The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.

Journal Article (Journal Article)

Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.

Full Text

Duke Authors

Cited Authors

  • Dohlman, AB; Arguijo Mendoza, D; Ding, S; Gao, M; Dressman, H; Iliev, ID; Lipkin, SM; Shen, X

Published Date

  • February 10, 2021

Published In

Volume / Issue

  • 29 / 2

Start / End Page

  • 281 - 298.e5

PubMed ID

  • 33382980

Pubmed Central ID

  • PMC7878430

Electronic International Standard Serial Number (EISSN)

  • 1934-6069

Digital Object Identifier (DOI)

  • 10.1016/j.chom.2020.12.001


  • eng

Conference Location

  • United States