Abstract
Glyphosate-based herbicides (GBHs) are ubiquitous agrochemicals whose ecological impacts extend beyond target weeds to non-target organisms, including key insect pollinators. The western honey bee (Apis mellifera) hosts a specialized, conserved gut microbiota that plays critical roles in nutrition, immune maturation, and defense against pathogens. Because several core bacterial taxa possess class I 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS)—the direct molecular target of glyphosate—herbicide exposure can disrupt microbial equilibrium. In this study, we evaluated the impacts of field-realistic concentrations of GBHs on the taxonomic diversity and functional capacity of the A. mellifera gut microbiome across intensive monoculture, mixed agricultural, and semi-natural forage landscapes. High-throughput 16S rRNA gene sequencing and shotgun metagenomics revealed a significant reduction in overall alpha diversity and marked shifts in community composition following chronic GBH exposure. Key core symbionts, particularly Snodgrassella alvi and Bifidobacterium asteroides, exhibited substantial declines in relative abundance, alongside an overrepresentation of opportunistic taxa such as Serratia marcescens. Metagenomic functional profiling demonstrated the downregulation of pathways associated with aromatic amino acid biosynthesis and short-chain fatty acid production. Notably, the severity of microbial dysbiosis was significantly amplified in intensive monoculture landscapes characterized by poor nutritional diversity. These findings demonstrate that glyphosate exposure synergizes with landscape-level habitat simplification to compromise honey bee gut health, emphasizing the urgent need to integrate microbiome endpoints into environmental risk assessments of modern agricultural practices.
