Effect of host genetics on gut microbiota composition in an Italian honeybee breeding population

Honeybees host a specialised gut microbiota composed of five ever-present bacteria, which undergo seasonal variation in their proportions. The objective of this study was to investigate how host genetics can affect the microbial composition of the honeybee gut over a 5-month sampling period. Seventy-seven colonies from eight maternal genetic lines were sampled from a breeding population located in Lombardy, Italy. The colonies have been selected since 2015 for three different traits, using isolated mating stations for reproduction. Worker bees were sampled three times: June, July and October 2021. From each colony, gut from ten worker bees were pooled, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Statistical analyses were conducted in the R environment to assess the impact of genetic lines, timepoints, and their interaction on a-diversity and b-diversity. Results for a-diversity showed a significant effect of genetic line on the Simpson index, as well as a consistent effect of the timepoint. Specifically, genetic line H showed a lower Simpson index, and this line also produced less honey in the same years, suggesting a genetic influence on both microbiota richness and honey yield. For b-diversity, results revealed that the month of sampling had the strongest effect, while no significant differences were identified for the genetic line or their interaction.