Single-cell metabolite detection and genomics reveals uncultivated talented producer

Abstract

The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), 1 of the oldest metazoans. However, most bacterial members of sponge microbiomes have not been cultivated or sequenced, and therefore, remain unrecognized. Unequivocally linking metabolic functions to a cellular source in sponge microbiomes is, therefore, a challenge. Here, we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge (sponge that hosts a rich bacterial community) Theonella swinhoei, previously shown to contain ‘Entotheonella’ symbionts that produce most of the bioactive substances isolated from the sponge. As an exception, the antifungal aurantosides had remained unassigned to a source. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, ‘Candidatus Poriflexus aureus’ from a new Chloroflexi lineage as the aurantoside producer. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.

Microbial communities associated with marine sponges from diverse geographic locations harbour biosynthetic novelty

“…Evidence is growing that various phyla associated with marine sponges produce bioactive compounds. Since the discovery of the Entotheonella genus from the Theonella swinhoei sponge 5,7 , Cyanobacteria 4 , Proteobacteria 44 , Verrucomicrobia 78 and Chloroflexota 79 have been conclusively linked to the production of natural products in marine sponges. Here, we present MetaSing, a reproducible bioinformatic pipeline that allows facile identification of sponge-associated taxa encoding biosynthetic potential.…”

Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals

“…Although the primary purpose of these proposed workflows is to accelerate novel microbial natural product discovery, they could be useful for chemical ecology research, particularly for deciphering the structure and/or function of specialized molecules produced by uncultivated microbes in marine symbiosis. A recent integrated genomic- and metabolic-based workflow was proposed by Kogawa and co-workers to isolate and analyze a single microbial cell obtained from a complex microbiome of the sponge Theonella swinhoei for the production of defensive compounds such as aurantosides, e.g., aurantoside A ( 112 ) ( Figure 16 ) [ 180 ]. The analysis pipeline combined microfluidic encapsulation, Raman microscopy and integrated digital genomics (MERMAID) for the efficient identification of uncultivated microbial producers.…”

Biosynthesis of Bioactive Natural Products Derived from Theonellidae Family Marine Sponges

“…3), the remaining metabolite originating in yellow chemotype T. swinohei, was identified as the different phylotype 'Candidatus Poriflexus aureus.' 19)…”