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Jones et al. Microbiome Res Rep 2024;3:24 https://dx.doi.org/10.20517/mrr.2023.78 Page 9 of 12

highlighting the utility of in silico screening studies to aid in the discovery of novel bacteriocins.

DISCUSSION
In conclusion, previous in silico screening techniques have successfully identified bacteriocin gene clusters
in the human microbiome [5,6,9-11,33] . However, given that urobiome research is in its nascent stages,
investigation of its bioactive products has remained relatively understudied to date. This in silico analysis
highlights the overall bacteriocin production ability of the urobiome. Bacteriocin production is a highly
regulated process and requires specific environmental conditions, which complicates in vitro screening for
bacteriocins. In silico screening, on the other hand, has allowed the rapid identification of bacteriocins
without the restrictions of in vitro screening [10,28] . However, it is important to note that in silico screening is
limited by the need for comparison to previously characterised bacteriocins, which can lead to completely
novel bacteriocin gene clusters being missed [28,33] . Furthermore, such in silico screens are based solely on
inference and can only be definitively verified by in vitro and or in vivo follow-up analysis. Notwithstanding,
the current study determined that 19.33% (35/181) of strains isolated from the urobiome encoded one or
more potentially active bacteriocin peptides. Despite these limitations, such studies remain an important
first step in identifying novel bacteriocins. Bacteriocins have been isolated from a variety of microbiomes,
demonstrating antimicrobial activity against clinically relevant pathogens. Bacteriocins have been used to
target pathogens both in vitro [45-47,54,62] and in vivo [48,63] , exerting probiotic effects [49,64] , inhibiting biofilm
formation , and resensitising resistant bacterial strains to antibiotics , while demonstrating limited
[60]
[65]
cytotoxic effects on the commensal healthy microbiomes. It is hoped that the identification of bacteriocins
from untapped niches such as the urobiome can aid in the transition into use in clinical settings to control
infections.

Overall, this study identified 53 putative novel bacteriocin peptides that have not been previously
characterised, suggesting a high degree of novelty and diversity of bacteriocin production within the
urobiome. These results indicate that the urobiome represents a comprehensive, and relatively untapped,
source of novel antimicrobials, some of which might well find application in the control of antibiotic
resistant infections.

DECLARATIONS
Authors’ contributions
Literature search: Culligan EP, Jones J
Data collection and analysis: Jones J
Writing and editing: Jones J
Review and editing: Culligan EP, Sleator RD, Murphy CP
Supervision of research project: Culligan EP, Sleator RD, Murphy CP

Availability of data and materials
The accession numbers for all genomes used for analysis in this manuscript can be found in Supplementary
Data. All BAGLE4 and antiSMASH data can be found in Supplementary Tables 1 and 2.

Financial support and sponsorship
This research was funded by an MTU RISAM PhD Fellowship to Jones J.

Conflicts of interest
All authors declared that there are no conflicts of interest.