Genomic and chemical analyses of 713 marine biofilm-derived bacterial strains

Abstract

ABSTRACT Marine biofilms are known as a reservoir of bacterial specialized metabolites, but the majority of these metabolites remain unexplored because most biofilm-associated bacteria have not yet been cultivated or genomically characterized. In a recent study, we isolated and cultivated 713 bacterial strains from marine biofilms and generated their nearly complete genomes. Here, we conduct a systematic analysis of biosynthetic gene clusters (BGCs) contained in these bacterial genomes. A total of 3,146 BGCs are predicted and organized into 2,176 mostly new gene cluster families (GCFs), in comparison with the GCFs in the Minimum Information about a Biosynthetic Gene cluster database, and those from genomes of global seawater bacteria. In particular, certain less-studied microorganisms, such as members of the Roseobacteriaceae family, possess a number of novel BGCs. Moreover, through bacterial antagonistic tests, 50 of the 713 strains inhibit the growth of at least one tested pathogenic bacterial strain. Furthermore, metabolomics followed by molecular networking reveals previously uncharacterized antimicrobial activities associated with known secondary metabolites, represented by the polycyclic tetramate macrolactam alteramide A. IMPORTANCE Marine microorganisms are important sources of natural products, yet quite a few studies have systematically explored the production of active molecules by marine biofilm-associated bacteria. In the present study, we analyzed nearly complete genomes of 713 strains isolated from marine biofilms to assess their biosynthetic potential. We further conducted experiments to discover compounds with a strong inhibitory effect against pathogenic bacterial strains. This work has laid the groundwork for further prospecting marine biofilm-associated bacterial strains for antibacterial agents.

Key findings

• ▸3,146 biosynthetic gene clusters were predicted in the 713 bacterial strains
• ▸50 of the 713 strains inhibit the growth of at least one tested pathogenic bacterial strain
• ▸2,176 mostly new gene cluster families were identified

Keywords

Identifiers

DOI

10.1128/aem.02593-25

Journal

Applied and Environmental Microbiology

Year

2026