Biodiversity and biogeography of the multi-kingdom cancer microbiome
Summary
Microorganisms represent an important component of the tumor microenvironment, but conflicting reports have left the extent of microbial prevalence across cancer types unclear, necessitating more robust methods for characterizing tumor-associated microbiomes. We built and benchmarked a host-subtraction and classification pipeline to identify microbiota in whole-genome sequencing data and applied it to 16,369 high-depth tumor whole genomes from the UK 100,000 Genomes Project. After decontam
Content
# Biodiversity and biogeography of the multi-kingdom cancer microbiome
*Published: 2026 May 5*
Microorganisms represent an important component of the tumor microenvironment,
but conflicting reports have left the extent of microbial prevalence across
cancer types unclear, necessitating more robust methods for characterizing
tumor-associated microbiomes. We built and benchmarked a host-subtraction and
classification pipeline to identify microbiota in whole-genome sequencing data
and applied it to 16,369 high-depth tumor whole genomes from the UK 100,000
Genomes Project. After decontamination, microbial signatures were
indistinguishable from the background in most cancer types. However, in
orodigestive tumors, we detected multi-kingdom polymicrobial communities,
including bacteria, fungi, viruses, archaea, and, in some cases, Trichomonas, a
protozoan parasite. These communities varied by tumor site and subtype, with
increased microbial colonization of microsatellite-instable and polymerase ε
(POLE)/polymerase δ (POLD1)-mutated tumors, supported by a correlation between
microbial load and tumor mutation burden observed across orodigestive cancers.
This analysis helps to resolve pan-cancer microbial structure and links the
tumor microbiome to host phenotype and tumor genomic context.
DOI: 10.1016/j.cell.2026.04.015