Gut microbiota structure in stingless bees is shaped by ontogeny, caste, and sex

Background Eusocial bee gut microbiota can be influenced by diet, environment, caste, sex, and developmental stage. While these dynamics are well studied in honey bees and bumble bees, they remain largely unknown in stingless bees. Here, we used 16S rRNA gene sequencing to characterize the gut microbiota of Melipona capixaba and Melipona mondury across developmental stages (larvae, nurses, and foragers), and across castes (workers and queens) and sexes (adult males and females) in M. mondury . We integrated taxonomic profiling, alpha and beta diversity analyses, differential abundance testing, and functional predictions to identify the ecological drivers of microbiome structure. Results Microbiota composition is structured by developmental stage, driven by an interaction of environmental contact through out-of-nest activities, social behaviour, and diet. Workers (nurses and foragers) and males harbour richer and more even communities. Socially integrated workers are dominated by typical bee-associated core taxa, including Lactobacillus , Bifidobacterium , and Commensalibacter , whereas males are enriched in transient and environmentally derived genera such as Erwinia and Morganella . Nurses exhibit intermediary microbiotas overlapping those of larvae, queens, and foragers, supporting a multidimensional model of bacterial acquisition mediated by in-nest social interactions. In contrast, larvae and queens possess less diverse and highly uneven communities dominated by fermentative and acid-tolerant taxa adapted to sugar-rich, low-oxygen diets. Both virgin and physogastric queens are consistently dominated by Erysipelatoclostridium sp., indicating that queen microbiota composition is relatively insensitive to reproductive physiology and hormonal state. Further predictive functional profiling indicates that worker and male microbiota are specialized for environmental resilience and oxidative metabolism, while larvae and queens are enriched in pathways for fermentation and detoxification. Conclusions Stingless bee gut microbiota is adjusted to host identity, developmental stage, and ecological role. Our findings reveal that the microbiotas of M. capixaba and M. mondury constitute a highly plastic system in which a multidimensional framework—encompassing social structure, caste, sex, developmental stage, diet, and environmental contact—interacts to calibrate microbial function according to the specific biological and energetic requirements of the colony’s members.