AbstractThe importance of the holobiont has been studied across many bee species, but less is known about the changes in the microbiome throughout the course of development, particularly in subsocial bees. This study used 16S rRNA and ITS amplicon sequencing of pollen provisions and individuals of the small carpenter bee, Ceratina calcarata, across stages of development to characterize the composition and diversity of bacteria and fungi in the microbiome. Pollen provisions and larval stages showed similar beta diversity, but differences in taxa composition. There was no significant decrease in diversity during the transition between larval and pupal stages that was expected post defecation. However, there were unexpected and progressive declines in diversity as development progressed from the early to late pupal stages and again from the callow to adult stages. Bees across all stages lacked members of the Lactobacillus (now Apilactobacillus) genus, which has been shown in other studies to be part of the core bacterial community in C. calcarata and all bees. Three correlations between bacteria and fungi were found, suggesting common beneficial bacteria may protect the bees from prevalent fungal pathogens. Low alpha diversity, particularly in the later stages of development through adulthood, is concerning as the microbiome plays an important role in maintaining wild bee health.