Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data

Area of Science:

• Microbiology
• Bioinformatics
• Oncology

Background:

• Colorectal cancer (CRC) is a leading cause of cancer death globally, necessitating novel therapeutic strategies.
• Tumor-infiltrating bacteria are increasingly recognized as significant contributors to CRC tumorigenesis, progression, and metastasis.
• Accurately quantifying these bacteria within tumor tissues presents a substantial analytical challenge.

Purpose of the Study:

• To develop and validate a bioinformatics pipeline for identifying and quantifying tumor-infiltrating bacteria using unmapped reads from host whole genome sequencing (hWGS) data.
• To compare the abundance and diversity of infiltrating bacteria in primary colorectal tumors versus normal blood samples.
• To establish a novel method for analyzing microbial communities within tumor microenvironments.

Main Methods:

• Utilized unmapped reads from colon adenocarcinoma hWGS data, including paired-end and single-end reads.
• Assembled unmapped read pairs and remapped all reads to a human microbiome reference database.
• Employed maximum likelihood estimation to compute microbial relative abundance and analyzed diversity differences between tumor and blood samples.

Main Results:

• Primary tumor tissues exhibited significantly higher diversity of infiltrating bacteria compared to normal blood samples.
• The relative abundance of *Bacteroides fragilis*, *Bacteroides dorei*, and *Fusobacterium nucleatum* was markedly elevated in primary colorectal tumors.
• These identified bacteria were among the most abundant in tumors but scarce in normal blood, with findings corroborated by previous studies.

Conclusions:

• The developed bioinformatics approach effectively identifies tumor-infiltrating bacteria from discarded hWGS data.
• This method provides a new avenue for investigating the role of the microbiome in colorectal cancer.
• The findings highlight specific bacterial species associated with CRC, potentially serving as diagnostic or therapeutic targets.