Fig. 1

In vivo experiments to investigate the effects of glyphosate and tylosin on the honey bee immune system. Three independent experiments were performed with newly emerged honey bees (Apis mellifera) originating from different hives from different seasons. In the fall 2018 and fall 2020 experiments, pupae were extracted from a brood frame and allowed to emerge under sterile conditions, whereas in the summer 2020 experiment, pupae were allowed to emerge naturally from a brood frame kept in the laboratory. In all experiments, healthy newly emerged workers were transferred to cup cages and allowed to acquire their microbiota simultaneously to treatment (0.1 mM glyphosate, 1 mM glyphosate or 0.1 mM tylosin in sucrose syrup) for 5 days. A control group was treated with sucrose syrup only. In the fall 2018 and summer 2020 experiments, RNA was extracted from individual bee guts and pooled for 3′-Tag RNA sequencing (3 pooled guts per sample, 5 samples sequenced per group), whereas in the fall 2020 experiment, RNA was extracted from whole bee bodies (15 individual bees per group) and used in downstream analyses