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Jones et al. Microbiome Res Rep 2024;3:24 Microbiome Research
DOI: 10.20517/mrr.2023.78
Reports

Original Article Open Access

An exploratory in silico analysis of bacteriocin gene
clusters in the urobiome

Jennifer Jones , Craig P. Murphy, Roy D. Sleator, Eamonn P. Culligan

Department of Biological Sciences, Munster Technological University, Bishopstown, Cork T12 P928, Ireland.
Correspondence to: Dr. Eamonn P. Culligan, Department of Biological Sciences, Munster Technological University, Bishopstown,
Cork T12 P928, Ireland. E-mail: Eamonn.culligan@mtu.ie

How to cite this article: Jones J, Murphy CP, Sleator RD, Culligan EP. An exploratory in silico analysis of bacteriocin gene clusters
in the urobiome. Microbiome Res Rep 2024;3:24. https://dx.doi.org/10.20517/mrr.2023.78

Received: 20 Dec 2023 First Decision: 26 Feb 2024 Revised: 4 Mar 2024 Accepted: 18 Mar 2024 Published: 27 Mar 2024

Academic Editor: Leonardo Mancabelli Copy Editor: Pei-Yun Wang Production Editor: Pei-Yun Wang

Abstract
Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of
the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have
identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to
screen the urobiome for genes encoding bacteriocin production.

Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin
gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7.

Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for
potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of
which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins.

Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.

Keywords: Urobiome, bacteriocins, antibiotic resistance, BAGEL4, bacteriocin gene cluster

INTRODUCTION
The human microbiome and its role in health and disease have been at the forefront of scientific research in

© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0
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