Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors

Abstract

Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.

Metabolomics and Marine Biotechnology: Coupling Metabolite Profiling and Organism Biology for the Discovery of New Compounds

“…Molecular networking is also a powerful tool in minor natural product dereplication (Cantrell et al, 2019). For example, sarasinosides and melophlins were identified using molecular networking tools, despite only small amounts of sponges being available (Mohanty et al, 2020). Finally, a recent tool called "bioactivity-based molecular networking" allows to accelerate the identification of bioactive candidate molecules by integrating data on the activity of extracts/fractions directly into the network via a bioactivity score (Nothias et al, 2018).…”

“…The development of high-throughput techniques such as genomics and metabolomics (i.e., the study of all small molecules, <2,000 Da, in an organism) promises to revolutionize natural product discovery, which according to some estimates, could outpace antibiotic discovery at its peak in the 1950s (Fortman and Mukhopadhyay, 2016). The use of these techniques, does not only offer an increase in the speed of natural product discovery and decrease in the rediscovery rate (Wolfender et al, 2019;van der Hooft et al, 2020), but provides a wide-array of unprecedented opportunities to discover unexplored chemical diversity and elucidate the biological and molecular mechanisms involved in metabolites production (e.g., Cantrell et al, 2019;Mohanty et al, 2020). Here, we provide a synthetic overview of the advantages of using metabolomic approaches in marine natural product discovery and marine biotechnology.…”

The Effects of Sampling and Storage Conditions on the Metabolite Profile of the Marine Sponge Geodia barretti

“…In the hunt for new bioactive compounds and natural products, metabolomics, especially liquid chromatography high-resolution mass spectrometry (LC-HRMS) based analysis, has gained interest owing to its capacity to analyze large numbers of metabolites simultaneously as well as its high sensitivity, reducing the amount of biological material necessary ( Paul et al, 2019 ). In sponge research metabolomics has been used to study differences in the metabolome depending on geographical location Bayona et al (2020) , between species Olsen et al (2016b) , Reverter et al (2018) or to investigate the chemical diversity of sponge extracts ( Cantrell et al, 2019 ; Mohanty et al, 2020 ). However, very few systematic investigations of method development for metabolomics of sponges have been performed.…”

“…Furthermore, factors such as sampling, quenching the metabolism, storage conditions as well as sample extraction parameters have great effects on the final metabolome as well as data quality Engskog et al (2016) , Vuckovic (2018) , and have been investigated and reviewed for plasma, serum and urine Bi et al (2020) , González-Domínguez et al (2020) , Smith et al (2020) , mammalian cells Dettmer et al (2011) , Bi et al (2013) , Engskog et al (2015) , bacteria and microbes Mashego et al (2007) , Rabinowitz (2007) , Kapoore and Vaidyanathan (2018) , as well as for plants ( Kim and Verpoorte, 2010 ; Rodrigues et al, 2019 ; Salem et al, 2020 ). For the collection of sponges for metabolomics, no guidelines or practical consensus exist and the procedures for sampling varies, in some cases the sponges are frozen directly upon collection, in some cases the time between collection and freezing is not stated in the publications and in some cases the sponges are immediately stored in ethanol where after the ethanol is often discarded prior to extraction of the sponge ( Olsen et al, 2016b ; Einarsdottir et al, 2017 ; Bayona et al, 2018 ; Bayona et al, 2020 ; Reverter et al, 2018 ; Mohanty et al, 2020 ).…”

Assessing the Diversity and Biomedical Potential of Microbes Associated With the Neptune’s Cup Sponge, Cliona patera

“…The sponge microbiome is known to provide a number of valuable contributions to many aspects of the host physiology and ecology as well as mediation of nutrient cycles, such as carbon, nitrogen, phosphorus, and sulfur cycles ( Webster and Thomas, 2016 ; Zhang et al, 2019 ). Due to the challenges associated with culturing microbial symbionts from sponges, culture-independent approaches, including metabarcoding, metagenomic, metaproteomic, metabolomic and metatranscriptomic techniques, have been instrumental in obtaining information to infer the putative functional roles of these sponge symbionts ( Thomas et al, 2010 ; Fan et al, 2012 ; Liu et al, 2012 ; Radax et al, 2012 ; Gauthier et al, 2016 ; Mohanty et al, 2020 ). Metagenomic differences between sponge-associated and seawater microbial consortia highlighted genes enriched only in sponge symbionts that are relevant to the symbiosis ( Fan et al, 2012 ; Hentschel et al, 2012 ; Horn et al, 2016 ).…”