Fig. 2

Framework of an ex vivo assay for screening drug-microbiome interactions. The individual’s microbiome is cultured and treated with drugs in anaerobic conditions simulating the in vivo environment. The cultured samples can then be analysed by 16S rRNA gene sequencing or single-shot metaproteomics to rapidly identify hit compounds taking advantage of well-established bioinformatic platforms. Detailed bidirectional drug-microbiome interactions for hit compounds can then be further evaluated with integrative multi-omics approaches