Dr Tommi Vatanen

PhD in computational biology

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Senior Research Fellow


I am a human microbiome expert specialising in the dynamic gut microbiomes in early childhood. I have a strong interest in understanding the microbiomes’ connection to autoimmune disorders and the role of fecal microbiota transplantations in therapy. My training covers stool sampling, laboratory protocols, DNA sequencing, computational analysis and knowledge transfer. I am experienced in working with multidisciplinary teams, including experimental microbiologists, immunologists, epidemiologists and clinicians.

Research | Current

My current research is focused on infant gut microbiomes in health and disease, and gut microbial manipulation by fecal microbiota transplantation. My overarching research goal is to combine ecological, evolutionary and microbiological concepts with state-of-the-art microbiome profiling to derive fundamental rules describing and predicting microbial colonization in the infant gut.

My ongoing projects include:

2020-2023, Principal Investigator of Marsden Fast-Start funded project “Phages as modulators of the human gut microbiome”. Direct costs NZD 300,000. I investigate the role of bacteriophages in the treatment efficacy of fecal microbiota transplantation from healthy stool donors to obese adolescents.

2017-present, I am a consortium member in the Global Microbiome Conservancy initiative (http://microbiomeconservancy.org/), led by researchers at the Massachusetts Institute of Technology (USA). This initiative aims to understand and conserve the human gut microbial heritage in a library of microbial strains from more than 40 countries.

2016-present, Microbiome Immunity Project (http://bit.ly/ibmmip) with IBM World Community Grid: I am the human gut microbiomes expert in this collaborative project. I work with researchers at University of California San Diego (USA), Flatiron Institute (USA), Małopolska Centre of Biotechnology (Poland) and IBM to predict 3D structures and functions of 100,000s of novel microbial proteins. IBM has, to date, provided compute resources of more than 100,000 CPU years for this project.

Teaching | Current

Visiting lecturer on MEDSCI710 - Nutrition Mechanisms


2021 - University of Auckland Early Career Research Excellence Award
2020 - Web of Science Highly Cited Researcher
2019 - Marsden FastStart Grant
2019 - Illumina™ Emerging Researcher Award 
2018 - Best Dissertation Award 2017, Department of Computer Science, Aalto University, Finland

Areas of expertise

Human gut microbiome, bioinformatics, microbial ecology, metagenomic assembly

Committees/Professional groups/Services

Member of the Liggins Institute Executive Committee
Liggins Institute representative in the Information Technology Faculties’ Forum
Co-chair of the steering committee of the TUMMI milk digestion trial

Selected publications and creative works (Research Outputs)

As of 29 October 2020 there will be no automatic updating of 'selected publications and creative works' from Research Outputs. Please continue to keep your Research Outputs profile up to date.
  • Vatanen, T., Plichta, D. R., Somani, J., Münch PC, Arthur, T. D., Hall, A. B., ... Young, R. A. (2019). Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nature microbiology, 4 (3), 470-479. 10.1038/s41564-018-0321-5
  • Stewart, C. J., Ajami, N. J., O'Brien JL, Hutchinson, D. S., Smith, D. P., Wong, M. C., ... Metcalf, G. A. (2018). Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature, 562 (7728), 583-588. 10.1038/s41586-018-0617-x
  • Vatanen, T., Franzosa, E. A., Schwager, R., Tripathi, S., Arthur, T. D., Vehik, K., ... She, J.-X. (2018). The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature, 562 (7728), 589-594. 10.1038/s41586-018-0620-2
  • Zhao, G., Vatanen, T., Droit, L., Park, A., Kostic, A. D., Poon, T. W., ... Hämäläinen A-M (2017). Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proceedings of the National Academy of Sciences of the United States of America, 114 (30), E6166-E6175. 10.1073/pnas.1706359114
  • Vaughn, B. P., Vatanen, T., Allegretti, J. R., Bai, A., Xavier, R. J., Korzenik, J., ... Moss, A. C. (2016). Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn's disease. Inflammatory Bowel Diseases, 22 (9), 2182-2190. 10.1097/MIB.0000000000000893
  • Yassour, M., Vatanen, T., Siljander, H., Hämäläinen A-M, Härkönen T, Ryhänen SJ, ... Gevers, D. (2016). Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Science Translational Medicine, 8 (343)10.1126/scitranslmed.aad0917
  • Vatanen, T., Kostic, A. D., d'Hennezel E, Siljander, H., Franzosa, E. A., Yassour, M., ... Hämäläinen A-M (2016). Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell, 165 (4), 842-853. 10.1016/j.cell.2016.04.007

Contact details

Primary office location

M&HS BUILDING 505 - Bldg 505
Level 2, Room 206
New Zealand

Social links

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