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

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Walsh, Calum J.
Guinane, Caitriona M.
Hill, Colin
Ross, R. Paul
O'Toole, Paul W.
Cotter, Paul D.
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Biomed Central Ltd.
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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.
Bacteriocin , Bacteriolysin , Lantibiotic , Sactipeptide , Unclassified drug , Actinobacteria , Bacterial genome , Bacteriocin gene , Bacterium , Bacterium isolate , Bacteroidetes , Bifidobacterium , Firmicutes , Fusobacteria , Gene cluster , Gram positive bacterium , Intestine flora , Proteobacteria , Roseburia , Ruminococcus , Synergistetes , Human Microbiome Project , Human gut microbiota
WALSH, C. J., GUINANE, C. M., HILL, C., ROSS, R. P., O’TOOLE, P. W. & COTTER, P. D. 2015. In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database. BMC Microbiology, 15:183, 1-11.
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