Figure 2. Targeted metabolomics analysis was performed on the extracts from ileum, colon, liver, and plasma samples from mice receiving oral gavages with several commensals or PBS (control), or continuous ATB, at days 3, 7 and 14 after the first oral gavage. Changes in metabolites relative abundance are illustrated. Ileum and colon showed the strongest treatment-dependent metabolites variations. Hierarchical clustering (euclidean distance, ward linkage method) of the metabolite abundance is shown. Note that Supplementary Figures 1, 2, 3 and 5 provide the names of each of the metabolites, for each of the different matrices. The purpose of this figure is to allow for a direct comparison of the amplitude of the metabolic effects of manipulation of the microbiota. ATB, antibiotics; PBS, phosphate buffer saline; FMT, fecal microbiota transplant; FC, fold change.