Characterizing the cancer-associated microbiome with small RNA sequencing data.

Document Type


Publication Date


Publication Title

Biochemical and biophysical research communications


Bacteria; Colonic Neoplasms; Colorectal Neoplasms; Dysbiosis; Gastrointestinal Microbiome; Humans; Microbiota; Phylogeny; Rectal Neoplasms


The microbiome is recognized as a quasi-organ in the human body. When dysbiosis of the microbiome occurs, this variation may contribute to alterations in the microenvironment, potentially inducing an inflammatory immune response and providing a niche for neoplastic growth. However, there is limited evidence regarding the correlation and interaction between the microbiome and tumorigenesis. By utilizing microRNA sequencing data of patients with colon and rectal cancer from The Cancer Genome Atlas, we designed a novel analytical process to extract non-human small RNA sequences and align them with the microbial genome to obtain a comprehensive view of the cancer-associated microbiome. In the present study, we identified >1000 genera among 630 colorectal samples and clustered these samples into three distinctive colorectal enterotypes. Furthermore, we found 12 genera from these clusters that are associated with cancer stages and revealed their putative functions. Our results indicate that the proposed analytical approach can effectively determine the cancer-associated microbiome. It may be readily applied to explore other types of cancer, in which specimens of the microbiome are difficult to collect.

Clinical Institute



Institute for Systems Biology