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

Abstract:

: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.

journal_name

Cell Host Microbe

journal_title

Cell host & microbe

authors

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

doi

10.1016/j.chom.2020.12.001

subject

Has Abstract

pub_date

2020-12-21 00:00:00

eissn

1931-3128

issn

1934-6069

pii

S1931-3128(20)30663-6

pub_type

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