This repo includes all data, code, and relevant results for the study "Route of oxytetracycline administration differentially impacts the growth and gut microbiome of pigs co-infected with Bordetella bronchiseptica and Pasteurella multocida"
| Chapter | Description |
|---|---|
| data | Includes data files needed to carry out R analysis. Also includes mock_community_16S3.fna file listing expected mock community sequences for mock sample Mock5 |
| scripts | R scripts for 16S data, qPCR, and other pig sample analyses. AbxConcWeightADGLungLesion.R and AMR_qPCR.R can be run anytime. Only fecal 16S data-related scripts are numbered and must be run in that order. |
| mothur.md | Commands used in mothur to process FS9 16S data, additional notes |
| Notes.md | To-do list for FS9, BioProject PRJNA693865 notes |
| Order | Script file name | Description |
|---|---|---|
| 1a | mothur.md | First run mothur.md to process 16S sequence data and generate output for R scripts. |
| 1b | 1_OTUtable.R | Generate OTU table from mothur output to use for creating phyloseq objects |
| 2a | 2a_phyloseq_NONINFnm_INFnm.R | Generate phyloseq object to use for 3a_alpha_beta_diversity_NONINFnm_INFnm.R. Run adonis function with distance matrices to assess how variation is attributed to different experimental treatments or uncontrolled covariates. |
| 2b | 2b_phyloseq_INFnmfeedinject.R | Generate phyloseq object to use for 3b_alpha_beta_diversity_INFnmfeedinject.R. Run adonis function with distance matrices to assess how variation is attributed to different experimental treatments or uncontrolled covariates. |
| 3a | 3a_alpha_beta_diversity_NONINFnm_INFnm.R | Run alpha (Shannon, Inverse Simpson) and beta diversity (generating NMDS, pairwise comparisons) analyses, data visualization |
| 3b | 3b_alpha_beta_diversity_INFnmfeedinject.R | Run alpha (Shannon, Inverse Simpson) and beta diversity (generating NMDS, pairwise comparisons) analyses, data visualization |
| 4a | 4a_DeSeq2_NONINFnm_INFnm.R | Identify differentially abundant bacterial taxa (order and genus levels) between groups within each day, data visualization |
| 4b | 4b_DeSeq2_INFnmfeedinject.R | Identify differentially abundant bacterial taxa (order level) between groups within each day, data visualization |
| 5b | 5b_NMDS_DeSeq2_INFnmfeedinject.R | Combined steps 2b, 3b, and 4b into one script to generate figure for manuscript |
| Anytime | AbxConcWeightADGLungLesion.R | Data visualization of oxytet concentration in various tissue sites, correlation between oxytet concentration and weight for each tissue site, average daily gain, and lung lesion severity |
| Anytime | AMR_qPCR.R | Data visualization of relative abundance (log10) of each AMR gene using scatter point box plots; and box plots of total abundance of each AMR gene using AULC calculation |
- Annotation Notes
(1/2/3/4)a= NONINFnm vs INFnm(1/2/3/4/5)b= INFnm vs INFfeed vs INFinject.