Deciphering the low abundance microbiota of presumed aseptic hip and knee implants
Authors/Creators
- 1. Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute
- 2. Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute and Department of Surgery, Schulich School of Medicine & Dentistry, Western University
- 3. Department of Surgery, Schulich School of Medicine & Dentistry, Western University and Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University
- 4. Department of Surgery, Schulich School of Medicine & Dentistry, Western University
- 5. Department of Surgery, Schulich School of Medicine & Dentistry, Western University and Department of Orthopaedics, Adult Hip and Knee Reconstruction Service, University of British Columbia
- 6. Department of Surgery, Schulich School of Medicine & Dentistry, Western University and Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University
Description
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
Files
aitch_dist.txt
Files
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Additional details
Related works
- Is supplement to
- Software: https://github.com/charlie-carr/implant_microbiota (URL)