In press at PeerJ
The natural product biosynthetic potential of Red Sea nudibranch microbiomes
Samar M. Abdelrahman1,2, Nastassia V. Patin3,4, Amro M. Hanora5, Akram A. Aboseidah2, Shimaa M. Desoky2, Salha G. Desoky2, Frank J. Stewart3,4,6, and Nicole B. Lopanik1,3
1School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta GA 30332
2Faculty of Science, Suez University, Suez, Egypt
3School of Biological Sciences, Georgia Institute of Technology, Atlanta GA 30332
4Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta GA 30332
5Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
6Department of Microbiology and Immunology, Montana State University, Bozeman MT 59717
Background. Antibiotic resistance is a growing problem that can be ameliorated by the discovery of novel drug candidates. Bacterial associates are often the source of pharmaceutically active natural products isolated from marine invertebrates, and thus, important targets for drug discovery. While the microbiomes of many marine organisms have been extensively studied, microbial communities from chemically-rich nudibranchs, marine invertebrates that often possess chemical defences, are relatively unknown.
Methods. We applied both culture-dependent and independent approaches to better understand the biochemical potential of microbial communities associated with nudibranchs. Gram-positive microorganisms isolated from nudibranchs collected in the Red Sea were screened for antibacterial and antitumor activity. To assess their biochemical potential, the isolates were screened for the presence of natural product biosynthetic gene clusters, including polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, using PCR. The microbiomes of the nudibranchs were investigated by high-throughput sequencing of 16S rRNA amplicons.
Results. In screens against five model microorganisms, 51% of extracts displayed antimicrobial activity against more than one organism, and 19% exhibited antitumor activity against Ehrlich’s ascites carcinoma (EAC). Sixty-four percent of isolates contained PKS and NRPS genes, suggesting their genomes contain gene clusters for natural product biosynthesis. Thirty-five percent were positive for more than one class of biosynthetic gene. These strains were identified as belonging to the Firmicutes and Actinobacteria phyla via 16S rRNA gene sequencing. In addition, 16S rRNA community amplicon sequencing revealed all bacterial isolates were present in the uncultured host-associated microbiome, although they were a very small percentage of the total community. Taken together, these results indicate that bacteria associated with marine nudibranchs are potentially a rich source of bioactive compounds and natural product biosynthetic genes.