Dr Tommi Vatanen

Biography

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

Postgraduate supervision

Open PhD/MSc positions:

• The role of phage in the gut microbiome of preterm babies
• Prevalence and spread of antibiotic resistance in New Zealand populations
• The rules governing microbial colonization in microbiome transplants - machine learning approach

Current PhD students:

Michele Zuppi

Former PhD students:

Brooke Wilson
Clara Yieh Lin Chong

Distinctions/Honours

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