Honey Bee (Apis mellifera) Raw sequence reads

The importance of gut microbial communities for animal health has become increasingly clear. Early gut succession and diet-related shifts in bacterial community composition can be associated with a variety of acute and chronic diseases. Here we determined the effect of host niche and nutrient source on gut bacterial composition of the honey bee (Apis mellifera). We provided caged bees with naturally collected pollen and pollen substitute, both fresh and aged, then recorded host development and bacterial community composition of four nutrient-processing host niches. Feeding fresh pollen or fresh substitute, we found no difference in host mortality, consumption rate, development, or microbial community composition. In contrast, bees fed aged nutrition differed markedly, suffering impaired development, increased mortality, and developed a significantly different microbiome throughout the alimentary tract. Consuming an aged nutrient source resulted in a significant reduction of the core ileum bacterium Snodgrassella alvi and a corresponding increase of opportunistic pathogen Frischella perrara. Moreover, the relative abundance of S. alvi in the ileum was positively correlated with host survival and development. The inverse was true for F. perrara, reinforcing its role as an opportunistic gut pathogen. Echoing results from bumble bees, Parasacharibacter apium was also associated with negative host effects in general. Collectively, our findings suggest that the early establishment of S. alvi is associated with healthy nurse development, potentially excluding F. perrara and P. apium from the ileum. The pattern of dysbiosis in the ileum was reflected in the rectum, mouthparts and hypopharyngeal glands, suggesting a systemic physiological response. Our findings provide insight into the role nutrition plays in host health and the establishment of a characeristic gut microbiome.