Extended Data Fig. 3: Z-score normalized metabolite abundances of compounds significantly affected by S. alvi colonization.

Box plots and individual data points display values across all 8 experimental conditions. Only metabolites in which a mixed linear model showed a significant effect of S. alvi colonization are plotted. Multiple types of metabolic interactions are shown. For example, metabolite depletion by S. alvi exclusively (2-ketoisocaproate, 3Hmg, caffeate, urea) or by both species (aspartate, citrate, glycerate), metabolite production by S. alvi exclusively (anthranilate, unknown 12.74), crossfeeding from Gilliamella to S. alvi (pyruvate, lactate), synergistic metabolite depletion (fumarate, malate) and production (acetate, benzoate). The dark and light grey asterisks show conditions significantly different from MF bees fed sugar water and pollen or only sugar water (also indicated by ± sign), calculated using a two-sided Wilcoxon rank sum test with BH correction, *P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. ((Pollen ±): P values are shown in Supplementary Table 3. No bacteria: n = 12/10; S. alvi: n = 11/12; S. alvi + Gilliamella: n = 13/14; Gilliamella: n = 10/13). The median and the inter-quartile range (IQR) are depicted by the box, with whiskers extending to the furthest data points up to 1.5*IQR. The dotted line represents the transformed LOD for each metabolite.