Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing

Abstract

Human gut microbiome studies typically focus on 16S RNA analyses and bacterial identification at the genus level. We analyzed bacterial and viral communities in colorectal tissue using both DNA and RNA sequencing and improved taxonomy resolution to species level. Specimens from 10 colorectal cancer patients and 10 matched control patients were DNA and RNA sequenced using Illumina Novaseq. Following taxonomy classification using Kraken 2, alpha and beta diversities (different metrics) as well as relative and differential abundance were calculated. There were no viral differences, but P. nesessarius had a highly increased presence in tumors (p=0.001). RNA analyses showed that A. massiliensis had a highly decreased transcription in tumors (p=0.002) while F. nucleatum transcription was highly increased in tumors (p=0.002). In conclusion, joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level identifies specific bacterial species as tumor-associated.