Data and code from: Environment and pollen diversity differentially affect the gut microbiomes of introduced honeybees and bumblebees
Data files
Jun 15, 2026 version files 157.54 KB
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Apis-gut-ASV.csv
21.43 KB
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Apis-merged-file_LME.csv
13.28 KB
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Apis-pollen-ASV.csv
11.10 KB
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Bombus-gut-ASV.csv
37.38 KB
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Bombus-merged-file_LME.csv
12.42 KB
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Bombus-pollen-ASV.csv
27.17 KB
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LME-chao1.R
13.01 KB
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LME-shannon.R
13.44 KB
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README.md
8.33 KB
Abstract
Invasive species may exhibit shifts in their gut microbiome in response to novel environments and diet, but this may differ across host species and their time since colonisation. We investigate if site environmental variables and foraged pollen resources differentially shape the gut microbiomes of two bee species with contrasting introduction histories: The European honeybee, Apis mellifera (introduced 1831), and the recently invasive bumblebee, Bombus terrestris (invaded 1992). Using landscape-scale metabarcoding across the island state of Tasmania in Australia, we characterised gut bacteria (16S rRNA) and corbicular pollen diversity (ITS2) for each species. Gut bacterial composition was significantly associated with mean annual temperature for A. mellifera and with mean annual precipitation and percentage of pasture for B. terrestris. In B. terrestris, the core and facultative gut microbial diversity and richness showed associations with precipitation, foraged pollen diversity, wind velocity, and temperature. Foraged pollen diversity of native plants more strongly predicted the facultative gut microbiome across species. Overall, the gut microbiome of B. terrestris shows a stronger response to abiotic and biotic predictors compared to A. mellifera. Our findings advance understanding of how environmental and dietary factors shape pollinator gut microbiomes at landscape scales, with implications for pollinator health and survival.
Dataset DOI: 10.5061/dryad.ngf1vhj6r
Description of the data and file structure
Female workers A. mellifera and B. terrestris were collected during peak summer activity (24 January –1 February 2023) from 14 sites across Tasmania.
Environmental data for the 14 sites were obtained as described in Kardum Hjort et al. (2023; 2024; Table 1). Mean annual temperature, precipitation, and average summer wind velocity were sourced from WorldClim v2.1 (Fick & Hijmans, 2017), and pasture percentage from the Dynamic Land Cover Dataset v2.1 within a 1 km radius of each site (Lymburner et al., 2015).
Gut microbiome 16S data
DNA was extracted using a modified DNeasy Blood & Tissue protocol (Qiagen) and quantified with a Qubit dsDNA High-Sensitivity kit (Text S1). The V4 region of the 16S rRNA gene was amplified and sequenced (2×250 bp paired-end) on an Illumina MiSeq at the Ramaciotti Centre, UNSW, Sydney, Australia (Text S2). Reads were processed in QIIME2 v2024.10 (Bolyen et al., 2019), denoised with Deblur (Amir et al., 2017), and classified using a Naïve Bayes classifier against Silva-138, with genus-level validation via blastn (e-value ≤ 1×10⁻³⁰; identity ≥ 95%; Text S3).
ITS2 Corbicular Pollen data
Corbicular pollen was removed from each bee (Text S4), pooled by site, and weighed, with 10–50 mg pollen per site used for DNA extraction following a modified NucleoSpin Food Kit protocol (Macherey Nagel; Text S4). DNA was quantified with a Qubit dsDNA High-Sensitivity kit and standardised to 10 ng/µl. PCR amplification of the ITS2 region was performed using S2F/S3R primers (as in Chen et al., 2010; Text S4). Amplicons were purified and sequenced (2×250 bp, Illumina MiSeq) at the Ramaciotti Centre, UNSW, Sydney.
Files and variables
File: LME-chao1.R
Description: R code for running the linear mixed effects models on A. mellifera and B. terrestris on the Chao1 taxonomic richness of 16S data.
LME-shannon.R
Description: R code for running the linear mixed effects models on A. mellifera and B. terrestris on Shannon's taxonomic diversity of 16S data.
File: Apis-gut-ASV.csv
Description: Amplicon Sequence Variant files for the 16S gut microbiome data from Apis mellifera (from Tasmania - sampled in 2023 from across Tasmania - female worker bees.
Variables
- SampleID: Sample name
- ASV1 - ASV84 - Amplicon Sequence Variant from ASV1-84
File: Apis-pollen-ASV.csv
Description: Amplicon Sequence Variant files for the ITS2 barcoding data from corbicular pollen collected from Apis mellifera (from Tasmania - sampled in 2023 from across Tasmania - female worker bees.
Variables
- SampleID: Sample name
- ASV1-ASV307: Amplicon Sequence Variant from ASV1-307
File: Bombus-gut-ASV.csv
Description: Amplicon Sequence Variant files for the 16S rRNA barcoding data from dissected guts collected from Bombus terrestris (from Tasmania - sampled in 2023 from across Tasmania - female worker bees.
Variables
- SampleID: Sample name
- Site: The name of the site collected from (as described in the paper)
- ASV1- ASV189: Amplicon Sequence Variant from ASV1-189
File: Bombus-pollen-ASV.csv
Description: Amplicon Sequence Variant files for the ITS2 barcoding data from corbicular pollen collected from Bombus terrestris (from Tasmania - sampled in 2023 from across Tasmania - female worker bees.
Variables
- Site: Sample name
- ASV1-ASV308: Amplicon Sequence Variant from ASV1-308
Apis-merged-file_LME.csv -
Description: Includes all data used in Linear Mixed Effects models for both gut microbial and pollen diversity for Apis mellifera. Includes Shannon's diversity, Chao1 Richness, and divisions of core and facultative microbiomes, and divisions of native, introduced, and 'both' pollen categories for Shannon's and Chao1 Richness.
Variables
Column headings are as follows:
- Sample ID (Site and sample number)
- Site (Site ID)
- all.gut_Chao1- total taxonomic (Chao 1) richness of gut bacteria
- all.gut_Shannon- Total diversity (Shannon's Index) of gut bacteria
- core.gut_Chao1- taxonomic richness (Chao1) of the core components of the gut microbiome (defined in paper)
- core.gut_Shannon- taxonomic diversity (Shannon's Index) of the core component of the gut microbiome (defined in paper)
- fac.gut_Chao1 - taxonomic richness (Chao1) of the facultative component of the gut microbiome (defined in paper)
- fac.gut_Shannon- taxonomic diversity (Shannon's) of the facultative component of the gut microbiome (defined in paper)
- Temp - Mean annual temperature of the site (BIO1)
- Rain - Mean annual precipitation of the site ( BIO12)
- Wind - Mean summer wind speed (WorldClim- methods in paper)
- Pasture - Percentage of pasture surrounding site (methods in paper)
- all.pollen_Shannon - total pollen taxonomic diversity (Shannon's Index)
- all.pollen_Chao1- total pollen taxonomic richness (Chao1)
- native.pollen_Shannon - pollen taxonomic diversity (Shannon's Index) of genera that are native to Tasmania or Australia
- native.pollen_Chao1- pollen taxonomic richness (Chao1) of genera that are native to Tasmania or Australia
- intro.pollen_Shannon- pollen taxonomic diversity (Shannon's Index) of genera that are introduced to Tasmania or Australia
- intro.pollen_Chao1-pollen taxonomic richness (Chao1) of genera that are introduced to Tasmania or Australia
- both.pollen_Shannon - pollen taxonomic diversity (Shannon's Index) of genera that contain species that are both introduced and invasive to Tasmania or Australia
- both.pollen_Chao1-pollen taxonomic richness (Chao1) of genera that contain species that are both introduced and invasive to Tasmania or Australia
Bombus-merged-file_LME.csv
Description: Includes all data used in Linear Mixed Effects models for both gut microbial and pollen diversity for Bombus terrestris. Includes Shannon's diversity, Chao1 Richness, and divisions of core and facultative microbiomes, and divisions of native, introduced, and 'both' pollencategories for Shannon's and Chao1 Richness.
Column headings are as follows:
- Sample ID (Site and sample number)
- Site (Site ID)
- all.gut_Chao1- total taxonomic (Chao 1) richness of gut bacteria
- all.gut_Shannon- Total diversity (Shannon's Index) of gut bacteria
- core.gut_Chao1- taxonomic richness (Chao1) of the core components of the gut microbiome (defined in paper)
- core.gut_Shannon- taxonomic diversity (Shannon's Index) of the core component of the gut microbiome (defined in paper)
- fac.gut_Chao1 - taxonomic richness (Chao1) of the facultative component of the gut microbiome (defined in paper)
- fac.gut_Shannon- taxonomic diversity (Shannon's) of the facultative component of the gut microbiome (defined in paper)
- Temp - Mean annual temperature of the site (degrees Celsius) (BIO1)
- Rain - Mean annual precipitation (mm) of the site ( BIO12)
- Wind - Mean summer wind speed (m/s) (WorldClim- methods in paper)
- Pasture - Percentage of pasture surrounding site (methods in paper)
- all.pollen_Shannon - total pollen taxonomic diversity (Shannon's Index)
- all.pollen_Chao1- total pollen taxonomic richness (Chao1)
- native.pollen_Shannon - pollen taxonomic diversity (Shannon's Index) of genera that are native to Tasmania or Australia
- native.pollen_Chao1- pollen taxonomic richness (Chao1) of genera that are native to Tasmania or Australia
- intro.pollen_Shannon- pollen taxonomic diversity (Shannon's Index) of genera that are introduced to Tasmania or Australia
- intro.pollen_Chao1-pollen taxonomic richness (Chao1) of genera that are introduced to Tasmania or Australia
- both.pollen_Shannon - pollen taxonomic diversity (Shannon's Index) of genera that contain species that are both introduced and invasive to Tasmania or Australia
- both.pollen_Chao1-pollen taxonomic richness (Chao1) of genera that contain species that are both introduced and invasive to Tasmania or Australia
Code/software
Best viewed in R Studio.
Access information
Other publicly accessible locations of the data:
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Data was derived from the following sources:
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