Characterizing Sponge Exo-metabolomes as Sustainable Sources of new AntiMicrobials – SESAM

Sponge biologists, marine ecologists and natural product chemists are working together to understand the cellular processes of metabolite storage and release by Mediterranean sponges that (1) harbor different types of specialized cells and (2) are known to produce structurally diverse alkaloids. Such interdisciplinarity within the research team fosters the development of efficient techniques for concentrating exo-metabolites in the marine environment, to evaluate their chemical characteristics and antimicrobial potentials.

Objective 1: Specialized sponge cells are separated from the total biomass using centrifugation and density gradient techniques. All these separated cells (symbiotic microorganisms and specialized sponge cells), are identified by DNA metabarcode and microscopy techniques.

Objective 1+2: Different systems of metabolite capture and concentration are developed in aquarium then in situ using various supports of solid phase adsorption. High resolution mass spectrometry (HR-MS) and nuclear magnetic resonance (NMR) will be used for comparative metabolomic analyses and for structural elucidation of compounds isolated from these sponges.

Objective 3: The measurement of antibiotic and antiviral activities of all prepared sponge extracts and isolated (exo)metabolites are performed on high-throughput screening platform from Aix-Marseille University ( BAC-SCREEN and AFMB, respectively). At BAC-SCREEN, assays are developed on multi-drug resistant bacteria of the ESKAPE group, on which direct cytotoxic activities and anti-biofilm properties are measured. Antiviral assays evaluate the inhibition of Dengue and Zika Flavivirus replication.

The first main results are related to aim 2 with the development of an analytical pipeline that enables qualitative and quantitative characterisation of specialized exometabolites released by the Mediterranean sponge Aplysina cavernicola. (see scientific production)

The data and results obtained during this project will lead
(1) to offer new insights as per the chemistry of Mediterranean sponges using eco-responsible methods
(2) to evaluate the biological properties of metabolites produced by sponges using the acquired knownledge from comparative metabolomic analyses
(3) to optimize the methods for the concentration of exometabolites in the marine environment
(4) to design chemical mediation experiments in the marine environment

Article:
Mauduit M, Greff S, Herbette G, Naubron JV, Chentouf S, Huy Ngo T, Nam JW, Molinari S, Mabrouki F, Garayev E, Baghdikian B, Pérez T, and Simmler C “Diving into the Molecular Diversity of Aplysina cavernicola’s Exometabolites: Contribution of Bromo-Spiroisoxazoline Alkaloids” ACS Omega 2022 DOI:10.1021/acsomega.2c05415

Zenodo community for sharing all related raw data:
zenodo.org/communities/sesam_anr/

The chemistry of sponge specialized metabolites (SpMs) has been extensively studied in the fields of anti-cancer and to a lesser extent anti-microbial drug discovery. The shrinking therapeutic choice for the treatment of multi-resistant bacterial infections or emerging viral infections, collectively underlines the necessity to maintain anti-microbial drug discovery endeavors. In that regards, sponge SpMs have displayed interesting anti-microbial properties, which are still relatively underexplored. Structurally complex, these SpMs are often purified in low yields. In some cases, massive harvests of sponge biomass were performed to obtain the most promising SpMs in sufficient quantities, thereby fragilizing the marine ecosystem. Clearly, the sustainable valorization of the chemical and biological potentials of marine SpMs should come hand in gloves with the implementation of eco-responsible supply methods.
Interestingly, sponges can release part of their SpMs into their surroundings (exo-SpMs) through the renewal or active expulsion of their cells. These exo-SpMs represent a source of bioactive molecules, which could be collected and concentrated from seawater without destroying the sponge biomass, thus, without affecting marine biodiversity. In this context, the SESAM project aims at (1) characterizing the chemical and biological properties of exo-SpMs, and (2) valorizing them as an additional and sustainable source of new antimicrobials.
An interdisciplinary approach will be developed to characterize the cells involved in the production and expulsion of exo-SpMs (AIM1), to develop efficient methods for concentrating exo-SpMs in aquaria and marine environments (AIM2), and to evaluate both their antibiotic properties against ESKAPE bacteria, and their antiviral activities against Dengue and Zika Flaviviruses (AIM3). This project, thus, brings together experts from different scientific fields: sponge biology and ecology, cellular and molecular biology, natural product chemistry, and microbiology. The SESAM team will study the chemical and antimicrobial properties of exo-SpMs from selected Mediterranean sponge species that contain different types of specialized cells possibly involved in the production and release of SpMs, all belonging to the alkaloid structural class. High-resolution mass spectrometry (HR-MS) and nuclear magnetic resonance (NMR) will be used for comparative metabolomic analyses and for the structural elucidation of isolated SpMs. Symbiotic cells (microorganisms and specialized sponge cells), isolated from the sponge biomass but also excreted in aquaria, will be identified by DNA metabarcode and microscopy techniques. The antibiotic and antiviral activities of sponge extracts, cellular fractions, and isolated SpMs will be measured on the renowned screening platforms (BAC-SCREEN and AFMB) of Aix Marseille University.
In the mid-to long terms, this project will lead to further development of techniques for a durable production and/or concentration of promising exo-SpMs. Additionally, data and results collected during this project will contribute to better characterize the ecosystemic functions of sponge exo-metabolites. Hence, this project combines marine chemical ecology with eco-responsible natural product drug discoveries. Thanks to its unique interdisciplinary approach, the SESAM project sets the ground foundation for evaluating all parameters involved in determining sponge exo-SpMs as a sustainable source of bioactive compounds.