In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database.

Colin Hill,Caitriona M Guinane,Paul W O’Toole,R Paul Ross,Calum J Walsh,Paul D Cotter

doi:10.1186/s12866-015-0515-4

Abstract

BackgroundThe human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated.ResultsWe identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides.ConclusionsMultiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0515-4) contains supplementary material, which is available to authorized users.

Highlights

The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function
Selection of the 74 Putative Bacteriocin Gene Cluster (PBGC) was achieved based on the presence of bacteriocin-associated genes, arrangement of those genes in the Area of Interest (AOI), and by overall similarity to previously described gene clusters
An overall breakdown of the 74 PBGCs according to phylum and predicted bacteriocin type can be seen in Fig. 1a, b, respectively

Summary

Introduction

The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. As a consequence of advances in DNA sequencing technologies, there is a clearer understanding of the composition of the GI microbiota and of associations between specific taxa with health and disease [6, 8] This knowledge can potentially be utilised through the modulation of the gut microbiota to address certain GI disorders [9, 10]. Bacteriocin production has been investigated to assess the extent to which it can control weight gain as a consequence of changing the composition of the gut microbiota [14, 15]

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Results

Conclusion