Enterotype signatures of multi-stressor exposure inform conservation strategies for mountain bumblebees of the subgenus Pyrobombus

Bees often exhibit gut microbiome-defined enterotypes impacting their health and pollination services. Bumblebees, keystone pollinators in montane and agriculture ecosystems, face significant population declines might linked to gut parasites, pathogens, and antibiotic exposure; however, whether their enterotypes reflect these specific stressors remains uncharacterized. Here, we investigate the gut microbiomes of two bumblebee species belonging to the subgenus Pyrobombus, which are commonly infested by the gut parasite Crithidia bombi and other pathogens with samples over four years in Hengduan Mountains in China. Metagenomic analysis of 175 individuals identified four distinct enterotypes in both bumblebee species. Enterotype I (23%) is characterized by Gilliamella sp. and a high metabolic activity. Enterotype II is associated with protist Crithidia bombi parasitism and shows a low bacterial relative abundance. Enterotype III exhibits proliferation of opportunistic pathogens and reduced metabolic potential. Enterotype IV is dominated by Burkholderia sp. and enriched in antibiotic resistance genes, virulence factors, and xenobiotic metabolism functions. This study establishes that bumblebee enterotypes reflect extensive (77%) exposure to parasites (Enterotype II), opportunistic pathogens (Enterotype III), and antibiotics/xenobiotics (Enterotype IV), calling for integrated conservation strategies targeting host-microbiome interactions under parasite, pathogen, and xenobiotic pressures for declining insect pollinators. Not applicable.