Deciphering the low abundance microbiota of presumed aseptic hip and knee implants

Deciphering the low abundance microbiota of presumed aseptic hip and knee implants

This data set includes input files and results associated with our work "Deciphering the low abundance microbiota of presumed aseptic hip and knee implants".

Contents

aitch_dist.txt: Aitchison distance matrix

clinical_envfit.RData: envfit results for clinical information

contam_by_freq_0.2.txt: decontam results (identifying contaminants by frequency)

contam_by_prev_0.2.txt: decontam results (identifying contaminants by prevalence)

counts.txt: counts table resulting from reads processed with custom demultiplexing script

cutadapt_counts.txt: counts table resulting from reads processed with cutadapt

cutadapt_meta.txt: metadata table accompanying cutadapt_counts.txt

cutadapt_tax.txt: taxonomy table resulting from reads processed with cutadapt

cutadapt_track.txt: table summarizing retention of reads processed with cutadapt throughout the DADA2 pipeline

dna_concs.txt: DNA concentrations per sample

extraction_aldex2.txt: ALDEx2 results for comparison of DNA extraction methodologies

extraction_envfit_and_pca.RData: envfit results and PCA biplot for DNA extraction methodologies

extraction_shannon_diversity.txt: Shannon diversity and extraction methodology per sample

fwd_barcodes.fasta: forward barcodes for use by cutadapt

meta.txt: metadata table accompanying counts.txt

meta_clinical.txt: metadata table for clinical information

meta_st.txt: metadata for use by SourceTracker

not_contam_0.05.txt: decontam results (identifying non-contaminants)

pt_oac_aldex2.txt: ALDEx2 results for comparison of sample type, controlling for the effect of DNA extraction methodology

pt_oac_envfit_and_pca.RData: envfit results and PCA biplot for sample type 

pt_oac_shannon_diversity.txt: Shannon diversity, sample type, and extraction methodology per sample

rev_barcodes.fasta: reverse barcodes for use by cutadapt

spike_1_dists.txt: Aitchison distances between spike 1 samples and other samples on the same plate

spike_2_dists.txt: Aitchison distances between spike 1 samples and other samples on the same plate

tax.txt: taxonomy table resulting from reads processed with custom demultiplexing script

track.txt: table summarizing retention of reads processed with custom demultiplexing script throughout the DADA2 pipeline

Code Availability

Scripts to process and produce these data are available at https://github.com/charlie-carr/implant_microbiota

Citation

Carr C, Wilcox H, Burton JP, Menon S, Al KF, O’Gorman D, et al. (2021) Deciphering the low abundance microbiota of presumed aseptic hip and knee implants. PLoS ONE 16(9): e0257471. https://doi.org/10.1371/journal.pone.0257471