BACKGROUND: Knowledge of microbiota composition, persistence, and transmission as well as the overall function of the bacterial community is important and may be linked to honey bee health. This study aimed to investigate the inter-individual variation in the gut microbiota in honey bee larvae and pupae. RESULTS: Individual larvae differed in the composition of major bacterial groups. In the majority of 5th instar bees, Firmicutes showed predominance (70%); however, after larval defecation and during pupation, the abundance decreased to 40%, in favour of Gammaproteobacteria. The 5th instar larvae hosted significantly more (P < 0.001) Firmicutes than black pupae. Power calculations revealed that 11 and 18 replicate-individuals, respectively, were required for the detection of significant differences (P < 0.05) in the Bacteroidetes and Firmicutes abundance between stages, while higher numbers of replicates were required for Actinobacteria (478 replicates) and Gammaproteobacteria (111 replicates). CONCLUSIONS: Although sample processing and extraction protocols may have had a significant influence, sampling is very important for studying the bee microbiome, and the importance of the number of individuals pooled in samples used for microbiome studies should not be underestimated.

Bee Research Institute Dol 94 252 66 Libcice nad Vltavou Czech Republic

Department of Agroecology and Crop Production Czech University of Life Sciences Prague Kamycka 129 165 00 Prague Czech Republic

Department of Food Science Czech University of Life Sciences Prague Kamycka 129 165 00 Prague Czech Republic

Department of Genetics and Breeding of Farm Animals Institute of Animal Science Pratelstvi 815 104 00 Prague Czech Republic

Department of Microbiology Nutrition and Dietetics Czech University of Life Sciences Prague Kamycka 129 165 00 Prague Czech Republic

Department of Zoology and Fisheries Czech University of Life Sciences Prague Kamycka 129 165 00 Prague Czech Republic

Institute of Animal Physiology and Genetics v v i Academy of Sciences of the Czech Republic Videnska 1083 142 20 Prague Czech Republic

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