Analysis from Klünemann et al. "Bioaccumulation of therapeutic drugs by human gut bacteria" publication.

Docker image

Dockerfile provides a recepie to reproduce our setup. A functional docker image with newest code is also avalable from Docker Cloud:

docker pull sandrejev/drugs_bioaccumulation
docker run -it sandrejev/drugs_bioaccumulation bash # to inspect contents of the container
docker run -it sandrejev/drugs_bioaccumulation # To repeat the analysis

Data files

• drug_map.csv General information about all the drugs used in this study
• bug_map.csv General information about all the bacteria used in this study
• go_terms.csv List of all GO terms for enrichment testing
• screenG_tax_info_specI_clusters.tab Core gut microbiome [1] composition average abundance and prevalence
• screenG_tax_input_specI_clusters.tab Core gut microbiome [1] cluster-to-strain (taxid) mapping
• kegg.db SQLite file containing information about all human gut bacteria and enzymes present in them taken from KEGG

Growth assay

• exp0growth/2016-11-28_curves_annotation.tab Processed growth curves data (maxOD, lag, mu) collected for all bacteria/drug combinations
• exp0growth/curves.rel_annotation_2016-11-28.tab Relative (to no-drug control) growth curves data (maxOD, lag, mu) collected for all bacteria/drug combinations

Bacteria-drug interaction screen.

• exp1depletion/170511_processingUPLCpeaks_data.clean_aftergrowthmerge_andfixingget.datacleanfunction.RData Data containing depletion of drugs from the media when a species is grown in presence (sample) and without (control) drug

Screen validation and bioaccumulation detection

• exp2metabolomics/data.depletionmodeassay_long.csv Drug UPLC measurements in absence (control) and in presence (sample) of species. Data collected from supernatant and total inoculum
• exp2metabolomics/hits.csv Relative drug UPLC measurements. Data collected from supernatant and total inoculum

NMR-based validation of duloxetine bioaccumulation and mass-spectrometry based secreted metabolite analysis

• exp3metabolomics/extraxset.fillden.noInj1.RData Untargeted metabolomics of extracellular composition
• exp3metabolomics/lysxset.fillden.noInj1.RData Untargeted metabolomics of lysed cells
• exp3metabolomics/clickxset.fillden.noInj1.RData Click-chemistry based pull down of duloxetine binding proteins
• exp3metabolomics/KEGG_metabolites_bugs.csv
• exp3metabolomics/KEGG_pathways.csv

Mass spectrometry-based protein identification

• exp3proteomics/Data_all.txt Quantitative abundance of etected proteins
• exp3proteomics/uniprot_C_saccharolyticum_enzymes.tab Uniprot annotation of C. saccharolyticum proteins

Untargeted metabolomics analysis of conditioned media assay

• exp4spentmedia/Salivarius_duloxetine.csv Metabolomics data from untargeted metabolomics analysis of E. rectale growth on S. salivarius spent media

Sensitivity of the five species used in the community assembly experiment

• exp5concentration/161118_dilution24h_rep[1-3].xlsx Growth data with different concentration of duloxetine
• exp5concentration/well2species.tsv Sample to condition mapping

Conditioned Media Assay an Community assembly assay

• exp6transfers/160916_160907_160823_transferassaydulox.xlsx Metabolomics data collected from Conditioned Media Assay
• exp6transfers/otu_table_wo_mono_normalized_by_gene_copy_mod.csv Metagenomic data for Community assembly assay
• exp6transfers/Sample_map_mod.csv Sample to condition mapping for Community assembly assay

References

[1] Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881–884 (2013).

Packages used in the analysis

• RSQLite:2.1.1
• ggrepel:0.8.0.9000
• scales:1.0.0
• stringi:1.2.4
• imputeLCMD:2.0
• pcaMethods:1.70.0
• norm:1.0-9.5
• tmvtnorm:1.4-10
• gmm:1.6-2
• sandwich:2.5-0
• Matrix:1.2-12
• impute:1.52.0
• gplots:3.0.1
• Mfuzz:2.38.0
• DynDoc:1.56.0
• widgetTools:1.56.0
• e1071:1.7-0
• rcdk:3.4.7.1
• rcdklibs:2.0
• rJava:0.9-10
• xcms:3.0.2
• MSnbase:2.4.2
• ProtGenerics:1.10.0
• mzR:2.12.0
• Rcpp:1.0.0
• qvalue:2.10.1
• mutoss:0.1-12
• mvtnorm:1.0-8
• purrr:0.2.5
• magrittr:1.5
• reshape2:1.4.3
• corpcor:1.6.9
• limma:3.34.9
• sva:3.26.0
• BiocParallel:1.12.0
• genefilter:1.60.0
• stringr:1.3.1
• locfit:1.5-9.1
• vsn:3.46.0
• DESeq2:1.18.1
• SummarizedExperiment:1.8.1
• DelayedArray:0.4.1
• matrixStats:0.54.0
• GenomicRanges:1.30.3
• GenomeInfoDb:1.14.0
• IRanges:2.12.0
• S4Vectors:0.16.0
• ade4:1.7-11
• boot:1.3-20
• LSD:4.0-0
• plyr:1.8.4
• multtest:2.34.0
• Biobase:2.38.0
• BiocGenerics:0.24.0
• readr:1.1.1
• networkD3:0.4
• rCharts:0.4.2
• data.table:1.11.4
• vegan:2.5-2
• lattice:0.20-35
• permute:0.9-4
• labdsv:1.8-0
• cluster:2.0.6
• MASS:7.3-50
• mgcv:1.8-23
• nlme:3.1-131
• widyr:0.1.1
• RColorBrewer:1.1-2
• tidyr:0.8.1
• bindrcpp:0.2.2
• dplyr:0.7.6
• xlsx:0.6.1
• ggplot2:3.0.0.9000