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Supplementary Information: Additional file 1: Supplementary Figure S1. Photorhabdus luminescens incubated with the KC-12 probe during 70 h. Supplementary Note 1. Taxonomic Appendix. Supplementary Figure S2. Hybridization of cells from nudibranch skin, gut, gills and gonads. Supplementary Figure S3. KEGG modules of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S4. Sulfur and nitrogen metabolism of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S5. ABC transporters of Ca. D. californiensis and medium quality Ca. Tethybacterales MAGs from sponges. Supplementary Figure S6. Phylogenetic tree of 16S rDNA gene sequences from public datasets. Supplementary Figure S7. Proportion of reads with >92% sequence similarity to Ca. D. californiensis in other nudibranchs. Supplementary Figure S8. Heatmap showing relative abundances of top ASVs across all 16S rDNA amplicon samples. Supplementary Figure S9. Core microbiome of D. fulva mantle. Supplementary Figure S10. ASVs determining the ordination of samples in the PCA anlaysis of nudibranch microbiome samples. Supplementary Figure S11. Phylogenetic tree of full length 16S rDNA gene sequences from nudibranch skin and mucus obtained by Sanger sequencing. Supplementary Figure S12. Ca. D. californiensis betalactone gene cluster compared to the best antiSMASH matches. Supplementary Figure S13. Similarity of the genes in the Ca. D. californiensis betalactone gene cluster with the 'nr' database of NCBI. Supplementary Figure S14. Similarity of the genes in the Ca. D. californiensis betalactone gene cluster with other members of the Ca. Tethybacterales order. Supplementary Figure S15. Biosynthetic pathway comparison to known betalactone natural product pathways. Supplementary Figure S16. NMR analysis of extracts from D. fulva nudibranchs. Supplementary Figure S17. Quantification of the dcbD expression in the CRAGE strains and nudibran

[Background] Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva., [Results] We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously., [Conclusions] Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.