Small molecules with highly diverse structures are produced by all animals and play essential functions in nearly all facets of their biology, including development, lifespan, reproduction, as well as interactions with other species. Identification of small molecule metabolites can reveal new biosynthetic and signaling pathways, with broad implications for medicine, human nutrition, but also agriculture. While great efforts over the past few decades have led to impressive discoveries in the field of metabolomics, the vast majority of metabolites still remain unknown and uncharacterized. Given the significance of metabolites and their biological functions, the development of new approaches toward a systematic structural and functional annotation of animal metabolomes is an important goal. In this dissertation, the author explores two highly conserved metabolic pathways with demonstrated relevance for human health and identifies diverse novel metabolites using the nematode Caenorhabditis elegans, a highly tractable model animal for biomedical research. Chapters 1–2 uncover new aspects of neurotransmitter metabolism of C. elegans, with a specific focus on serotonin metabolism. We uncovered a parallel pathway for serotonin biosynthesis and identified modular glucosides as novel down-stream metabolites of serotonin in C. elegans, and further investigated their biological activities. In chapter 3, the author investigates the metabolomes of C. elegans mitochondrial mutants, which revealed distinctive metabolic signatures in long-lived mutants, suggesting that amino acid metabolism and mitochondria-related longevity are linked. In chapter 4, the author developed selective synthetic strategies that allow to access structurally diverse modular glucosides, providing authentic samples for confirmation of proposed structures studying their biological functions.