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

Publication ,  Journal Article
Dohlman, AB; Arguijo Mendoza, D; Ding, S; Gao, M; Dressman, H; Iliev, ID; Lipkin, SM; Shen, X
Published in: Cell Host Microbe
February 10, 2021

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.

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Published In

Cell Host Microbe

DOI

EISSN

1934-6069

Publication Date

February 10, 2021

Volume

29

Issue

2

Start / End Page

281 / 298.e5

Location

United States

Related Subject Headings

  • Immunology
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genetic Markers
  • Gastrointestinal Tract
  • Gastrointestinal Neoplasms
  • Gastrointestinal Microbiome
  • Decontamination
  • Chromosome Mapping
  • Bacteria
 

Citation

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Dohlman, A. B., Arguijo Mendoza, D., Ding, S., Gao, M., Dressman, H., Iliev, I. D., … Shen, X. (2021). The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe, 29(2), 281-298.e5. https://doi.org/10.1016/j.chom.2020.12.001
Dohlman, Anders B., Diana Arguijo Mendoza, Shengli Ding, Michael Gao, Holly Dressman, Iliyan D. Iliev, Steven M. Lipkin, and Xiling Shen. “The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.Cell Host Microbe 29, no. 2 (February 10, 2021): 281-298.e5. https://doi.org/10.1016/j.chom.2020.12.001.
Dohlman AB, Arguijo Mendoza D, Ding S, Gao M, Dressman H, Iliev ID, et al. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe. 2021 Feb 10;29(2):281-298.e5.
Dohlman, Anders B., et al. “The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants.Cell Host Microbe, vol. 29, no. 2, Feb. 2021, pp. 281-298.e5. Pubmed, doi:10.1016/j.chom.2020.12.001.
Dohlman AB, Arguijo Mendoza D, Ding S, Gao M, Dressman H, Iliev ID, Lipkin SM, Shen X. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe. 2021 Feb 10;29(2):281-298.e5.
Journal cover image

Published In

Cell Host Microbe

DOI

EISSN

1934-6069

Publication Date

February 10, 2021

Volume

29

Issue

2

Start / End Page

281 / 298.e5

Location

United States

Related Subject Headings

  • Immunology
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genetic Markers
  • Gastrointestinal Tract
  • Gastrointestinal Neoplasms
  • Gastrointestinal Microbiome
  • Decontamination
  • Chromosome Mapping
  • Bacteria