Diet outweighs genetics in shaping gut microbiomes in Asian honeybee

Abstract

Background: The gut microbiome is a crucial element that facilitates a host adaptation to a changing environment. Host-specificity often coincides with distinctions in gut microbes, suggesting a co-evolution of the holobionts. However, it is unclear how gut microbiota shared by a common host ancestor would co-diversify with hosts and eventually become distinct among sister hosts. In this context, understanding the evolutionary pathway of gut microbiomes of the same host species could provide insight on how holobionts co-adapt along environmental gradients. Specifically, we ask which factor, nature or nurture, i.e., genetics or diets, contributes more to the shaping of gut microbiome, along with host diversification and range expansion. Results: We compared and analyzed the gut microbiomes of 99 Asian honeybees, Apis cerana, from genetically diverged populations covering 13 provinces across China. Bacterial composition varied significantly across populations at phylotype, sequence-discrete population (SDP), and strain levels, but with extensive overlaps, indicating the diversity of microbial community among A. cerana populations is driven by nestedness. Taken together, genetics exhibited tangential impacts, while pollen diets were significantly correlated with both the composition and function of gut microbiome. Core bacteria, Gilliamella and Lactobacillus Firm-5, showed antagonistic turnovers and contributed to the enrichment in carbohydrate transport and metabolism. By feeding and inoculation bioassays, we confirmed that the variations in pollen polysaccharide composition contributed to the trade-off of these core bacteria. Conclusions: Progressive change, i.e., nestedness, is the foundation of gut microbiome evolution in the Asian honeybee. Such a transition during the co-diversification of gut microbiomes is shaped primarily by environmental factors, diets in general, pollen polysaccharide in particular.

Community Dynamics in Structure and Function of Honey Bee Gut Bacteria in Response to Winter Dietary Shift

“…The remaining reads were de novo assembled using Megahit (v1.1.2, k-list 51,61,71,81,91,101,111) ( 89 ) for each metagenome, where contigs longer than 500 bp were kept and blast analyzed against the NCBI nr database using DIAMOND (v0.9.22.123, blastx -f 102 -k 1 -e 1e-3) ( 90 ) for taxonomic assignment. A customized bacterial database was combined with the NCBI bacterial genomes ( 37 ). Assemblies assigned to bacteria were then blast analyzed against the customized bacterial database (blastn -outfmt 6 -e 1e-5 -max_target_seqs 5).…”

“…In particular, food can drive the differentiation of gut bacterial strains in various animals, from Drosophila ( 33 ) to humans ( 34 , 35 ). In bees, pollen diet is critical to the colonization of bee gut bacteria ( 36 ), therefore playing a vital role in shaping the gut microbiomes of the honey bees ( 37 ) and bumble bees ( 30 ). Moreover, the composition and quality of pollen may affect colony health via changing the gut community structure ( 31 ).…”

Different Diets Modulate the Gut Microbiome Compositions and Promote the Health of <em>Apis mellifera</em>

“…Diets have effects on shaping the gut microbiota in insect species [19,20]. In contrast with genetic factors, diet outweighs genetics in shaping gut microbiota in Asian honey bees [21].…”

Different Diets Modulate the Gut Microbiome Compositions and Promote the Health ofApis mellifera

“…Diets have effects on shaping the gut microbiota in insect species [19,20]. In contrast with genetic factors, diet outweighs genetics in shaping gut microbiota in Asian honey bees [21].…”