Immune stimulation induced changes to the native gut microbiota of bumble bees

Understanding factors influencing the maintenance and membership of beneficial host-associated microbial communities is central to understanding ecological, evolutionary, and health consequences of these communities for their hosts. Host immunity is often implicated as a potential regulator of these microbiota. However, conversely, immunity may play a disruptive role, with immune responses to infection causing collateral damage. Such effects may be more prominent from innate immune responses, with more rapid-acting and relatively non-specific components. We investigated how upregulation of antibacterial immunity in the bumble bee Bombus impatiens affects the core gut microbiota, testing the hypothesis of immunity-induced perturbation of the beneficial microbiota structure. Freshly emerged adult bees received a native microbiota inoculation before being subjected to non-pathogenic immune stimulation treatments. We quantified the microbial community using 16S rRNA amplicon sequencing and targeted qPCR. We find colonization of the core member Gilliamella is altered by immune stimulation treatment. Additionally, a positive association in communities between Gilliamella and another core bacteria, Snodgrassella alvi, is perturbed. These changes are indicative of immune-response-induced dysbiosis. As such, the potential for collateral perturbation of beneficial microbial communities upon a host's innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment.See the uploaded readme (ReadME.md). In addition to this, the latest version of R statistical software and the latest versions of the following packages: MASS, car, plyr, dplyr, lme4, msme, emmeans, phyloseq, ggplot2, cowplot, vegan, dplyr, metagMisc, glmmTMB, DHARMa, NetCoMi, AICcmodavg and a Linux system with the latest version of Ubuntu, Conda, and QIIME2 will be required to recreate the analysis. Funding provided by: National Institute of General Medical SciencesCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000057Award Number: R15GM1296