Full-length 16S rRNA gene sequencing of gut compartments from in vitro reared and hive reared honey bees (Apis mellifera)
Adult worker honey bees acquire their gut microbiota horizontally in the days after emergence, and the resulting community is compartmentalized along the alimentary tract. Separating the contribution of the social environment from that of the microbial inoculum requires rearing bees under controlled conditions, but in vitro rearing is itself a perturbation, and the extent to which an in vitro reared worker reproduces the hive reared gut community has not been resolved at species level.This BioProject reports full-length (V1-V9) 16S rRNA gene sequences from the midgut, ileum, and rectum of individual adult workers under three rearing treatments. Newly emerged workers were either marked and returned to a source hive, reared in vitro and inoculated at emergence with a homogenate of adult worker hindguts, or reared in vitro with no microbial inoculum. Individual bees were dissected at 3, 9, and 15 days post emergence, and each bee contributed three separately sequenced gut compartments, allowing community assembly to be followed within an individual rather than inferred across pooled samples.The BioProject also carries 49 full-length queen hindgut libraries from the banked-queen experiment (Copeland et al., 2022): 10 sampled at the start of the experiment (TimeZero), 19 free-running queens sampled from their colonies (Colony), and 20 queens held in a queen bank (QueenBank). These were sequenced on the same platform and assigned against the same reference, so the worker and queen compartments can be read on one scale.Sequencing used the PacBio Revio platform with Kinnex full-length 16S library preparation. Full-length reads resolve the core honey bee gut symbionts to species, including members of Lactobacillus, Gilliamella, Snodgrassella, Bifidobacterium, and Bombilactobacillus that shorter hypervariable regions cannot separate. The dataset is intended as a species-level reference for gut community assembly in the worker, and as a benchmark against which short-read amplicon surveys of the honey bee microbiota can be compared.