Highly significant distances between untreated, antibiotic and probiotic treated groups were observed in the intestinal tracts emerging as main bacterial functional sites from our PET images, namely the caecum for [ 18 F]FDG and [ 18 F]FDS and the proximal and central small gut for [ 11 C]cho (Fig. 6 b, Supplementary Information S1 a, S1 c, S1 g).
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Functional PET imaging of gut microbiota with [<sup>18</sup>F]fluorodeoxyglucose, [<sup>18</sup>F]fluorodeoxysorbitol and [<sup>11</sup>C]choline reflects Clostridia and Lactobacillales abundance in caecum and small intestine and host metabolic interactions.
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