Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome

Fergus W J Collins,Mary C Rea,Colin Hill,Orla O’Sullivan,Paula M O’Connor,R Paul Ross,Beatriz Gómez-Sala

doi:10.1038/s41598-017-03339-y

Abstract

Lactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains’ environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments.

Highlights

Bacteriocins are ribosomally-synthesised antimicrobial peptides which generally act by inducing pore formation or inhibiting cell wall synthesis in target cells[1]
From the information identified by BAGEL, we used a phylogenetic tree to visualise the distribution of bacteriocin operons within the genus (Fig. 1)
While this study focuses on the type strain of each Lactobacillus species, Table 1 identifies those bacteriocins which have been previously identified and characterised from all strains in the Lactobacillus Genus Complex

Summary

Introduction

Bacteriocins are ribosomally-synthesised antimicrobial peptides which generally act by inducing pore formation or inhibiting cell wall synthesis in target cells[1] Some bacteriocins such as nisin have found widespread applicability as bio preservatives in food systems where they have been used for decades. Whilst the areas of interest identified by BAGEL represent potential bacteriocin operons, this does not always translate into functional bacteriocin production for many reasons including problems with mutation, regulation or target specificity. Despite no longer formally being considered as bacteriocins, large (>30 kDa) helveticin-like antimicrobial proteins were included in the study Based on those results, we analysed strains which were identified as encoding putative bacteriocin operons for in vitro production using well diffusion assays (WDAs) and MALDI TOF MS. This redundancy allows for a more comprehensive analysis of bacteriocin gene clusters in the sequenced strains

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Conclusion