Giacomo Vitali, Johannes R. Björk, Oleg Kambur, Marine Fidelle, Einar Birkeland, Lindsay Goulet, Emmanuelle Le Chatelier, Yani Ren, Robert Benamouzig, Patrick Veiga, Trine Ballestad Rounge, Barbara Pardini, Teemu Niiranen, Mārcis Leja, Juozas Kupčinskas, Bertrand Routy, Arielle Elkrief, Joana Ribeiro, Lisa Derosa, Nikos Paragios, Jan Baumbach, Leo Lahti, Le French Gut Consortium, Mathieu Almeida, Rinse K. Weersma, Laurence Zitvogel, and Stanislav Dusko Ehrlich
- Gut microbiome alterations predictive of cancer risk, MedRxiv. doi: 10.64898/2026.09.09.26362628
This preprint is the first in a newly started collaboration with gut microbiome researchers from across Europe. Here, microbial associations with disease status are assessed in different population-based and clinical cohorts, identifying shared patterns of associations in cases compared to controls.
ES. Karstad, E. Birkeland, E. Avershina, E. Botteri, I Odsbu, P. Berstad, HS. Blix, I. Robertsen, TB. Rounge
- Metformin, antibiotics, painkillers, and proton pump inhibitors shape the gut microbiome, including microbial signatures associated with colorectal neoplasia, MedRxiv. doi: 10.64898/2026.08.12.26360274
Prescriptions drugs can alter the gut microbiome, and may thus affect microbiome-based biomarkers for colorectal cancer screening. In a cohort of 1,034 screening participants, we found that 38 of 83 drugs were associated with changes in microbial diversity and specific bacterial species. These drugs include painkillers, metformin, antibiotics, and proton pump inhibitors, which were associated with species previously identified as CRC biomarker candidates in the same cohort: Escherichia coli, Eggerthella lenta, Flavonifractor plautii, Streptococcus salivarius, and Streptococcus parasanguinis. Our findings indicate that routine drug use and cumulative drug burden are important determinants of gut microbiome composition, underscoring the need to account for drug exposure when developing and applying microbiome-based screening tools.
Einar Birkeland, Paula Istvan, Ekaterina Avershina, Torbjørn Rognes, Trine B Rounge (2025).
- VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data, BioRxiv. doi:10.1101/2025.02.07.637044
Exploring the viral landscape via shotgun metagenome sequencing is challenging due to data complexity. Here we present VirMake, a tool designed for efficient, high-throughput processing — from data assembly to annotation — enhancing viral sequence identification and classification. VirMake’ modular framework offers detailed taxonomic and functional insights into viral genomes and integrates seamlessly into various metagenomic analysis stages. Visit https://github.com/Rounge-lab/VirMake to explore VirMake and incorporate this resource into your next research endeavor.