Identification of low abundance microbiome in clinical samples using whole genome sequencing Academic Article uri icon


MeSH Major

  • Genome, Human
  • Helicobacter pylori
  • Microbiota
  • Stomach Neoplasms


  • Identifying the microbiome composition from primary tissues directly affords an opportunity to study the causative relationships between the host microbiome and disease. However, this is challenging due the low abundance of microbial DNA relative to the host. We present a systematic evaluation of microbiome profiling directly from endoscopic biopsies by whole genome sequencing. We compared our methods with other approaches on datasets with previously identified microbial composition. We applied this approach to identify the microbiome from 27 stomach biopsies, and validated the presence of Helicobacter pylori by quantitative PCR. Finally, we profiled the microbial composition in The Cancer Genome Atlas gastric adenocarcinoma cohort.

publication date

  • November 27, 2015



  • Academic Article



  • eng

PubMed Central ID

  • PMC4661937

Digital Object Identifier (DOI)

  • 10.1186/s13059-015-0821-z

PubMed ID

  • 26614063

Additional Document Info

start page

  • 265


  • 16


  • 1