Conserved gut microbiomes with cross-species spillover between sympatric Neotropical stingless bees and honey bees

Stingless bees (Meliponini) are ecologically vital pollinators with deep cultural and economic importance in the Neotropics; however, the biogeographic structure of their gut microbiota and the extent of microbial exchange with managed honey bees (Apis mellifera) remain insufficiently understood. Using full-length 16S rRNA gene sequencing of individually sampled workers from 167 colonies across Brazil, we compared gut bacterial communities of Melipona quadrifasciata and Melipona mondury with those of co-occurring A. mellifera through an integrated taxonomic, phylogenetic, and community ecological framework. The core microbiota of Melipona species was dominated by Lactobacillus, Bifidobacterium, Apilactobacillus, Bombella, and Floricoccus, whose relative abundances covaried inversely with a set of low-prevalence taxa. Although the core communities of stingless bees overlapped only partially with those of honey bees, both groups displayed comparable alpha- and beta-diversity dispersion, suggesting broadly similar assembly dynamics. Notably, 6% of all amplicon sequence variants (ASVs) were shared across hosts, encompassing nearly all canonical honey bee symbionts, consistent with frequent cross-species spillover. Among these, several Snodgrassella ASVs-typically rare in these stingless bee species-reached high abundance in M. quadrifasciata and formed a deeply divergent clade (~96% 16S rRNA identity to Snodgrassella alvi). These patterns indicate that human-mediated management practices, such as mixed apiaries and artificial feeding, create ecological opportunities for interspecific microbial exchange. Overall, our results show that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped jointly by long-term host specificity and recent anthropogenic contact.IMPORTANCEStingless bees are key pollinators in tropical ecosystems and hold long-standing cultural significance in the Neotropics; however, their microbiomes remain far less studied than those of managed honey bees. Understanding how gut bacterial communities vary across landscapes, and whether microbes move between native and non-native hosts, is essential for predicting the ecological consequences of increasing meliponiculture and urban beekeeping. Our study reveals that stingless bee gut microbiota are generally stable and host-associated but nonetheless acquire bacterial symbionts typical of honey bees, indicating that human management practices facilitate cross-species microbial transmission. These findings broaden current knowledge of bee-microbe evolution by showing that gut symbiont boundaries are not fixed but can become permeable under anthropogenic influence. This has important implications for pollinator health, conservation, and biosecurity as managed and native bees increasingly co-occur in human-modified environments.