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A balanced, diverse gut microbiota is vital for animal health. The microbial population is shaped by multiple factors including genetic background and environment, but other determinants remain controversial. Numerous studies suggest that the dominant factor is genetic background while others emphasize the environmental factors. Here, we bred asexual hybridization queens (AHQs) of honeybees through nutritional crossbreeding (laid in  Apis mellifera  colony but bred in  Apis cerana  colony), sequenced their gut microbiome, and compared it with normally bred sister queens to determine the primary factor shaping the gut microbiota. Our results showed that the dominant genera in the gut microbiota of AHQs were  Brevundimonas ,  Bombella , and  Lactobacillus , and its microbial community was more related to  A. mellifera  queens. The AHQs had a moderate number of different bacterial species and diversity, but total bacterial numbers were low. There were more significant taxa identified in the comparison between AHQ and  A. cerana  queen according to LEfSe analysis results. The only genetic-specific taxon we figured out was  Brevundimonas . The growth of core bacterial abundance showed different characteristics among different queen groups in the first week after emerging. Collectively, this study suggested that the genetic background played a more dominant role than environmental factors in shaping the gut microbiota of honeybee queen and the microbiota of midgut was more sensitive than that of rectum to this impact.

The Dominating Role of Genetic Background in Shaping Gut Microbiota of Honeybee Queen Over Environmental Factors