Antibiotic production and resistance in the microbial community of Ulva australis

Abstract

Shigella flexnery and Shigella sonnei isolated from several countries have shown resistance to most antibiotics used for shigellosis treatment and therefore new antibiotics against the two bacteria are urgently needed. Although most antibiotics were discovered from soil microorganisms, the marine environment, such as the microbial communities of the macro-alga Ulva australis, is a potential source for finding new antibiotics. Since most of the bacteria living in the alga are not readily cultured or “not-yet” cultured, metagenomics was applied to access the uncultured properties for antibacterial activity against the two Shigella species. To optimally capture antibiotic synthesis genes, two host systems (Escherichia coli and Streptomyces lividans) were used. Moreover, to obtain a link of antibiotic function and phylogenetic origin, Homing Endonuclease Restriction and Marker Insertion (HERMI) was applied. The functional screening of the metagenomic library expressed in the two host cells resulted in the antibacterial activity against Shigella and it is thought that the activity was due to production by a microcin-like compound by the host cell and microcin maturation through genes encoded by the cosmid. HERMI, a valuable technique for the phylogenetic analysis of metagenomic libraries, has produced a clone for phylogenetic analysis and identification of gene properties. This HERMI clone was identified as belonging to a new, uncultured bacterium with only 79% 16S rRNA gene identity to Hyphomonas oceanitis. Five antibiotic resistant clones were obtained from the HERMI application and five genes encoding for beta-lactamases were characterized. It was revealed that both clinical and novel beta-lactamases were present in the microbial communities. The gene encoding for putative cell wall-associated hydrolase, which are distantly related to the existing sequences were also identified. Furthermore, genes for virulence (Toll/ interleukin-1 receptor protein and leucine-rich repeat protein-like protein) were identified, indicating the presence of pathogens on the alga. Overall, the microbial communities of U. australis have possibly important properties for pharmaceutical applications and further work will be needed to uncover its full potential.