DOI: 10.5061/dryad.ncjsxkt8v
title: Data from: Host-associated beneficial gut microbiota boosts induced immunity and limits immune deployment costs in bumblebees

description: Ecological immunology posits that variation in host resistance to
 infection may be attributed partly to the ecological and evolutionary
 costs of immunity. While the deployment of immune defense is necessary to
 combat pathogenic infection, host pay energetic and other costs for
 activation. Host-associated beneficial microbiota have been shown to
 affect multiple host traits, including immunity, but how interactions with
 these microbial communities may mitigate the costs of immune activation
 remains an open question. For apid bees, including eusocial bumblebees,
 core members of the adult gut microbiota contribute to a variety of
 fitness-relevant traits and provide a key ecological and evolutionary
 relationship contributing to ecological success. Here, we test the
 hypothesis that the host-associated microbiota provides benefits to bumble
 bee immunity, including the mitigation of the costs associated with
 inducible immune responses. Freshly emerged germ-free adult workers were
 supplemented with their native microbiota via experimental fecal
 transplants from nestmates or kept deprived of their native microbiota
 inoculum. We assessed functional measures of induced immunity and assessed
 the costs of non-pathogenic immune activation for survival. In support of
 our hypothesis, we find that microbiota supplementation strengthened
 functional antibacterial immunity. Moreover, although we observed a cost
 of immune activation for survival, the cost was much greater for bees
 deprived of their native gut microbiota compared to those supplemented.
 Thus, we provide evidence that in addition to other roles, the microbiota
 mitigates costs of immune deployment. This demonstrates a key role for
 host-associated microbiota in the realization of induced immune defense,
 and contributes more broadly to our understanding of microbiota-immune
 interactions in the context of ecological immunology.
description: # Data from: Host-associated beneficial gut microbiota boosts induced
 immunity and limits immune deployment costs in bumblebees Dataset DOI:
 [10.5061/dryad.ncjsxkt8v](https://doi.org/10.5061/dryad.ncjsxkt8v) ##
 Description of the data and file structure To assess the effects of the
 native microbiota on functional immunity and the cost of immune deployment
 for bumblebee survival, otherwise microbiota-free workers were
 supplemented or left naturally deprived of their native microbiota
 immediately following adult eclosion. At a fixed later time point,
 allowing for microbial colonization of supplemented bees, individuals were
 injected with a heat-killed bacteria cocktail to stimulate an immune
 response. Immune-challenged individuals from the two microbiota treatments
 (i.e., supplemented versus deprived) had their hemolymph extracted two
 days post challenge for functional immune assays. In a separate experiment
 assessing the cost of immune activation, an uninjected naïve group was
 included for each microbiota treatment and the four reciprocal treatment
 combinations were tracked daily for survival. ### Files and variables ####
 **File: Immune_activation_Shosanya.csv** **Description:** Data for immune
 activation and effects on AMP expression across two tissues. 
 **Variables** * Sample: individual ID's  * Hym_EF: normalized
 expression of Hymenoptaecin to elongation factor housekeeping gene (EF 1
 Alpha) * Def_EF: normalized expression of Defensin to elongation factor
 housekeeping gene (EF 1 Alpha) * Tissue: source tissue from which RNA was
 extracted (i.e., abdomen or gut) * Treat: treatment delivered to
 individuals (i.e., naive or immune challenged) **File:
 Microbiota_immunity_FINAL03262025.csv** **Description:** Data for the main
 overall experiments. **Variables** * colony: source colony of bumblebees *
 ID: individual ID's * microbiota: microbiota deprived (i.e., 0) or
 microbiota supplemented (i.e., 1) * treatment: designated response for
 bees allocated to track survival or immune responses * Universal_adj: qPCR
 values of 16S rRNA. NA's (Not Applicable) indicate if sample was not
 included in qPCR run (i.e., samples in the survival treatment), or if qPCR
 runs were inconclusive/samples were contaminated. * Snod_adj: qPCR values
 of Snodgrassella. NA's (Not Applicable) indicate if sample was not
 included in qPCR run (i.e., samples in the survival treatment), or if qPCR
 runs were inconclusive/samples were contaminated. * Snod_LoD:
 Snodgrassella limit of detection where qPCR values &lt;1000 = 0, and qPCR
 values &gt;1000 = 1. NA's (Not Applicable) indicate if sample was not
 included in qPCR run (i.e., samples in the survival treatment), or if qPCR
 runs were inconclusive/samples were contaminated. * emergence: date
 individual emerged from pupal clump * challenge: immune challenged (i.e.,
 1) or left naive (i.e., 0) * challenge_date: date of immune challenge *
 date_dead: date of death * survival_since_challenge: days surviving since
 immune challenge. NA's (Not Applicable) indicate if the sample died
 before receiving the challenge (i.e., across all treatment groups), or if
 the sample died prior to hemolymph collection (i.e., within immune
 treatment group, before the 2 days post-challenge collection). *
 dead_prior: if individual died prior to immune challenge (i.e., 1), or not
 (i.e., 0), * dead: dead individuals * size_mm: size based on length of
 radial cell in forewing. NA's (Not Applicable) indicate a wing was
 damaged and unable to be measured.  * ZIA_length_A: length in mm for zone
 of inhibition for replicate A. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * ZIA_width_A: width in mm for zone of
 inhibition for replicate A. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * ZIA_diam_A: diameter in mm for zone
 of inhibition for replicate A. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * ZIA_length_B: length in mm for zone
 of inhibition for replicate B. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * ZIA_width_B: width in mm for zone of
 inhibition for replicate B. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * ZIA_diam_B: diameter in mm for zone
 of inhibition for replicate B. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * tetra_A: zone of inhibition
 diameters converted to tetracycline units (ug/mL) for antibacterial
 activity for replicate A * Zone: if a zone was visible (i.e., 1) or not
 (i.e., 0). NA's (Not Applicable) indicate no hemolymph was extracted
 intentionally (i.e., samples dedicated to survival), or due to
 contamination. * tetra_B: zone of inhibition diameters converted to
 tetracycline units (ug/mL) for antibacterial activity for replicate
 B. NA's (Not Applicable) indicate no hemolymph was extracted
 intentionally (i.e., samples dedicated to survival), or due to
 contamination. * tetra_avg: average tetracycline units. NA's (Not
 Applicable) indicate no hemolymph was extracted intentionally (i.e.,
 samples dedicated to survival), or due to contamination. * PO_abs_1:
 phenoloxidase absorbance for replicate 1. NA's (Not Applicable)
 indicate no hemolymph was extracted intentionally (i.e., samples dedicated
 to survival), or due to contamination. * PO_abs_2: phenoloxidase
 absorbance for replicate 2. NA's (Not Applicable) indicate no
 hemolymph was extracted intentionally (i.e., samples dedicated to
 survival), or due to contamination. * PO_abs_avg: average phenoloxidase
 absorbance. NA's (Not Applicable) indicate no hemolymph was extracted
 intentionally (i.e., samples dedicated to survival), or due to
 contamination. * PO_abs_avg_adj: phenoloxidase adjusted values where
 negatives were treated as zeroes, but all else remained the
 same. NA's (Not Applicable) indicate no hemolymph was extracted
 intentionally (i.e., samples dedicated to survival), or due to
 contamination. * notes: notes needed for any sample #### File:
 Immunity_Study_comparison.csv **Description:** Supplementary data to
 compare our immune effects with previously published work. ##### Variables
 * Study: Last name of First author from which data were collected. * Inj:
 injection with ES (*Escherichia* *coli* and *Staphyloccocus
 epidermidis* cocktail) or A (*Arthrobacter globiformis)* * Time: hours
 post injection when response was measured * Colony: source colony of
 bumblebees * Tetra_ug_ml: tetracycline units #### File:
 Survival_Study_comparison.csv **Description:** Supplementary data to
 compare our survival response with previously published work. #####
 Variables * Study: Last name of First author from which data were
 collected. * Colony: source colony of bumblebees * Survival_days: days
 surviving since challenge * Death: death as yes/no (i.e., 1/0). #### File:
 Microbiota_immunity__study_comparison06212025.R **Description:** R script
 for comparing our research to previously published work. #### File:
 Immune_act_Shosanya_03262025.R **Description:** R script for immune
 activation of AMP genes. #### File: Microbiota_immunity_02172025_(4).R
 **Description:** R script for the overall experiment. ## Code/software All
 workflow and packages are described within the respective R scripts. ##
 Access information Data was derived from the following sources: * For
 comparing our immunity and survival responses to other published work,
 data were pulled from Tobin et al. 2024 (Journal of Animal Ecology)
 and Czerwinski and Sadd 2017 (Journal of Experimental Zoology).