Data from: Life history stage-dependent effects of food supplementation on gut microbiome diversity in Sialia sialis (Eastern Bluebird)
Data files
Apr 09, 2026 version files 1.22 MB
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2021_decontam.R
4.50 KB
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2021_pbs_qiime_workflow1.pbs
1.46 KB
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2021_pbs_qiime_workflow2_assignTaxSilva.pbs
2.50 KB
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2021_pbs_qiime_workflow3_postDecontam.pbs
2.65 KB
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2022_decontam.R
4.75 KB
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2022_pbs_qiime_workflow1.pbs
1.49 KB
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2022_pbs_qiime_workflow2_assignTaxSilva.pbs
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2022_pbs_qiime_workflow3_postDecontam.pbs
2.62 KB
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adult_microbiome_2021_metadata.xlsx
9.49 KB
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adult_microbiome_2021.csv
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adult2022_carryover_metadata.xlsx
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adult2022_carryover.csv
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arbeaNestID1_metadata.xlsx
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arbeaNestID1.csv
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chickmaturity1_metadata.xlsx
10 KB
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chickmaturity1.csv
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consensus_sex.csv
41.74 KB
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dryadBaizCornell.R
5.52 KB
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Fecal_inventory_2022_EABL_ALLISON.csv
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figure2data_metadata.xlsx
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figure2data.csv
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metadata_16s_vermivora2.tsv
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metadata_nestboxes2.csv
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nestlings_model_input_medatadata.xlsx
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nestlings_model_input.csv
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phyloseq_eabl2022.R
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phyloseq_supp_feed2.R
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ps_eabl2022.rds
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README.md
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Abstract
Diet can be an important health factor that links fitness to an individual’s ecology. The gut microbiome responds to diet changes and plays an important role in host physiology. Dietary interventions are known to impact gut microbiome composition, but long-term effects and to what extent these impacts vary among individuals at different life history stages is unclear. To address this question, we performed a supplemental feeding experiment by providing live mealworms (Tenebrio molitor) to Sialia sialis (Eastern Bluebirds) during the chick-rearing period. We produced 16S metabarcoding data to quantify gut microbiome diversity from fecal samples of adults and nestlings collected during our experimental period, and again one year later when individuals returned to breed at the study site. Food supplementation was associated with shifts in gut microbiome composition for adults, but not early (8-day-old) or late stage (15-day-old) nestlings. In particular, one bacterium in the genus Staphylococcus was more abundant in food-supplemented adults. Nestling gut microbiomes were similar among nest-mates, and differed between the sexes during early development, but sex-differences disappeared before fledging (nest departure). Microbiome richness was higher in female nestlings, but not related to chick maturity. We did not observe any effects of the previous year’s diet treatment among returning breeders. Humans commonly provide mealworms for S. sialis in order to attract them to their property and to help them achieve nutritional requirements. Our results suggest this practice has limited, short-term effects on gut microbiome diversity that differ among individuals of different life history stages.
Dataset DOI: 10.5061/dryad.sqv9s4ngv
Description of the data and file structure
Supplemental feeding experiment on gut microbiome variation in Eastern Bluebirds. Files with the extension .pbs are shell scripts containing directives for a Portable Batch System (PBS) job scheduler. These analyses were run on a High-Performance Computing (HPC) environment. Files with the extension .rds are objects that can be imported to a working environment within R. These files are associated with R scripts (file extension .R). Files with .csv extension are comma-separated values and .xlsx are excel files. Empty cells and "NA" values in spreadsheets represent missing data or "not applicable" to be read as "NA".
Files and variables
File: 2021_pbs_qiime_workflow1.pbs
Description: Sequence data processing script, step 1 (2021 sequencing data)
File: 2021_pbs_qiime_workflow2_assignTaxSilva.pbs
Description: Sequence data processing script, step 2 (2021 sequencing data)
File: 2021_pbs_qiime_workflow3_postDecontam.pbs
Description: Sequence data processing script, step 3 (2021 sequencing data)
File: 2022_pbs_qiime_workflow1.pbs
Description: Sequence data processing script, step 1 (2022 sequencing data)
File: 2022_pbs_qiime_workflow2_assignTaxSilva.pbs
Description: Sequence data processing script, step 2 (2022 sequencing data)
File: 2022_pbs_qiime_workflow3_postDecontam.pbs
Description: Sequence data processing script, step 3 (2022 sequencing data)
File: 2021_decontam.R
Description: Identify contaminant ASVs (2021 dataset)
File: 2022_decontam.R
Description: Identify contaminant ASVs (2022 dataset)
File: phyloseq_supp_feed2.R
Description: Statistical analysis of ASVs, beta diversity, figure creation (2021 dataset)
File: phyloseq_eabl2022.R
Description: Statistical analysis of ASVs, beta diversity, figure creation (2022 dataset)
File: Fecal_inventory_2022_EABL_ALLISON.csv
Description: Input for phyloseq_eabl2022.R - variables are defined in accompanying consensus_sex.csv
File: consensus_sex.csv
Description: Object input for phyloseq_supp_feed2.R
Variables
- Site: Sampling site
- Date: Samling date
- Time: Sampling time (hr:min)
- Box: Nest box ID
- Treatment: Treatment group (control or food)
- Species: Species code (EABL=Eastern bluebird)
- Age: Bird age (AHY=after hatch year)
- Sex: Bird sex (M=male, F=female)
- ID.Band.no.: Bird USGS band number
- Type: Sample type
- Color.right: Color band (right) (R=red , B=blue , O=orange , X=aluminium , W=white , G=green , Y=yellow , K=black)
- Color.left: Color band (left) (R=red , B=blue , O=orange , X=aluminium , W=white , G=green , Y=yellow , K=black)
- Colors: Color band code (R=red , B=blue , O=orange , X=aluminium , W=white , G=green , Y=yellow , K=black)
- Bird.weight..in.bag.: Weight of bird in bag (g)
- Bird.weight.in.bag.: Bird weighed in bag (Y=yes/N=no)
- True.weight..subtract.bag.: Bird weight - bag weight (g)
- Tarsus..left.: Tarsus length (mm)
- Wing..right.: Wing length (mm)
- Fecal: Fecal sample collected (Y=yes/N=no)
- Blood.glucose: Blood glucose measurement (mg/dl)
- Hct: Hematocrit measurement (%)
- Stage: Bird stage at sampling
- Clutch: Clutch number
- Clutch.mortality.: Clutch mortality (Y/N)
- Camera: Photograph location (device)
- Notes: Notes about sampling
- stage2: Bird stage at sampling for analysis
- age2: Bird age at sampling for analysis
- Observed: Richness
- Shannon: Shannon index
- pd: Phylogenetic diversity
- clutch.size: Clutch size
- brood.size.at.hatching: Brood size at hatching
- brood.size.day.8: Brood size at day 8
- brood.size.day.15: Brood size at day 15
- record: Sample ID
- label: Sample ID 2
- pcr_sex: Result of CHD genotyping (F=female, M=male)
- cons_sex: Sex (consensus between CHD genotyping and phenotypic sexing) (F=female, M=male)
File: ps_eabl2022.rds
Description: Phyloseq object input for phyloseq_eabl2022.R script. Requires the phyloseq R package. See the phyloseq_eabl2022.R for relevant details.
File: metadata_16s_vermivora2.tsv
Description: Metadata associated with ps_eabl2022.rds
Variables
- id: Sample ID
- Species: Species ID (GWWA=golden-winged warbler, BWWA=blue-winged warbler, BRWA=brewster's warbler, PRWA=prairie warbler, EABL=eastern bluebird, INTR=intrograde Vermivora warbler)
- Year: Sampling year
- Type: Sample type
- State: Sampling site (state) (PA=Pennsylvania, MI=Michigan)
- Date: Sampling date
- Location: Sampling locality
- Latitude: Latitude coordinates
- Longitude: Longitude coordinates
- Range: Species range
- Region: Sampling region
- Elevation: Elevation (m)
- Time: Sample collection time
- Band.: USGS band number
- Sex: Individuals sex (F=female, M=male)
- Age: Individual age (AHY=after hatch year, ASY=after second year, SY=second year, HY=hatch year)
- Blood: Blood sample collected (Y=yes/N=no)
- Fecal: Fecal sample collected (Y=yes/N=no)
- CP: Cloacal protuberance
- Photo: Photo taken (device)
- Measurer: Initials of measurer
- Wing: Wing chord length (mm)
- Tail: Tail length (mm)
- Tarsus: Tarsus length (mm)
- Notes: Notes about sample collection
- Bill_Culmen: Culmen length (mm)
- Bill_Exposed: Exposed culmen length (mm)
- Bill_Depth: Bill depth (mm)
- Bill_Width: Bill width (mm)
- W_bar: Wing bar plumage score
- W_bar_width: Wing bar plumage score
- Chin_throat: Chin/throat plumage score
- Chin: Chin plumage score
- Throat: Throat plumage score
- Nape: Nape plumage score
- Back: Back plumage score
- Rump: Rump plumage score
- Breast: Breast plumage score
- Belly: Belly plumage score
- Sum: Sum plumage scores
- Complete_plumage: Complete scores collected (Y/N)
- Plumage_score: Plumage score
- Treatment.2021: Supplemental feeding treatment (control/food)
- Age.2021: Age in 2021
- Mass: Mass (g)
- Box: Nest box ID
- Nest: Nest ID
- sum2: Sum2 plumage score
- Plumage_score2: Plumage score 2
- Tot_for_plu_sc: Total for plumage score
File: metadata_nestboxes2.csv
Description: Metadata for phyloseq_suppfeed2.R - variables are defined in consensus_sex.csv
File: adult_microbiome_2021.csv
Description: Input file for dryadBaizCornell.R - variables are defined in adult_microbiome_2021_metadata.xlsx
File: adult_microbiome_2021_metadata.xlsx
Description: Column headers and their description in adult_microbiome_2021.csv
File: adult2022_carryover.csv
Description: Input file for dryadBaizCornell.R - variables are defined in adult2022_carryover_metadata.xlsx
File: adult2022_carryover_metadata.xlsx
Description: Column headers and their description in adult2022_carryover.csv
File: arbeaNestID1.csv
Description: Input file for dryadBaizCornell.R - variables are defined in arbeaNestID1_metadata.xlsx
File: arbeaNestID1_metadata.xlsx
Description: Column headers and their description in arbeaNestID1.csv
File: chickmaturity1.csv
Description: Input file for dryadBaizCornell.R - variables are defined in chickmaturity1_metadata.xlsx
File: chickmaturity1_metadata.xlsx
Description: Column headers and their description in chickmaturity1.csv
File: dryadBaizCornell.R
Description: Statistical analysis of ASVs, alpha diversity, figure creation
File: figure2data.csv
Description: Input file for dryadBaizCornell.R - variables are defined in figure2data_metadata.xlsx
File: figure2data_metadata.xlsx
Description: Column headers and their description in figure2data.csv
File: nestlings_model_input.csv
Description: Input file for dryadBaizCornell.R - variables are defined in nestlings_model_input_medatadata.xlsx
File: nestlings_model_input_medatadata.xlsx
Description: Column headers and their description in nestlings_model_input.csv
Code/software
Scripts use R and QIIME2 for analysis of data.
Access information
Other publicly accessible locations of the data:
- NCBI SRA accession numbers: PRJNA1308634 and PRJNA1023537
