# How Environmental and Ecological Stressors Reprogram Honey Bee Chemistry Through the Microbiome–Metabolome Axis

## TL;DR

This review explains how various environmental stressors disrupt honey bee health by altering their gut microbiome and metabolism.

## Contribution

The paper introduces a conceptual model showing how stressors converge to disrupt the microbiome-metabolome axis in honey bees.

## Key findings

- Stressors like pesticides and poor nutrition cause similar metabolic issues in honey bees.
- Minor changes in gut microbes can significantly impact honey bee metabolism.
- Functional dysbiosis is linked to impaired energy and detoxification systems in bees.

## Abstract

Honey bee gut microbiota aids immune system function, detoxification, nutritional absorption, and digestion. Pesticides, antibiotics, diseases, inadequate nutrition, temperature stress, habitat change, and pollution all have an impact on honey bee metabolism and gut microbiome. This review demonstrates that a range of stressors frequently cause similar metabolic disorders, such as decreased energy generation, lower levels of beneficial microbial metabolites, impaired antioxidant and detoxification systems, and impaired immunity. Crucially, even minor changes in the composition of microorganisms can have a significant impact on metabolism. Focusing on how stressors affect microbial function, rather than only microbial composition, can improve our understanding of honey bee health decline and help develop better strategies for protection and conservation.

Honey bees are exposed to a wide range of environmental and ecological stressors that threaten individual health and colony sustainability. Growing evidence suggests that many of these stressors converge on a common target: the gut microbiome and its metabolic functions. The honey bee microbiome–metabolome axis represents a central regulatory system linking microbial symbionts with host nutrition, detoxification, immune competence, neural signaling, and social behavior. This review synthesizes current knowledge on how major stressors—including pesticides, antibiotics, pathogens, nutritional imbalance, thermal stress, habitat change, and environmental contaminants—reprogram honey bee chemistry by disrupting microbial community structure and, importantly, microbial and host metabolic pathways. We highlight recurring patterns consistent with functional dysbiosis, characterized by impaired energy metabolism, reduced production of short-chain fatty acids, altered amino acid and lipid metabolism, compromised antioxidant and detoxification capacity, and weakened immune regulation. However, much of the current evidence is correlative and derived from short-term or laboratory-focused studies; longitudinal and multi-site field validation of causal links remains limited. Importantly, emerging multi-omics studies suggest that profound metabolic disturbances can occur even when taxonomic changes in the microbiome are modest, emphasizing the need to move beyond descriptive community profiling toward functional and mechanistic assessments. We further discuss how stress-induced metabolic reprogramming at the individual level scales up to influence behavior, division of labor, and colony-level resilience. Finally, we propose a conceptual model illustrating how diverse stressors converge to disrupt the microbiome–metabolome axis, potentially leading to functional dysbiosis and host impairment.