Authors
Nguyen, J. N., Testerman, T., McBride, K., Donohue, H., Marden, J., Balunas, M., Graf, J.
Abstract
The antimicrobial resistance crisis, driven by excessive use of antimicrobials in medical and agricultural settings, has spurred the search for alternative strategies. In the present study, we investigated surface biofilms from a rainbow trout aquaculture facility to identify bacteria with inhibitory activity against fish and human pathogens. A total of 906 isolates were obtained, of which 478 were taxonomically classified using full-length 16S rRNA gene sequencing, revealing Pseudomonas, Aeromonas, and Flavobacterium as the most abundant genera. Twenty-nine isolates, predominantly novel Pseudomonas species, inhibited one or more fish pathogen strains, with two P. aphyarum strains inhibiting every fish pathogen tested. All human pathogen strains were inhibited by at least one trout farm isolate. A biofilm assay identified strains capable of excluding F. columnare from established biofilms. Numerous strains reduced biofilm colonization, with P. aphyarum and P. idahonensis strains exhibiting the greatest reduction. Genome analysis and biosynthetic gene cluster (BGC) identification from a subset of isolates revealed shared and unique clusters with strong potential for antimicrobial production, correlating in part with observed inhibition patterns. Metabolomics profiling identified a suite of strain-specific siderophores that may mediate biofilm disruption. Additionally, co-culture of these isolates with the human pathogen Pseudomonas aeruginosa enhanced the production of specialized metabolites with reported antimicrobial activities. Collectively, these findings highlight trout farm biofilms as a promising source of bacteria that could be developed as probiotics or investigated for novel antimicrobial discovery.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 07 Nov 2025.
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