Data from: Sparse gut microbiomes in solitary bees and wasps
Data files
Jul 20, 2026 version files 25.92 MB
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Ch2metadataJNS_16Aug2025_mctoolsr_qPCR.txt
162.69 KB
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README.md
10.99 KB
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repset.fasta
5.96 MB
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seqtab_wTax_mctoolsr.txt
19.71 MB
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SparseMicrobiomesJNS_11June2026_R_Code.Rmd
76.30 KB
Abstract
Bees and wasps are ecologically vital, but many species are declining due to anthropogenic stressors. Social bees harbour host-specific and dense gut microbiomes that affect their resilience to stress. However, there are tens of thousands of other bee and wasp species that vary in sociality and diet (including pollen-feeding and predatory guilds), traits known to influence host-microbe symbioses. The role of gut microbes in the biology of these species is largely unknown. Here, we measured the composition and absolute abundance of bacterial communities in adult abdomens across 61 genera and 14 families of field-collected bees, predatory wasps, and pollen wasps. We found that solitary bees and both wasp guilds harbor distinct bacterial taxa and lower bacterial abundances as compared with social bees. Bacterial abundances also varied extensively among and within genera of solitary bees, with little variation explained by body size, diet breadth, or nesting ecology. Further, microbiome composition was only weakly differentiated among solitary bees and the two wasp groups, even comparing herbivorous (pollen-feeding) and carnivorous taxa. We suggest that the sparse and somewhat stochastic microbiomes of solitary bees and wasps reflect weak host dependence on microbially mediated functions, a trait that may influence their resilience to environmental change.
Dataset DOI: 10.5061/dryad.4qrfj6qt2
Description of the data and file structure
A total of 443 wild adult bee and wasp specimens were sampled for this study. Data for the collection of these specimens, as well as the qPCR concentration, is in the metadata file. The bacterial taxonomic information is in the seqtab file.
Of these, 310 specimens were collected in California and Arizona from April to August of 2023 and stored in 95% ethanol. An additional 100 samples from South Africa, the Canary Islands, California, and the southwestern United States were included; these were collected via hand net between January 2022 and March 2025 and stored in 95% ethanol. Thirty of the South African specimens were euthanized via a cyanide killing jar, stored at -20 ℃ briefly, then transferred to 95% ethanol. One pollen wasp from Arizona was stored at -20 ℃ for a few days, then transferred to 95% ethanol. Thirty-three Meliponini samples, stored in 95% ethanol, were included in the dataset; these samples are described in Rasmussen & Cameron 2010 and were previously sequenced (Villabona et al. 2026). All specimens besides the Meliponini were identified at least to genus by J. Schlauch, using Danforth et al. 2023 and Gess & Gess 2010, with help from Jaime Palewek.
Files and variables
File: SparseMicrobiomesJNS_11June2026_R_Code.Rmd
Description: the R code for the publication.
File: Ch2metadataJNS_16Aug2025_mctoolsr_qPCR.txt
Description: the metadata for the host specimens used in this project. None of these host species have a conservation status that is endangered or threatened.
Variables
- SampleID_dup: the accession number of the host specimen, duplicated to preserve any changes made in the code
- SampleID: the accession number of the host specimen
- full_num_order: this allows for re-ordering after any data shuffling / sorting
- project: This is the name of the project for which the host specimen was collected. Includes JNS_CAWBM (This is the author's "CAlifornia Wetland Bee Microbiome" project, the primary collection reason, and thus why most of the data is populated for this project specifically), BURPP & SeqRun2 (extra specimens included from the lab's Bombus and other bee projects), MJL_MiscHym & Unk[own] (Additional Hymenoptera specimens gathered by various collectors, and NV_Meliponini (Nickole Villabona's processed stingless bee specimens from Villabona et al. 2026).
- accession_alphabet: this changed the "-1" numerical hyphen of specimens to "A, B, C..." for some processing
- accession_period: this changed the "-1" numerical hyphen of specimens to a period for some processing
- concentration_ngPERul: the DNA concentration of the specimen at the end of the extraction. Same for all samples or not relevant.
- volume_ul: the DNA volume of the specimen at the end of the extraction. Same for all samples or not relevant.
- library_size_bp: 400 or NA for all specimens. Sequencing information.
- NumOfReads_M: 0.0764 or NA for all specimens. Sequencing information.
- index_name_i7: Specific information for sequencing, not used for the rest of the R analysis
- i7_BarcodeSequence: Specific information for sequencing, not used for the rest of the R analysis
- i7_ReverseComplement: Specific information for sequencing, not used for the rest of the R analysis
- library_type: amplicon or NA for all.
- date_coll: calendar date of specimen collection
- site: location name of specimen collection. D_DSC (Desert Studies Center, ZZyzx); D_MDL (Mojave Desert Land Trust Nancy Karl Trail); W_TSN (Tijuana Slough NWR, San Diego); W_KFM (Kendall Frost Marsh Reserve, San Diego); W_SJM (UCI San Joaquin Marsh); W_IRW (IRWD San Joaquin Marsh); W_CSM (Carpinteria Salt Marsh); W_COP (Coal Oil Point Reserve); W_YLR (Younger Lagoon Reserve); W_BMR (Bodega Marine Reserve)
- lat: latitude of collection
- long: longitude of collection
- site_survey: for the CAWBM project, the survey number that this was for the site for the year
- site_type: desert or wetland, CAWBM project only
- site_size: in km2, for the CAWBM project wetland sites only
- transect_point: CAWBM project only. Collections were done along a 1-km transect labelled T1 - T11. Mostly irrelevant for coding, use lat long
- specimen_descriptor: placeholder for specimen ID while processing. Use genus_species column for analysis
- sex: male or female, when identifiable
- host_category: same as host guild in paper. Eusocial bee, solitary bee, omnivorous wasp (changed to predatory wasp), and pollen wasp
- family: taxonomic family
- subfamily: taxonomic subfamily
- tribe: taxonomic tribe
- genus: taxonomic genus
- species: taxonomic species
- genus_species: taxonomic full scientific name of specimen
- ITD: Intertegular distance, measured in millimeters by Mandy Huang. A proxy for body size for bees
- diet: categorized using Danforth et al. 2019 for bees only. Generalists feed on multiple flower families. Specialists feed on approximately 1 flower family. "Clepto" is for kleptoparasites, as they do not provision their own nests
- sociality: life strategy for bees only. Eusocial (Apis, Bombus, Meliponini) and solitary
- nest_guild: Using Danforth et al. 2019. Nest type for the bee genus. Hive (all eusocial are here); stem (pithy stems or reeds); ground (digs or uses a hole in the ground); leaf_cutter (all leafcutters are here); clepto (kleptoparasitic species)
- floral_assoc_notes: field description of the flower from which the bee was collected. "Net collection" from JNS_CAWBM project only.
- flower_genus: genus of flower from which the host was collected
- flower_sp: species of flower from which the host was collected
- flower_genussp: full scientific name of flower from which the host was collected
- plant_code: 6 letter plant code for quick field notetaking
- flower_fam: family of flower from which the host was collected
- sample_type: all adult insect for specimens, distinguishes "blank" and "mock" samples from the extraction process
- collector: first initial and last name of the human collector of the specimens
- notes: details about the specimen or collection
- Mean_Conc: mean concentration value from the qPCR of the specimen
File: seqtab_wTax_mctoolsr.txt
Description: the ASV taxa table compiled by TJH, a matrix with the host specimen accession numbers and the relative abundances of the bacterial taxa present in each sample.
Variables
- matrix of host specimen accession numbers and bacterial taxa data
File: repset.fasta
Description: the representative sequences file
Variables
- 16S rRNA bacterial sequences
Code/software
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] emmeans_1.11.1 pairwiseAdonis_0.4.1 cluster_2.1.8.1 devtools_2.4.5 usethis_3.1.0
[6] forcats_1.0.0 calecopal_0.1.0 ggplot2_3.5.2 vroom_1.6.5 decontam_1.22.0
[11] RColorBrewer_1.1-3 magrittr_2.0.3 broom_1.0.8 lubridate_1.9.4 patchwork_1.3.1
[16] nlme_3.1-168 dplyr_1.1.4 tibble_3.3.0 tidyr_1.3.1 vegan_2.7-1
[21] permute_0.9-8 mctoolsr_0.1.1.9 lmerTest_3.1-3 lme4_1.1-37 Matrix_1.6-5
loaded via a namespace (and not attached):
[1] rstudioapi_0.17.1 TH.data_1.1-3 estimability_1.5.1 rmarkdown_2.29 farver_2.1.2
[6] nloptr_2.2.1 fs_1.6.6 fields_16.3.1 zlibbioc_1.48.2 vctrs_0.6.5
[11] memoise_2.0.1 minqa_1.2.8 RCurl_1.98-1.17 terra_1.8-54 htmltools_0.5.8.1
[16] polynom_1.4-1 raster_3.6-32 Formula_1.2-5 htmlwidgets_1.6.4 pbkrtest_0.5.4
[21] sandwich_3.1-1 plyr_1.8.9 zoo_1.8-14 cachem_1.1.0 mime_0.13
[26] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3 R6_2.6.1 fastmap_1.2.0
[31] GenomeInfoDbData_1.2.11 rbibutils_2.3 shiny_1.11.1 digest_0.6.37 numDeriv_2016.8-1.1
[36] S4Vectors_0.40.2 pkgload_1.4.0 labeling_0.4.3 randomForest_4.7-1.2 gbm_2.2.2
[41] timechange_0.3.0 abind_1.4-8 mgcv_1.9-1 compiler_4.3.2 remotes_2.5.0
[46] bit64_4.6.0-1 withr_3.0.2 doParallel_1.0.17 backports_1.5.0 carData_3.0-5
[51] viridis_0.6.5 spThin_0.2.0 pkgbuild_1.4.8 maps_3.4.3 MASS_7.3-60.0.1
[56] quantreg_6.1 sessioninfo_1.2.3 ggpp_0.5.9 tools_4.3.2 httpuv_1.6.16
[61] nnet_7.3-20 glue_1.8.0 promises_1.3.3 grid_4.3.2 reshape2_1.4.4
[66] generics_0.1.4 maxnet_0.1.4 gtable_0.3.6 tzdb_0.5.0 sp_2.2-0
[71] car_3.1-3 XVector_0.42.0 BiocGenerics_0.48.1 ggrepel_0.9.6 foreach_1.5.2
[76] pillar_1.11.0 stringr_1.5.1 spam_2.11-1 later_1.4.2 splines_4.3.2
[81] lattice_0.22-7 survival_3.8-3 bit_4.6.0 SparseM_1.84-2 tidyselect_1.2.1
[86] Biostrings_2.70.3 miniUI_0.1.2 knitr_1.50 ggpmisc_0.6.2 reformulas_0.4.1
[91] gridExtra_2.3 IRanges_2.36.0 stats4_4.3.2 xfun_0.52 Biobase_2.62.0
[96] stringi_1.8.7 yaml_2.3.10 boot_1.3-31 evaluate_1.0.4 codetools_0.2-20
[101] kernlab_0.9-33 cli_3.6.5 xtable_1.8-4 Rdpack_2.6.4 Rcpp_1.1.0
[106] GenomeInfoDb_1.38.8 coda_0.19-4.1 flexsdm_1.3.6 parallel_4.3.2 MatrixModels_0.5-4
[111] ellipsis_0.3.2 ggh4x_0.3.1 dotCall64_1.2 profvis_0.4.0 urlchecker_1.0.1
[116] bitops_1.0-9 mvtnorm_1.3-3 viridisLite_0.4.2 scales_1.4.0 purrr_1.0.4
[121] crayon_1.5.3 rlang_1.1.6 multcomp_1.4-28
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
