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 ..., , 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. , Explanation of files for Sauers et al. \"Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction\"

File: Immune_PerturbationData_06042023.csv

Data sheet containing sample meta data, qPCR determined values for total bacterial 16S rRNA, downstream relative abundances calculated from 16S amplicon sequencing analysis with QIIME2 and phyloseq, the adjusted amplicon read values for core bacteria (Relative abundance * total bacteira 16S rRNA for the sample), and species-specific qPCR values.

Analytical script: Immune_perturbation_R_Code_06042023

sampleID: The unique sample id for each sample collected in the experiment.
Colony: The colony of origin for each sample
Bee_ID: The initial ID, nested within colony, before assignment of the unique ID
Block: Sampling block for each sample
ImmuneChallenge: The immune challenge treatment for each sample, N = naive, C = wounding, E = gram negative, and S = gram positive
TreatmentDay: The da...