Gut microbiota variation across sympatric stingless bee species and honey bees in the Neotropics

Stingless bees (Meliponini) are ecologically and culturally important pollinators with a long tradition of human management in the Neotropics. Yet, little is known about how their gut microbiota vary across geographic regions or whether microbial exchange occurs with managed honey bees ( Apis mellifera ), which are often kept in close proximity. Using full-length 16S rRNA gene sequencing of individual bees sampled from 167 colonies, we characterized gut microbial community structure through a hierarchical, taxonomic and phylogenetic comparative framework, contrasting the microbiota of Melipona quadrifasciata and Melipona mondury with that of Apis mellifera across their shared geographic range in Brazil. The core microbiota of Melipona was dominated by Lactobacillus , Bifidobacterium , Apilactobacillus , Bombella , and Floricoccus , and showed inverse variation in relative abundance with lower-prevalence bacterial taxa. Although the core microbiota of the two stingless bee species overlapped only partially with that of Apis mellifera , they exhibited comparable alpha-diversity and beta-diversity dispersion, indicating broadly similar community assembly processes and dynamics. Nevertheless, we found that 6% of all amplicon sequence variants (ASVs) were shared between hosts, encompassing nearly all canonical honey bee “core” symbionts, indicating frequent spillover. Remarkably, several ASVs of Snodgrassella , a genus typically rare in stingless bees, reached high abundance in several M. quadrifasciata individuals and formed a deeply divergent clade (∼96% 16S rRNA gene identity to S. alvi ). These patterns are consistent with the hypothesis that human-mediated management practices, such as mixed apiaries and artificial feeding, create opportunities for microbial exchange between native and non-native bees. Together, our findings indicate that stingless bee gut microbiomes are compositionally stable yet ecologically permeable, shaped by both long-term host specificity and recent anthropogenic contact.