Measuring Microbial Community-Wide Antibiotic Resistance Propagation via Natural Transformation in the Human Gut Microbiome

Description

This repository includes the raw data, analysis code, and results of a systematic analysis of natural transformation (i.e., horizontal gene transfer; HGT) of bacteria in a naturally occurring microbiome (human stool) following exposure to free extracellular DNA (eDNA) that coded for antibiotic resistance. A full description of this effort is available in the associated publication. 

Resources

Name Format Description Link
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/ddPCR/FIG1-ddPCR-Analysis.Rmd.sha256
5 FIG4-WGS-AnalyzingProcessedReads.Rmd https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG4-WGS-AnalyzingProcessedReads.Rmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Data.zip.sha256
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG4-WGS-AnalyzingProcessedReads.Rmd.sha256
5 FIG5-WGS-AnalyzingProcessedReads.Rmd https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG5-WGS-AnalyzingProcessedReads.Rmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG5-WGS-AnalyzingProcessedReads.Rmd.sha256
53 HGT_STORMS_Checklist.xlsx https://data.nist.gov/od/ds/ark:/88434/mds2-3579/HGT_STORMS_Checklist.xlsx
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/HGT_STORMS_Checklist.xlsx.sha256
47 This file describes the organization of this data record. https://data.nist.gov/od/ds/ark:/88434/mds2-3579/00README.txt
47 This READEME file describes the organization this data record. https://data.nist.gov/od/ds/ark:/88434/mds2-3579/00README.txt.sha256
5 This READEME file describes the organization this data record. https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/CFU/FIG2-CFU-Analysis.Rmd
47 https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/CFU/FIG2-CFU-Analysis.Rmd.sha256
57 This compressed folder contains the raw data collected in the analysis of aforementioned samples. This includes CFU count results, ddPCR gene quantification, long-read next-generation sequencing (Nanopore) of isolates, and shotgun metagenomic sequencing characterization of microbiome samples. https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Data.zip
5 Analysis code of ddPCR data. https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/ddPCR/FIG1-ddPCR-Analysis.Rmd

Tags

  • microbiome
  • antibiotic-resistance
  • natural-transformation
  • horizontal-gene-transfer

Topics

Categories