Data from: Host-associated beneficial gut microbiota boosts induced immunity and limits immune deployment costs in bumblebees
Data files
Oct 30, 2025 version files 132.67 KB
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Immune_act_Shosanya_03262025.R
5.92 KB
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Immune_activation_Shosanya.csv
1.72 KB
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Immunity_Study_comparison.csv
1.53 KB
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Microbiota_immunity__study_comparison06212025.R
41.27 KB
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Microbiota_immunity_02172025_(4).R
40.19 KB
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Microbiota_immunity_FINAL03262025.csv
33.06 KB
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README.md
7.92 KB
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Survival_Study_comparison.csv
1.06 KB
Abstract
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.
Dataset DOI: 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 <1000 = 0, and qPCR values >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).
