Dynamics of the hindgut microbiota of the Japanese honey bees (Apis cerana japonica) throughout the overwintering period

This study compared the hindgut microbiota of the Japanese honey bees (Apis cerana japonica), a subspecies of A. cerana, during the overwintering period (December) with that before overwintering (October) and after overwintering (March) to estimate beneficial hindgut bacteria contributing to survival during the overwintering period.This dataset includes R code (.Rmd) and .csv files that are necessary for DADA2 analysis of raw amplicon sequences and downstream analysis conducted in this study. The raw amplicon sequence datasets generated in this study are available in the DDBJ Sequence Read Archive (accession numbers: DRR685263–DRR685298 for DRA Run and PRJDB20791 for BioProject).This dataset is used in a published article; Suzuki A, Hisamoto S, Sakamoto Y. 2025. Dynamics of the hindgut microbiota of the Japanese honey bees (Apis cerana japonica) throughout the overwintering period. PeerJ 13:e20050 https://doi.org/10.7717/peerj.20050.