# Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome

## TL;DR

This study uses metagenomic sequencing to show how neonicotinoid pesticides disrupt the gut microbiome of honey bees, potentially affecting their health.

## Contribution

The study identifies specific microbial signatures of dysbiosis caused by two neonicotinoid insecticides in honey bees.

## Key findings

- Chronic exposure to neonicotinoids increases Bifidobacterium spp. in the bee gut.
- Acute exposure leads to an increase in Apibacter adventoris.
- Each pesticide causes unique microbial changes, such as increased Snodgrassella alvi for clothianidin and decreased Lactobacillus spp. for thiamethoxam.

## Abstract

The Western honey bee (Apis mellifera) plays an essential role in agriculture around the world. In Canada, honey bees contribute up to $7 billion in economic value annually by pollinating crops and producing honey. However, since 2006–2007 North American beekeepers have lost more than a quarter of their colonies each winter. In recent years, the losses have been up to 50% in some regions. The causes of losses are complex, including the interacting effects of nutrition, pathogens, and pesticides. Although the bee gut microbiome plays a crucial role in colony health and disease, studies on the effects of agricultural pesticides on the bee microbial community are sparse. We report the use of shotgun metagenomic sequencing to investigate bee gut microbiota changes, or dysbiosis, in response to two neonicotinoid insecticides, clothianidin and thiamethoxam. Common dysbiosis signatures included an increase in Bifidobacterium spp. after chronic sublethal exposure and an increase in Apibacter adventoris after short-term acute exposure. Other dysbiosis signatures were unique to each compound, such as an increase in Snodgrassella alvi for clothianidin and a decrease in Lactobacillus spp. for thiamethoxam. These findings enhance our understanding of how the honey bee gut microbiome responds to stressors and highlight identifiable microbial profile signatures which underscores the potential utility of gut microbiome profiling as a bee health diagnostic tool. Access to timely and accurate bee health diagnosis will inform regulatory actions to decrease and mitigate exposure to stressors and will facilitate managing and improving bee health.

The online version contains supplementary material available at 10.1038/s41598-025-30907-4.