VGO Oropharyngeal Resistome Data Analysis

Authors: Beatrice Cornu Hewitt
Contact: b.cornuhewitt@uu.nl
Date: "r Sys.time()"

Description

The scripts in this repository are related to a COPD case-control study conducted with data from the VGO project which involves study participants living in a livestock dense region in the South Eastern Netherlands (https://www.rivm.nl/veehouderij-en-gezondheid/onderzoek-veehouderij-en-gezondheid-omwonenden-vgo). We aimed to investigate associations between the OP resistome composition and (1) COPD status, (2) the OP microbiome composition and (3) residential exposure to livestock-related microbial emissions.

Scripts

All scripts are saved as Rmarkdown files in the folder 'Rscripts' within this repository. Scripts are separated into the following sections: * [1 - Load data and create phyloseq.Rmd]: Load data for whole project and create phyloseq objects ready for analysis * [2 - Identify contaminants.Rmd]: Script to identify contaminants using decontam combined method * [3 - Resistome basics.Rmd]: Basic analysis of the resistome including abundance analysis, bacterial load analysis * [4 - Visualisations.Rmd]): Visualisations of the resistome including stacked bar charts and heatmaps on different taxonomic levels * [5 - Alpha diversity.Rmd]: Alpha diversity analyses in relation to COPD status and livestock exposure status * [6 - Beta diversity.Rmd]: Community composition analyses in relation to COPD status and livestock exposure status * [7 - Differential abundance analysis.Rmd]: Differential abundance analysis of resistance genes in relation to COPD status and livestock exposure status using DESeq and ALDEx algorithms * [8 - Bacteriome and resistome.Rmd]: Comparison of the composition of the bacteriome and the resistome using Procrustes analysis and co-occurrence networks * [9 - Manuscript Figure 3.Rmd]: Script to create figure 3 in manuscript

Session Info

``` R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited Kingdom.utf8 LCCTYPE=EnglishUnited Kingdom.utf8
[3] LCMONETARY=EnglishUnited Kingdom.utf8 LCNUMERIC=C
[5] LCTIME=English_United Kingdom.utf8

time zone: Europe/Berlin tzcode source: internal

attached base packages: [1] grid stats graphics grDevices utils datasets methods base

other attached packages: [1] ALDEx21.34.0 latticeExtra0.6-30 zCompositions1.5.0-1 truncnorm1.0-9
[5] NADA1.6-1.1 survival3.5-7 MASS7.3-60 renv1.0.3
[9] annotater0.2.3 here1.0.1 decontam1.22.0 phyloseq1.46.0
[13] writexl1.4.2 vegan2.6-4 permute0.9-7 lubridate1.9.3
[17] purrr1.0.2 tidyr1.3.0 tidyverse2.0.0 tibble3.2.1
[21] stringr1.5.1 scales1.3.0 readr2.1.4 RColorBrewer1.1-3
[25] plyr1.8.9 patchwork1.1.3 openxlsx4.2.5.2 olsrr0.5.3
[29] matrixStats1.1.0 magrittr2.0.3 lattice0.21-9 knitr1.45
[33] igraph1.5.1 Hmisc5.1-1 styler1.10.2 TempPackage1.0
[37] docstring1.0.0 ggpubr0.6.0 ggplot23.4.4 foreach1.5.2
[41] forcats1.0.0 e10711.7-13 DT0.30 dplyr1.1.4
[45] cowplot1.1.1 corrplot0.92 car3.1-2 carData3.0-5
[49] BiocManager1.30.22 lintr3.1.1

loaded via a namespace (and not attached): [1] splines4.3.2 bitops1.0-7 R.oo1.26.0
[4] rpart4.1.21 rex1.2.1 lifecycle1.0.4
[7] rstatix0.7.2 rprojroot2.0.4 processx3.8.2
[10] backports1.4.1 sass0.4.7 rmarkdown2.25
[13] jquerylib0.1.4 yaml2.3.7 remotes2.4.2.1
[16] zip2.3.0 pkgbuild1.4.2 ade41.7-22
[19] abind1.4-5 pkgload1.3.3 zlibbioc1.48.0
[22] quadprog1.5-8 GenomicRanges1.54.1 R.cache0.16.0
[25] R.utils2.12.3 BiocGenerics0.48.1 RCurl1.98-1.13
[28] nnet7.3-19 GenomeInfoDbData1.2.11 IRanges2.36.0
[31] S4Vectors0.40.2 nortest1.0-4 goftest1.2-3
[34] DelayedArray0.28.0 codetools0.2-19 xml21.3.5
[37] tidyselect1.2.0 stats44.3.2 base64enc0.1-3
[40] roxygen27.2.3 jsonlite1.8.7 multtest2.58.0
[43] Formula1.2-5 iterators1.0.14 tools4.3.2
[46] Rcpp1.0.11 glue1.6.2 SparseArray1.2.2
[49] gridExtra2.3 xfun0.41 mgcv1.9-0
[52] MatrixGenerics1.14.0 GenomeInfoDb1.38.1 withr2.5.2
[55] fastmap1.1.1 rhdf5filters1.14.1 fansi1.0.5
[58] callr3.7.3 digest0.6.33 timechange0.2.0
[61] R62.5.1 colorspace2.1-0 jpeg0.1-10
[64] R.methodsS31.8.2 utf81.2.4 generics0.1.3
[67] data.table1.14.8 class7.3-22 S4Arrays1.2.0
[70] prettyunits1.2.0 htmlwidgets1.6.3 pkgconfig2.0.3
[73] gtable0.3.4 XVector0.42.0 htmltools0.5.7
[76] biomformat1.30.0 Biobase2.62.0 png0.1-8
[79] cyclocomp1.1.1 rstudioapi0.15.0 tzdb0.4.0
[82] reshape21.4.4 checkmate2.3.1 nlme3.1-163
[85] proxy0.4-27 cachem1.0.8 rhdf52.46.1
[88] parallel4.3.2 RcppZiggurat0.1.6 foreign0.8-85
[91] desc1.4.2 pillar1.9.0 vctrs0.6.4
[94] cluster2.1.4 htmlTable2.4.2 evaluate0.23
[97] cli3.6.1 compiler4.3.2 rlang1.1.2
[100] crayon1.5.2 ggsignif0.6.4 interp1.1-6
[103] ps1.7.5 fs1.6.3 stringi1.8.2
[106] BiocParallel1.36.0 deldir2.0-2 munsell0.5.0
[109] Biostrings2.70.1 lazyeval0.2.2 Matrix1.6-1.1
[112] hms1.1.3 Rhdf5lib1.24.0 SummarizedExperiment1.32.0 [115] Rfast2.1.0 broom1.0.5 RcppParallel5.1.7
[118] bslib0.6.1 directlabels2024.1.21 xmlparsedata1.0.5
[121] ape_5.7-1
```