Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China

Abstract

Sponge-derived bacteria are considered to be a promising source of novel drugs, owing to their abundant secondary metabolites that have diverse biological activities. In this study, we explored the antimicrobial biosynthetic potential and phylogenetics of culturable bacteria associated with the sponge Ophlitaspongia sp. from the Yellow Sea, China. Using culture-dependent methods, we obtained 151 bacterial strains, which were then analysed for their antimicrobial activities against seven indicator strains. The results indicate that 94 (62.3%) of the 151 isolated strains exhibited antimicrobial activities and inhibited at least one of the indicator strains. Fifty-two strains were selected for further phylogenetic analysis using 16S rRNA gene sequencing, as well as for the presence of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes. These 52 strains belonged to 20 genera from 18 families in 4 phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Five strains with PKS genes and ten strains with NRPS genes were detected. Among them, two strains contained both PKS and NRPS genes. Notoacmeibacter sp. strain HMA008 (class Alphaproteobacteria) exhibited potent antimicrobial activity; thus, whole genome sequencing methods were used to analyse its secondary metabolite biosynthetic gene clusters. The genome of HMA008 contained 12 biosynthetic gene clusters that potentially encode secondary metabolites belonging to compound classes such as non-ribosomal peptides, prodigiosin, terpene, β-lactones, and siderophore, among others. This study indicates that the sponge Ophlitaspongia sp. harbours diverse bacterial strains with antimicrobial properties and may serve as a potential source of bioactive compounds.

Prioritization of Microorganisms Isolated from the Indian Ocean Sponge Scopalina hapalia Based on Metabolomic Diversity and Biological Activity for the Discovery of Natural Products

“…Marine macroorganisms such as sponges are already known to produce metabolites with structural originality and remarkable biological activities [ 11 , 12 ]. Within these hosts, there are microbiota that can consist of hundreds of bacteria belonging to different genera [ 22 , 23 , 24 ]. These bacteria may be responsible for the production of specialized metabolites in holobionts and exhibit a great potential for the discovery of new molecules with diverse biological activities [ 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ].…”

“…Within these hosts, there are microbiota that can consist of hundreds of bacteria belonging to different genera [ 22 , 23 , 24 ]. These bacteria may be responsible for the production of specialized metabolites in holobionts and exhibit a great potential for the discovery of new molecules with diverse biological activities [ 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. However, the large number of microorganisms isolated from these complex systems makes their exploration fastidious, time-consuming and expensive for research.…”

“…One article gives the chemical composition of this sponge [ 19 ], highlighting the presence of butenolide derivatives, phospholipids or even brominated compounds. These compounds can be synthetized by the macro-organisms themselves or by their associated microbial community [ 22 , 23 ]. Another hypothesis is that the production of bioactive metabolites is possibly due to the existence of this holobiont composed of the macroorganism and its microbiome, which together form a discrete ecological unit through symbiosis or various thin interactions.…”

Isolation, characterization and identification of sponge-associated bacteria producing antimicrobial compounds

“…To date, more than 23,000 natural Poliketides (PKs) and Non Ribosomal Protein (NRP) products have been identified and characterised, including antibiotics (Chen et al 2022). Although the presence of these genes in the genome does not suggest their expression or function, their presence raises the possibility of identifying organisms capable of producing bioactive compounds (Amoutzias et al 2016).…”