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. 2017 Jun 26;12(6):e0176801.
doi: 10.1371/journal.pone.0176801. eCollection 2017.

In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives

Hikmate Abriouel  1 , Beatriz Pérez Montoro  1 , María Del Carmen Casado Muñoz  1 , Charles W Knapp  2 , Antonio Gálvez  1 , Nabil Benomar  1
Affiliations

In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented Aloreña green table olives

Hikmate Abriouel et al. PLoS One. .

Abstract

Lactobacillus pentosus MP-10, isolated from brines of naturally fermented Aloreña green table olives, exhibited high probiotic potential. The genome sequence of L. pentosus MP-10 is currently considered the largest genome among lactobacilli, highlighting the microorganism's ecological flexibility and adaptability. Here, we analyzed the complete genome sequence for the presence of acquired antibiotic resistance and virulence determinants to understand their defense mechanisms and explore its putative safety in food. The annotated genome sequence revealed evidence of diverse mobile genetic elements, such as prophages, transposases and transposons involved in their adaptation to brine-associated niches. In-silico analysis of L. pentosus MP-10 genome sequence identified a CRISPR (clustered regularly interspaced short palindromic repeats)/cas (CRISPR-associated protein genes) as an immune system against foreign genetic elements, which consisted of six arrays (4-12 repeats) and eleven predicted cas genes [CRISPR1 and CRISPR2 consisted of 3 (Type II-C) and 8 (Type I) genes] with high similarity to L. pentosus KCA1. Bioinformatic analyses revealed L. pentosus MP-10 to be absent of acquired antibiotic resistance genes, and most resistance genes were related to efflux mechanisms; no virulence determinants were found in the genome. This suggests that L. pentosus MP-10 could be considered safe and with high-adaptation potential, which could facilitate its application as a starter culture and probiotic in food preparations.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Circular representation of the Lactobacillus pentosus MP-10 chromosome (A) and 5 plasmids (B).
(A) The circles from outside to inside are the annotated CDS elements in forward orientation, the annotated CDS elements in the reverse orientation, several COG functions, the structural RNA, the GC content and the GC screw. (B) The circles from outside to inside of each plasmid are the annotated CDS elements in forward orientation, the annotated CDS elements in the revers orientation, several COG functions, the GC content and the GC screw.
Fig 2
Fig 2. Mauve visualization of whole genome alignment of L. pentosus MP-10 with L. pentosus IG1 and L. pentosus KCA1 (A) and the phylogenetic tree (B).
Fig 3
Fig 3. Localization of CRISPR elements and prophage regions in L. pentosus MP-10 genome.
(A) Schematic view of the genomic locations of CRISPR arrays (CR) numbered according to the CRISPRdb database. The locations of associated cas Operons (CRISPR1 and CRISPR2) and prophage regions (Region 1, Region 2, Region 3, Region 4 and Region 5), which are numbered according to PHAST are indicated. The asteriscs indicated the questionable CRISPR arrays. (B) Organization of the cas operons (CRISPR1 and CRISPR2) of L. pentosus MP-10 and L. pentosus KCA1. The same color was used for homologous cas genes. The start and end positions are indicated in each case.
Fig 4
Fig 4. Phylogenetic relationships of L. pentosus inferred from the alignment of the CRISPR-associated proteins encoding genes [cse1 (A) and cse2 (B)].
The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 14 (MegAlign 14, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.
Fig 5
Fig 5. Phylogenetic relationships of L. pentosus and L. plantarum inferred from the alignment of the transposase encoding genes.
The sequences were aligned and the most parsimonious phylogenetic trees were constructed using the CLUSTAL W of Lasergene program, version 14 (MegAlign 14, Inc., Madison, WI, USA). The scale below indicates the number of nucleotide substitutions. Accession numbers are indicated in parentheses.
Fig 6
Fig 6. Screening of the whole genome of Lactobacillus pentosus MP-10 by using the perfect and strict algorithms in the Resistance Gene Identifier (RGI) with overall resistance in the center, resistance classes in the middle, and individual resistance genes on the outer (open reading frames).
See this image and copyright information in PMC

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