Extended Data Fig. 1: Total number of bacteria and fungi and colonization levels of Gilliamella per bee gut.

(A) Total number of bacteria (both S. alvi and Gilliamella) was determined by plating homogenized guts on BHIA and counting CFUs. Horizontal dotted line represents LOD < 70. No colonies were observed in samples plotted below the LOD line. Significant differences in CFUs between dietary conditions was determined with a two-sided Wilcoxon rank sum test (S. alvi: ***P = 3.9x10^-4; S. alvi + Gilliamella: *P = 0.031) NS, non-significant. (B) Bacterial cells (number of bacterial genome equivalents) per bee gut determined by qPCR using genus-specific Gilliamella 16 S rRNA gene primers. The horizontal dotted line represents qPCR LOD < 10⁴. A two-sided Wilcoxon rank sum test was used with Gilliamella (Pollen -) as reference group, NS, non-significant; (No bacteria: ****P = 4.43x10^-7, No bacteria (Pollen) ****P = 4.25x10^-7, Gilliamella (Pollen): *P = 3.7x10^-2, S. alvi + Gilliamella: **P = 6x10^-3. (C) Number of 16 S rRNA gene copies per bee gut and in three different quantities of sterilized bee pollen as determined by qPCR using universal 16 S rRNA gene primers. The horizontal dotted line represents qPCR LOD < 8x10³. Wilcoxon rank sum test was used with MF (Pollen -) as reference group, (No bacteria: ****P = 3.16x10^-5, S. alvi: ****P = 1.71x10^-9, S. alvi (Pollen) ****P = 1.71x10^-9, Gilliamella: ****P = 3.18x10^-11, Gilliamella (Pollen): ****P = 4.93x10^-10, S. alvi + Gilliamella: ****P = 1.35x10^-13, S. alvi + Gilliamella (Pollen): ****P = 1.93x10^-13 NS, non-significant). The number of 16 S rRNA gene copies detected in DNA extracted from different quantities of sterile pollen used in the bee diet is shown in a separate plot. The high background signal in samples containing pollen comes from the amplification of chloroplast DNA as shown in previous studies⁴⁵. (D) Number of 18 S rRNA gene copies per bee gut and in three different quantities of sterilized bee pollen as determined by qPCR using universal 18 S rRNA gene primers. The horizontal dotted line represents qPCR LOD < 10⁴. Wilcoxon rank sum test was done with MF (Pollen -) as reference group, NS, non-significant. In all plots, each dot represents a single bee gut and red bars represent the median value for each group. The absence or presence of pollen in the diet is indicated by (-/+).