Honey bees subsist on a pollen and nectar-specialized diet, which underpins their critical role in pollination. However, bees are unable to metabolize pollen polysaccharides on their own and depend on their gut microbiome to break them down. Due to the wide range of plants that honey bees pollinate, the composition of nectar and pollen in their diet is highly diverse, which consequently influences the structure of their gut microbiome. The honey bees host a simple and conserved gut microbiome. The five core gut bacterial taxa have a clear division of labor in polysaccharide metabolism. However, the combined metabolic functions of individual microbial members alone are clearly insufficient to handle the diversity of dietary polysaccharides. Therefore, interactions between different gut bacterial members are necessary for degrading complex polysaccharides in the diet. Furthermore, interactions between gut bacteria driven by polysaccharide metabolism may play a significant role in shaping the dynamics of the gut microbiome under varying pollen conditions. However, relevant studies on the interactions among bee gut microbes are scarce.
Here, we demonstrate a conditional reciprocal relationship between Bifidobacterium asteroides and Gilliamella apicola, two core gut bacterial species of honey bees, driven by their synergistic degradation of homogalacturonan (HG), the backbone structure of pectin. Our results indicate that the degree of HG methylation, which varies among plants, mediates the shift in interactions between the two parties and dictates the dynamics of the gut microbiome.
Specifically, Gilliamella is a key bacterium for pectin degradation, encoding all the necessary enzymes for the breakdown and utilization of homogalacturonan (HG), except for the pectin methylesterase enzyme (CE8). Therefore, highly methylated pectin inhibits the utilization by Gilliamella, thereby impairing its growth. Large-scale comparative genomics analysis based on hundreds of bacterial genome sequences coupled with protein predictions indicated that another core bacterium, Bifidobacterium asteroids was specialized for CE8 encoding, suggesting a potential cooperation in pectin deconstruction between the two parties. Through heterologous expression and purification of the pectin lyase PL1 from Gilliamella and the pectin methylesterase CE8 from Bifidobacterium, we confirmed that the enzyme activities and synergistic relationship in pectin digestion occurred in vitro. Growth inhibition on Gilliamella by highly methylated pectin was released after CE8 precondition. At the same time, oligo galacturonic acid liberated from Gilliamella’s digestion could also cross-feed Bifidobacterium and promoted its growth, thus a reciprocal interaction between the two bacteria was established.
Interestingly, experiments based on in vitro culture revealed that the reciprocal interactions between the two bacteria vanished under low-methylated pectin conditions, when Gilliamella alone was able to degrade pectin without having to rely on the demethylated function of Bifidobacterium. At the same time, Gilliamella no longer shared pectin metabolites with Bifidobacterium, resulting a transition to a neutral interaction between the two bacteria.
This shift in the interaction between bacteria results in alterations in bacterial community dynamics under varying pectin conditions. In vivo colonization experiments showed that under highly methylated pectin conditions, the abundance of both bacteria was significantly increased in co-colonization than each being cultured alone. However, a low-level methylation in pectin increased the abundance of Gilliamella but did not change the abundance of Bifidobacterium despite the presence of Gilliamella. Therefore, the conditional interaction relationship between the two bacteria was also confirmed under varied diet conditions in the honey bee gut.
We further explored the mechanism underlying the shift in bacterial interactions. By performing a metabolite assay using the high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD), we found that the ratio of metabolic intermediates galacturonic acid disaccharide (di-GalA) and monosaccharide (GalA) varied under the different levels of HG methylation. Therefore, we predicted that the variation in the composition of publicly accessible substrate affected their utilization by the two bacteria and, thus, their growth. However, these substrates were not available to us, which prevented us from validating the effects of their ratio on the growth of the two bacteria. Given this, we opted to measure the expression of bacterial genes related to the utilization of these metabolites and to construct a consumer resource model to tackle this question. Taken together, these findings suggest that the ratio of public goods influences their utilization by the two bacteria, resulting in shifts in their interactions.
This study underscores the significance of bacterial interactions in shaping gut microbiome dynamics under various disturbances, offering insights into the interactions between gut bacteria mediated by polysaccharide metabolism. These findings contribute to predicting population dynamics in the bee gut microbial ecosystem in response to environmental changes.
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For more details, please see our article: www.nature.com/articles/s41467-024-51365-y