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This Special Issue is dedicated to recent advances in natural products chemistry related to metabolites and microbiomes. In the present Special Issue, the following topics have been covered: . Isolation of novel microbial compounds using metabolomic approaches; . Molecules and metabolomes related to agricultural applications (crop and animal productions); . Microbiomes and related natural products with beneficial effects in agriculture; . Plant metabolites with bioactive properties; . Influence of beneficial microbes and/or their metabolites on plant metabolomes; . Microbial metabolites involved in plant or animal interactions; . Influence of production technologies on animal metabolomes and microbiomes.