A network-based meta-analysis of the honeybee gut microbiome: geographic, seasonal, and pesticide-associated shifts.

The honeybee (Apis mellifera) gut microbiome is essential for pollinator health, yet its functional responses to environmental stressors remain poorly understood. We conducted a global meta-analysis of honeybee gut microbiomes from seven geographic regions, including newly generated data from Armenia, and applied a novel co-abundance network approach, tsantsR, to uncover community-level co-abundance patterns and functional adaptations. We identified a conserved core of six and ten phylotypes in 16 S and WGS datasets, respectively. In Armenia, seasonal and environmental factors, such as urbanization, were linked to compositional shifts, including higher relative abundance of Commensalibacter in autumn and of Bombilactobacillus in urban colonies. Analysis of pesticide and dietary exposure revealed distinct microbial responses. Oxalic acid and neonicotinoid exposure were associated with shifts in opportunistic pathogens, including Klebsiella, Hafnia-Obesumbacterium, and Serratia. In contrast, the herbicide glyphosate was linked to a potential adaptive response characterized by disruption of core taxa such as Snodgrassella alvi and upregulation of pathways hypothesized to be involved in glyphosate degradation, primarily linked to enrichment of Pseudomonas.