

A genomic view of food-related and probiotic Enterococcus strains.

Author information

1
Laboratorio de Genética y Biología Molecular, CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán (T4000ILC), Tucumán, Argentina.
2
Department of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany.

Abstract

The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner. Thus, the genome sequences of 25 Enterococcus strains, from 7 different species, were examined and compared. Their phylogenetic relationship was reconstructed based on orthologous proteins and whole genomes. Likewise, markers associated with a successful colonization (bacteriocin genes and genomic islands) and genome plasticity (phages and clustered regularly interspaced short palindromic repeats) were investigated for lifestyle specific genetic features. At the same time, a search for antibiotic resistance genes was carried out, since they are of big concern in the food industry. Finally, it was possible to locate 1617 FIGfam families as a core proteome universally present among the genera and to determine that most of the accessory genes code for hypothetical proteins, providing reasonable hints to support their functional characterization.

KEYWORDS:

Enterococcus; food; genomics; niche; probiotics

PMID:
27773878
PMCID:
PMC5381348
DOI:
10.1093/dnares/dsw043
[Indexed for MEDLINE]
Free PMC Article

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