Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq

Area of Science:

• Microbiology
• Oncology
• Bioinformatics

Background:

• Emerging research indicates breast tissue is a habitat for diverse microorganisms, contrary to previous beliefs of sterility.
• The human microbiome plays a crucial role in health and disease, including cancer development and progression.

Purpose of the Study:

• To analyze and compare the microbial composition of primary breast tumor tissue and adjacent normal breast tissue.
• To investigate differences in breast tissue microbial communities across various breast cancer phenotypes.
• To evaluate the reliability of bioinformatics tools (Kraken2, Metaphlan3) for analyzing microbial composition in RNA-seq data.

Main Methods:

• RNA sequencing (rRNA depleted) of breast tumor and normal tissue samples from 23 Slovak individuals.
• Bioinformatic analysis using Kraken2 and Metaphlan3 to identify microbial species.
• Analysis of an additional 91 breast tissue samples from the SRA database (China).

Main Results:

• Significant differences in microbial composition were observed between cancerous and healthy breast tissues.
• Distinct microbial profiles were identified among different breast cancer phenotypes.
• Proteobacteria, Firmicutes, and Actinobacteria were the most enriched bacterial phyla in breast tissue across both datasets.
• Bacteroides were enriched in Slovak samples, while Cyanobacteria were more frequent in Chinese samples.

Conclusions:

• Breast tissue is not sterile and harbors a complex microbiome that varies between healthy and cancerous states.
• The composition of the breast tissue microbiome differs based on breast cancer subtypes and geographic origin.
• Kraken2 demonstrated higher reliability for analyzing microbial communities in rRNA-depleted RNA-seq data.