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Data from: Transgenerational effects of doxycycline and anhydrotetracycline on the microbiome of the Australian sheep blowfly, Lucilia cuprina

Cite this dataset

Kriete, Alexis; Scott, Maxwell (2024). Data from: Transgenerational effects of doxycycline and anhydrotetracycline on the microbiome of the Australian sheep blowfly, Lucilia cuprina [Dataset]. Dryad. https://doi.org/10.5061/dryad.76hdr7t4h

Abstract

Tetracyclines are a family of broad-spectrum antibiotics commonly used in agriculture, medicine, and research. However, exposure to tetracyclines is associated with a wide range of negative health outcomes. In some cases, these negative effects are transgenerational: when individuals are treated with tetracyclines, their untreated offspring exhibit phenotypic abnormalities. The causes of such transgenerational effects are not well-understood, but disruption of the microbiome and/or mitochondria may play an important role. Transgenerational effects from tetracyclines may threaten the success of an environmentally-friendly form of pest control, the release of transgenic males carrying a tetracycline-repressible female lethal gene. In this study, we investigated the direct and transgenerational effects of two tetracycline-class antibiotics, doxycycline (DOX) and anhydrotetracycline (ATC), on the blowfly Lucilia cuprina, a facultative parasite of sheep. To simulate the rearing conditions used in a male-only release program, blowflies were reared on diet alone, or diet plus DOX or ATC, for three generations, then reared for an additional fourth generation off tetracyclines. We used 16S amplicon sequencing and qPCR to examine whole-body microbiome composition and bacterial and mitochondrial DNA abundance in third and fourth generation flies. The microbiomes of third generation flies reared on DOX or ATC were similar in composition and diversity to the microbiomes of flies reared exclusively on the control diet. However, we found that the untreated fourth generation offspring of DOX- or ATC-treated flies displayed major shifts in microbiome composition relative to both their treated parents and untreated control groups. Our study supports a growing body of evidence that tetracyclines exert both direct and transgenerational effects on arthropods, and highlights the need to address these impacts in the context of insect pest management.

README: Transgenerational effects of doxycycline and anhydrotetracycline on the microbiome of the Australian sheep blowfly, Lucilia cuprina

https://doi.org/10.5061/dryad.76hdr7t4h

This dataset contains additional files associated with the manuscript "Transgenerational effects of doxycycline and anhydrotetracycline on the microbiome of the Australian sheep blowfly, Lucilia cuprina."

Description of the data and file structure

qPCR input data for R.csv: This .csv file contains qPCR data formatted for importing into R for statistical analysis. Metadata and delta-delta Ct values are provided.

qPCR raw data and stats.xlsx: This .xlsx file contains several tabs consisting of the raw qPCR data and statistical output (unpaired t-tests with Benjamini-Hochberg correction for multiple comparisons).

  • Raw data and calculations: This tab contains the raw qPCR measurements (i.e., Cq values) for the GST-1, 16S, and COXI genes for each of the 54 samples used in this study. The calculations used to produce the delta-delta Cq values and associated fold changes reported in the manuscript are also shown in this tab.
  • R input for stats: This tab contains the matrix of sample data (including metadata) and associated delta-delta Cq values for importation into R.
  • p-values 16S adult comps: This tab displays the p-values (adjusted for multiple comparisons using the Benjamini-Hochberg correction) from pairwise comparisons of delta-delta Cq values for the 16S gene across adult sample groups using an unpaired t-test. 
  • p-values 16S larva comps: This tab displays the p-values (adjusted for multiple comparisons using the Benjamini-Hochberg correction) from pairwise comparisons of delta-delta Cq values for the 16S gene across larva sample groups using an unpaired t-test. 
  • p-values COXI adult comps: This tab displays the p-values (adjusted for multiple comparisons using the Benjamini-Hochberg correction) from pairwise comparisons of delta-delta Cq values for the COXI gene across adult sample groups using an unpaired t-test. 
  • p-values COXI larva comps: This tab displays the p-values (adjusted for multiple comparisons using the Benjamini-Hochberg correction) from pairwise comparisons of delta-delta Cq values for the COXI gene across larva sample groups using an unpaired t-test. 
  • t-values 16S adult comps -t -va: This tab displays the t-values (test statistic) from pairwise comparisons of delta-delta Cq values for the 16S gene across adult sample groups using an unpaired t-test. 
  • t-values 16S larva comps -t -va: This tab displays the t-values (test statistic) from pairwise comparisons of delta-delta Cq values for the 16S gene across larva sample groups using an unpaired t-test. 
  • t-values COXI adult comps -t -va: This tab displays the t-values (test statistic) from pairwise comparisons of delta-delta Cq values for the COXI gene across adult sample groups using an unpaired t-test. 
  • t-values COXI larva comps -t -va: This tab displays the t-values (test statistic) from pairwise comparisons of delta-delta Cq values for the COXI gene across larva sample groups using an unpaired t-test. 
  • How to interpret NA values: A value of "NA" in a cell means "not applicable." For example, the value of the column "Sex" for larval samples is NA because larvae were not sexed in this study. Similarly, matrices of statistical output (p-values and t-values) contain NA values to avoid redundancy (showing the same comparison twice) and can be ignored. 

ANCOMBC2_comps_pairwise_allgroups.csv: This .csv file contains the output from pairwise analysis of differentially-abundant taxa in ANCOM-BC2.

sample-metadata.csv: This .csv file contains the sample metadata for this study, formatted for importation into R.

SampleSeq_info coded.pdf: This PDF file displays the forward and reverse barcodes, and associated linker sequences, used for 16S sequencing in this study.

PD_pvals_pairs.csv: This .csv file contains the corrected p-values from comparisons of Faith’s Phylogenetic Diversity, a measure of alpha diversity, across all sample groups (pairwise Wilcoxon rank sum test with Benjamini-Hochberg correction for multiple comparisons)

Evenness_pvals_pairs.csv: This .csv file contains the corrected p-values from comparisons of Pielou’s Evenness, a measure of alpha diversity, across all sample groups (pairwise Wilcoxon rank sum test with Benjamini-Hochberg correction for multiple comparisons)

Shannon_pvals_pairs.csv:  This .csv file contains the corrected p-values from comparisons of the Shannon Index, a measure of alpha diversity, across all sample groups (pairwise Wilcoxon rank sum test with Benjamini-Hochberg correction for multiple comparisons).

Sharing/Access information

The raw 16S sequence reads and associated metadata from this study are available at NCBI Sequence Read Library BioProjectID: PRJNA1118283 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1118283/).
The R code used in this study can be accessed on GitHub (https://github.com/AlexisKriete/microbiome-project-code).

Funding

Animal and Plant Health Inspection Service, Award: AP21IS000000C003, International Services