Type

Journal Article

Authors

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

Subjects

Veterinary

Topics
proteobacteria bacterium isolate synergistetes gastrointestinal tract intestine flora gram positive bacterium human microbiota human gut microbiota gut microbiota fusobacteria lantibiotic bacteriocins bacteriocin gene clusters bifidobacterium next generation sequencing bacteriocin gene gene bacteriolysin bacterium firmicutes unclassified drug actinobacteria sactipeptide ruminococcus bacterial genome roseburia human genome project bacteriocin inflammatory bowel disease gastrointestinal tract git human microbiome project bacteroidetes gene cluster

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database. (2015)

Abstract 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. 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. We 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. Multiple 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.
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Full list of authors on original publication

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

Experts in our system

1
Paul D. Cotter
Teagasc
Total Publications: 253
 
2
Paul W O’ Toole
University College Cork
Total Publications: 92
 
3
R Paul Ross
Teagasc
Total Publications: 441
 
4
Colin Hill
University College Cork
Total Publications: 351
 
5
Caitriona M Guinane
Teagasc
Total Publications: 35
 
 
7
Paul W O’Toole
Teagasc
Total Publications: 6