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.
Ekaterina Avershina, Einar E. Birkeland, Cecilie Bucher-Johannessen, Trine B Rounge (2026)
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut, BioRxiv. doi:10.64898/2026.03.18.712547
Bacteria are pivotal to human health, yet their ecology is shaped by mobile genetic elements (MGEs) such as viruses and plasmids. Because of the gut microbiome complexity, these components are often studied separately. We built an integrated resource of bacterial, viral, and plasmid data from 1,000+ Norwegian metagenomes and used CRISPR-Cas as a record of past encounters to map their interactions. CRISPR-Cas repertoires were highly individualized and primarily reflected the local microbial environment rather than human host factors. Bacteria preferentially targeted co-occurring MGEs, with interaction patterns structured by taxonomy and MGE lifestyle. Overall, this work views the microbiome as a dynamic ecosystem defined by interactions. It also raises the possibility that interaction-based signatures, alongside current approaches, could help refine how we think about microbiome-informed diagnostics.
C. Bucher-Johannessen, AS. Kværner, E. Birkeland, E. Botteri, E. Avershina, V. Bemanian, G. Hoff, KR. Randel, E. Hovig, P. Berstad, TB. Rounge (2025)
- Women and men exhibit distinct gut microbial profiles linked to colorectal cancer development, MedRxiv. doi:10.1101/2025.05.16.25327767
This study found that men and women have distinct gut microbiome profiles, which appear to influence their risk of developing colorectal lesions differently. Analyzing data from over 1,000 Norwegian screening participants, we observed that men were more likely to have both non-advanced and advanced lesions. We also found significant sex-based differences in the types and functions of gut bacteria, with certain microbial patterns linked to lesion development in women but not in men. These findings suggest that sex should be considered in future research and strategies for colorectal cancer prevention and early detection.
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.
Ane Sørlie Kværner, Einar Birkeland, Ekaterina Avershina, Edoardo Botteri, Cecilie Bucher-Johannessen, Markus Dines Knudsen, Anette Hjartåker, Christian M. Page, Johannes R. Hov, Mingyang Song, Kristin Ranheim Randel, Geir Hoff, Trine B. Rounge, Paula Berstad (2025).
The association between alcohol consumption and colorectal carcinogenesis is partially mediated by the gut microbiome, MedRxiv. doi:10.1101/2024.10.17.24315656