Recent progress in sequencing technology have enabled large scale sequencing of mixtures of DNA and RNA from all the organisms present in a sample simultaneously. We are developing computational tools to analyse this kind of data in order to identify and classify the species present and their abundances. We are focusing on bacteria as well as viruses and bacteriophages. Microbiome analysis is now making an impact in many areas, including marine biology, medical sciences, forensic science and agriculture.
Principal investigators
Research groups involved
- Rounge group at the Centre for Bioinformatics.
- Rognes group at the Centre for Bioinformatics.
Projects
- Effects of pandemic protective of Covid-19/SARS-Cov-2 measures on the human gut microbiome and resistome (postdoctoral fellow Paula Istvan)
Recent publications
- Kværner AS, Birkeland E, Bucher-Johannessen C, Vinberg E, Nordby JI, Kangas H, Bemanian V, Ellonen P, Botteri E, Natvig E, Rognes T, Hovig E, Lyle R, Ambur OH, de Vos WM, Bultman S, Hjartåker A, Landberg R, Song M, Ursin G, Randel KR, de Lange T, Hoff G, Holme Ø, Berstad P, Rounge TB (2021)
The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants
BMC Cancer (in press) - Mahé F, Czech L, Stamatakis A, Quince C, de Vargas C, Dunthorn M, Rognes T (2021)
Swarm v3: towards tera-scale amplicon clustering
Bioinformatics (in press) - Engberg E, Raju SC, Figueiredo RAO, Weiderpass E, Rounge TB, Viljakainen H (2021)
Saliva microbiota differs between children with low and high sedentary screen times
Human Microbiome Journal, 20. doi 10.1016/j.humic.2021.100080 - Snipen L, Angell IL, Rognes T, Rudi K (2021)
Reduced Metagenome Sequencing for strain-resolution taxonomic profiles
Microbiome, 9, 79. doi: 10.1186/s40168-021-01019-8 - Raju SC, Viljakainen H, Figueiredo RAO, Neuvonen PJ, Eriksson JG, Weiderpass E, Rounge TB (2020)
Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition
Microbiome, 8 (1), 121. doi 10.1186/s40168-020-00893-y - Viljakainen J, Raju R, Viljakainen H, Figueiredo RAO, Roos E, Weiderpass E, Rounge TB (2020)
Meal Regularity Plays a Role in Shaping the Saliva Microbiota
Front Microbiol, 11, 757. doi 10.3389/fmicb.2020.00757 - Raju SC, Lagström S, Ellonen P, de Vos WM, Eriksson JG, Weiderpass E, Rounge TB (2019)
Gender-specific associations between saliva microbiota and body size
Front Microbiol, 10, 767. doi 10.3389/fmicb.2019.00767 - Rounge TB, Meisal R, Nordby JI, Ambur OH, de Lange T, Hoff G (2018)
Evaluating gut microbiota profiles from archived fecal samples
BMC Gastroenterol, 18 (1), 171. doi 10.1186/s12876-018-0896-6 - Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016)
VSEARCH: a versatile open source tool for metagenomics
PeerJ, 4, e2584. doi 10.7717/peerj.2584 - Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R (2016)
Open-Source Sequence Clustering Methods Improve the State Of the Art
mSystems, 1 (1). doi 10.1128/mSystems.00003-15 - Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2015)
Swarm v2: highly-scalable and high-resolution amplicon clustering
PeerJ, 3, e1420. doi 10.7717/peerj.1420 - Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M (2014)
Swarm: robust and fast clustering method for amplicon-based studies
PeerJ, 2, e593. doi 10.7717/peerj.593
Collaborations
- Frédéric Mahé (CIRAD, France)
- Lars Snipen, Knut Rudi (NMBU, Ås)