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

Author:

Garcia‐Serrano Ainhoa1,Mukhedkar Dhananjay12,Hultin Emilie1ORCID,Rudsander Ulla1,Wettergren Yvonne3,Ure Agustín Enrique1,Dillner Joakim14ORCID,Arroyo‐Mühr Laila Sara14ORCID

Affiliation:

1. Department of Clinical Science, Intervention and Technology (CLINTEC) Karolinska Institutet Stockholm Sweden

2. Hopsworks AB Stockholm Sweden

3. Department of Surgery Sahlgrenska University Hospital, Sahlgrenska Academy at University of Gothenburg Gothenburg Sweden

4. Center for Cervical Cancer Elimination Forskningsgatan F56 Karolinska University Hospital Huddinge Stockholm Sweden

Abstract

AbstractBackgroundColorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non‐targeted deep‐sequencing strategies enable nowadays full microbiome characterization up to species level.AimWe aimed to analyze both bacterial and viral communities in CRC using these strategies.Materials & MethodsWe analyzed bacterial and viral communities using both DNA and RNA deep‐sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples.ResultsNo viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002).DiscussionSequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC.ConclusionJoint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.

Funder

Horizon 2020 Framework Programme

Publisher

Wiley

Subject

Cancer Research,Radiology, Nuclear Medicine and imaging,Oncology

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