Abstract
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
Highlights
Probiotics are living microorganisms, which, when administered in adequate amounts, confer a health benefit to the host (Kechagia et al, 2013)
TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
Genome drafts for non-probiotic strains of Shewanella putrefaciens With the aim of detecting genes or genomic regions from the probiotic strain that are distinctive with respect to NPSs, the recently published (Tapia-Paniagua et al, 2017) genome draft of Shewanella putrefaciens Pdp11 in one single scaffold was used
Summary
Probiotics are living microorganisms, which, when administered in adequate amounts, confer a health benefit to the host (Kechagia et al, 2013). Very interesting results have been recently reported regarding fish benefits with respect to digestive enzymes, growth, and immune response when probiotics are included in feed (Akhtar et al, 2015; Banerjee et al, 2017). Probiotic candidates are screened and isolated from the indigenous microbiota of fish as an advantage over exogenous sources (Boutin et al, 2013). Different mechanisms have been demonstrated by probiotics and have been used to. TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp. The potential mechanisms involved in the probiotic character remains obscure
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