A comparative metagenomics approach to marine natural product drug discovery in Hippospongia lachne

*These authors contributed equally.

With the increasing availability of deeply sequenced data sets, it has become clear that the biosynthetic potential of uncultured microbes remains largely untapped [1]. Uncultured, symbiotic bacteria associated with marine invertebrates often protect and interact with their hosts through the production of secondary metabolites, which can exhibit a broad spectrum of clinically relevant bioactivities. The microbial consortia of marine sponges (phylum Porifera), for instance, are known or suspected to produce a number of interesting bioactive compounds [2].

Fig. 1: Bacterial contigs over 10 kbp assembled from the metagenome of a single Hipposongia lachne sample and binned into distinct clusters based on kmer frequencies. Each cluster of grey points represents an individual bacterial genome separated from the overall sponge metagenome. Colored points represent contigs with biosynthetic pathways; these contigs are colored by biosynthetic pathway type and scaled by length.

To explore this source of biosynthetic talent, we collected ˜100 sponge samples from the Florida Keys. Amplicon sequencing of 16S rRNA genes by next-generation sequencing revealed differences in sponge microbiome compositions, and evaluation of crude organic extracts by HPLC analysis showed differences in chemical composition between sponges of the same species. Furthermore, biofilm inhibition assays suggested that perturbations in microbiota and variation in the chemical profiles of individual sponges can be associated with the bioactivity of their organic extracts. For two Hippospongia lachne sponge samples where perturbations in the microbiome were associated with a change in chemical composition and bioactivity, we implemented a culture-independent, shotgun metagenomics approach to reconstruct whole bacterial genomes from sponge microbiomes. With this technique, we were able to recover over 100 high quality genome assemblies, many of which diverge significantly from known bacterial lineages, and identify over 300 biosynthetic pathways distributed throughout the microbial community of a single sponge (Fig. 1). In conjunction with analytical chemistry techniques as well as targeted culturing and heterologous expression efforts, we hope to develop culture-independent sequencing methods to explore uncultured bacteria and their otherwise inaccessible biosynthetic potential in complex microbial systems.

Acknowledgements: This research was performed in part using the compute resources and assistance of the UW-Madison Center For High Throughput Computing (CHTC) in the Department of Computer Sciences. The CHTC is supported by UW-Madison, the Advanced Computing Initiative, the Wisconsin Alumni Research Foundation, the Wisconsin Institutes for Discovery, and the National Science Foundation, and is an active member of the Open Science Grid, which is supported by the National Science Foundation and the U.S. Department of Energy's Office of Science. This work was supported by the National Institutes of Health, NIAID Grant R21AI121704, the American Foundation for Pharmaceutical Education (IJM) and the School of Pharmacy, the Graduate School, and the Institute for Clinical & Translational Research at the University of Wisconsin-Madison.

Keywords: comparative metagenomics, shotgun sequencing, de novo assembly, bioinformatics, marine drug discovery.

References:

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