gut_microbiome_shift_and_resistome_diversity

Table_otu.raw.txt.xls: OTU table processed by Uparse(97% similarity) on the Magigene Cloud Platform. Chloroplasts, mitochondria, Unclassified, archaea otus were removed. rpkm.type.txt: Abundance of Antibiotic-resistant genes (ARGs) grouped by types processed by ARGs-OAP v3.0 rpkm.subtype.txt: ARGs grouped by subtypes processed by ARGs-OAP v3.0 rpkm.genes.txt: ARGs grouped by genes processed by ARGs-OAP v3.0 lefse_results.txt.xls: lefse analysis result produced by Magigene Cloud Platform. otus.fa: Representative otu sequences processed by Uparse(97% similarity) on the Magigene Cloud Platform. Chloroplasts, mitochondria, Unclassified, archaea otus were removed. otus_aligned.fasta: Aligned otu sequences by mafft. Bash: mafft otus.fa > otus_aligned.fa otus_fasttree.tre: Construct phylogenic tree from otus_aligned.fa by fasttree. data_analysis_visualization.ipynb: Script for Relative Abundance, Microbial Diversity analysis and Data visualization. SpeciesAbundance.py: Script for calculating the species abundance for given otu table at given genus BetaDiversity.py: Script for calculating the distance matrix and PCoA analysis. Fixed the bug of confidence ellipse function. args_oap.sh: Shell script for ARGs analysis. analysis_16s.yml: conda environment config file with all necessary packages. LDA.plot: Figure S1A, LDA bar plot produced by Magigene Cloud Platform. lefse_cladogram_plot.pdf: LEfSe cladogram plot produced by Magigene Cloud Platform. polymyxin.svg & multidrug.svg: Figure S1B&C. Figure1.svg: figure1 produced by our python script. figureS1.svg: figure s1 produced by our python script. Table1.xlsx: Predominant bacterial genera percentage of all pandas at two stages. TableS1.xlsx: Information about the pandas and fecal samples. TableS2.xlsx: Top 10 bacterial genera percentage of all pandas at two stages. otu_table_individuals.biom: temporary data produced by our scripts. otu_table_individuals_rearranged_merged.tsv: temporary data produced by our scripts. otu_table_samples.biom: temporary data produced by our scripts. otu_table_samples_rearranged.tsv: temporary data produced by our scripts. analysis_16s.yml: conda environment configuration file.