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

Published by National Institute of Standards and Technology | National Institute of Standards and Technology | Catalog Last Checked: August 03, 2026 at 03:52 AM | Dataset Last Updated: September 26, 2024
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. 

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Complete Metadata
@type dcat:Dataset
accessLevel public
accrualPeriodicity irregular
bureauCode 
[
  "006:55"
]
contactPoint 
{
  "fn": "Samuel P. Forry",
  "hasEmail": "mailto:samuel.forry@nist.gov"
}
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. 
distribution 
[
  {
    "title": "Figure 1 - ddPCR Analysis",
    "mediaType": "application/octet-stream",
    "description": "Analysis code of ddPCR data.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/ddPCR/FIG1-ddPCR-Analysis.Rmd"
  },
  {
    "title": "README",
    "mediaType": "text/plain",
    "description": "This READEME file describes the organization this data record.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/00README.txt.sha256"
  },
  {
    "title": "Read Me",
    "mediaType": "application/octet-stream",
    "description": "This READEME file describes the organization this data record.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/CFU/FIG2-CFU-Analysis.Rmd"
  },
  {
    "title": "Data",
    "mediaType": "application/zip",
    "description": "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.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Data.zip"
  },
  {
    "title": "READEME file",
    "mediaType": "text/plain",
    "description": "This file describes the organization of this data record.",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/00README.txt"
  },
  {
    "title": "README",
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/CFU/FIG2-CFU-Analysis.Rmd.sha256"
  },
  {
    "mediaType": "application/octet-stream",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG4-WGS-AnalyzingProcessedReads.Rmd"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG4-WGS-AnalyzingProcessedReads.Rmd.sha256"
  },
  {
    "mediaType": "application/octet-stream",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG5-WGS-AnalyzingProcessedReads.Rmd"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/WGS%20-%20Illumina/FIG5-WGS-AnalyzingProcessedReads.Rmd.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Analysis&Visualization/ddPCR/FIG1-ddPCR-Analysis.Rmd.sha256"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/Data.zip.sha256"
  },
  {
    "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/HGT_STORMS_Checklist.xlsx"
  },
  {
    "mediaType": "text/plain",
    "downloadURL": "https://data.nist.gov/od/ds/ark:/88434/mds2-3579/HGT_STORMS_Checklist.xlsx.sha256"
  }
]
identifier ark:/88434/mds2-3579
issued 2024-11-07
keyword 
[
  "antibiotic resistance",
  "horizontal gene transfer",
  "microbiome",
  "natural transformation"
]
landingPage https://data.nist.gov/od/id/mds2-3579
language 
[
  "en"
]
license https://www.nist.gov/open/license
modified 2024-09-26 00:00:00
programCode 
[
  "006:045"
]
publisher 
{
  "name": "National Institute of Standards and Technology",
  "@type": "org:Organization"
}
theme 
[
  "Bioscience:Microbial measurements"
]
title Measuring Microbial Community-Wide Antibiotic Resistance Propagation via Natural Transformation in the Human Gut Microbiome

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