Figure 2. Overview of two main strategies to integrate metabolomics in the context of IBD research. Differentially abundant metabolites in patients with IBD compared with non-IBD controls can be further investigated by integrating additional omics layers. For metabolites with a known identity, knowledge-guided approaches can be used to place metabolites in their metabolic context, allowing the identification of genes involved in their production and degradation. In the case of human genes, further investigation of its expression or the presence of polymorphisms in individuals with IBD can provide novel hypotheses of the pathomechanism of the disease. Similarly, faecal metagenomics and metatranscriptomics datasets can be used to explore the capacity of the gut microbiota to transform these molecules. When the information on the metabolic pathway is unavailable or the identity of the associated metabolites cannot be established, co-abundance analyses with other omics layers can help establish which environmental, host and microbial factors impact the levels of a specific metabolite. IBD, inflammatory bowel diseases.