Combined imidacloprid and chlorpyrifos disrupt gut microbiota-host interactions and reduced performance and survival in honey bees.

Gut microbiota plays a central role in insect physiology and health. However, how agrochemical exposure perturbs gut microbiota of the host and its downstream functional consequences remains understudied. Here, we employed an integrative multi-omics framework combining microbiome profiling, transcriptomics, and metabolomics to investigate how field-realistic exposures to the insecticides chlorpyrifos (CPF), imidacloprid (IMD), and their combination (IC) affect gut microbial composition as well as sucrose consumption, body weight dynamics, and survival in bees. We found that sucrose consumption was significantly reduced in bees exposed to IMD and IC, but not in the CPF group. Survival probability was significantly lower only in the IC group, whereas IMD and IC treatments caused greater weight loss compared to controls. Furthermore, IC exposure induced pronounced gut dysbiosis, and severe midgut structural damage, including epithelial degeneration and disruption of gut barrier integrity. At the functional level, IC exposure suppressed key detoxification enzymes, including glutathione S-transferase (GST) and cytochrome P450, indicating impaired xenobiotic metabolism. Multi-omics integration revealed 842 differentially expressed genes and 193 metabolites under IC exposure, with alterations in key pathways associated with energy metabolism, oxidative stress response, immune regulation, and host-microbiome interactions. These findings demonstrate that combined pesticide exposure disrupts gut microbiota composition and function, leading to cascading effects on host metabolic and detoxification processes as well as the overall health, and highlights the need for careful pesticide management to mitigate adverse impacts of combined pesticides across the environment.