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. Author manuscript; available in PMC: 2025 Sep 1.
Published in final edited form as: Nat Metab. 2025 Feb 18;7(3):617–630. doi: 10.1038/s42255-025-01220-1

Fig. 3 ∣. MEDI recapitulates data from controlled-feeding studies.

Fig. 3 ∣

a, Outline and cohort sizes of the controlled-feeding studies used. b, Non-metric multidimensional scaling of MEDI food abundance beta diversity (Bray–Curtis distance) for the MBD study (n = 30, only samples with detected food (30 out of 34)). Individual lines connect each sample with the group centroid. Colours denote diet group (WD, Western diet; MBD, microbiome enhancer diet). Asterisks denote significance from a PERMANOVA (**P = 0.005). c, Relative abundance of foods (food reads / total reads) for all samples with detected foods in the MBD study (n = 30 metagenomes from n = 17 individuals, each subjected to both diets). Boxplots show 25%, 50% and 75% quantiles; the centre denotes the median and whiskers extend to the smallest and largest data points within 1.5 interquartile ranges. Asterisks denote significance under a two-sided Mann–Whitney U-test (***P = 0.0007). d, Volcano plot for differential abundance analysis of food abundances in the PATH study. Each point denotes a food species detected by MEDI. Red colour denotes food item with an FDR-adjusted P < 0.05 limma-voom regression of read counts vs intervention group (n = 48). e, MEDI predictions from faecal DNA (y axis) and nutrient consumption obtained from food diaries (x axis) in a controlled-feeding study (PATH), in which the dietary intake recorded in the daily food record precedes the stool sample by at least 48 h. Each point denotes a single individual. For the food diaries, points represent means over all measured intake amounts; error bars, s.e.m. (s.d. / sqrt(n)), normalized to a 100 g portion (all samples within the offset, 38 individuals with 124 food record diary entries). For the MEDI data, x-coordinate points represent estimates of intake based on weighting nutrient profiles of food items by food item relative abundance and assuming a 100 g portion. Blue lines denote regression slopes and grey areas represent 95% confidence intervals. Annotations denote correlation r and P value from a two-sided Pearson product-moment correlation test.