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

<strong>Deciphering the low abundance microbiota of presumed aseptic hip and knee implants</strong> This data set includes input files and results associated with our work "Deciphering the low abundance microbiota of presumed aseptic hip and knee implants". <strong>Contents</strong> <em>aitch_dist.txt</em>: Aitchison distance matrix <em>clinical_envfit.RData</em>: envfit results for clinical information <em>contam_by_freq_0.2.txt</em>: decontam results (identifying contaminants by frequency) <em>contam_by_prev_0.2.txt</em>: decontam results (identifying contaminants by prevalence) <em>counts.txt</em>: counts table resulting from reads processed with custom demultiplexing script <em>cutadapt_counts.txt</em>: counts table resulting from reads processed with cutadapt <em>cutadapt_meta.txt</em>: metadata table accompanying <em>cutadapt_counts.txt</em> <em>cutadapt_tax.txt</em>: taxonomy table resulting from reads processed with cutadapt <em>cutadapt_track.txt</em>: table summarizing retention of reads processed with cutadapt throughout the DADA2 pipeline <em>dna_concs.txt</em>: DNA concentrations per sample <em>extraction_aldex2.txt</em>: ALDEx2 results for comparison of DNA extraction methodologies <em>extraction_envfit_and_pca.RData</em>: envfit results and PCA biplot for DNA extraction methodologies <em>extraction_shannon_diversity.txt</em>: Shannon diversity and extraction methodology per sample <em>fwd_barcodes.fasta</em>: forward barcodes for use by cutadapt <em>meta.txt</em>: metadata table accompanying <em>counts.txt</em> <em>meta_clinical.txt</em>: metadata table for clinical information <em>meta_st.txt</em>: metadata for use by SourceTracker <em>not_contam_0.05.txt</em>: decontam results (identifying non-contaminants) <em>pt_oac_aldex2.txt</em>: ALDEx2 results for comparison of sample type, controlling for the effect of DNA extraction methodology <em>pt_oac_envfit_and_pca.RData</em>: envfit results and PCA biplot for sample type <em>pt_oac_shannon_diversity.txt</em>: Shannon diversity, sample type, and extraction methodology per sample <em>rev_barcodes.fasta</em>: reverse barcodes for use by cutadapt <em>spike_1_dists.txt</em>: Aitchison distances between spike 1 samples and other samples on the same plate <em>spike_2_dists.txt</em>: Aitchison distances between spike 1 samples and other samples on the same plate <em>tax.txt</em>: taxonomy table resulting from reads processed with custom demultiplexing script <em>track.txt</em>: table summarizing retention of reads processed with custom demultiplexing script throughout the DADA2 pipeline <strong>Code Availability</strong> Scripts to process and produce these data are available at https://github.com/charlie-carr/implant_microbiota <strong>Citation</strong> 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