Agromics
is a research group at the Department of Food Quality and Safety, Czech University of Life Sciences Prague, led by Assoc. Prof. Jaroslav Havlík. We measure small molecules in complex samples – in faeces, in the bee gut, in a leaf, in wine. From a single spectrum we read out hundreds of metabolites at once and look for patterns that mean something for human health, food quality and agriculture.
Our analytical facilities include a Bruker 500 MHz NMR spectrometer (liquid and solid state), a timsTOF LC-QTOF, equipment for the isolation of chemical compounds, robotic sample preparation and a tissue culture laboratory focused on cell lines of the digestive tract. The main domains of the group are NMR and LC-MS metabolomics and in vitro models of digestion.
What we do
Across fields we use the same approach: untargeted 1H NMR and LC-MS metabolomics, chemometrics and machine learning. Only the matrix and the question change. We specialise in environmental matrices – soil, plant tissues, food and faeces – that is, everything related to nutrition and agriculture, hence AGROMICS. In addition, in collaboration with hospitals at home and abroad, we also analyse clinical samples.
Our main research questions of the past five years include:
Gut microbiome and the faecal metabolome
What happens in the gut in Crohn's disease, coeliac disease or type 1 diabetes – and can the metabolome predict how well a treatment will work?
Polyphenol catabolism and models of digestion
Plant phenolics are broken down differently in every person's gut. We follow who metabolises what and how fast – in in vitro fermentations and on cell lines.
Honey bee metabolomics and colony health
We have long worked on the gut microbiota of honey bees. From describing its dynamics during development we have moved on to developing a probiotic preparation, Včelí štít (Bee Shield), based on lactobacilli and bifidobacteria that showed activity against American foulbrood. We are now optimising it and testing, under ordinary beekeeping conditions, how it affects bee health, brood rearing and immunity. We also hold a large collection of further bee-derived strains with potential as probiotics and in food biotechnology.
Food quality and authenticity
An NMR spectrum works like a fingerprint. From it we can identify the grape variety of a wine, the admixture of bovine milk in caprine milk, and the compounds behind a sensory profile. We collaborate with the National Wine Centre – Salon of Wines of the Czech Republic.
Plant metabolomics and the response to stress
How does a plant's chemistry change under pathogen attack, under salinity or after harvest – and which metabolites does the plant use to defend itself against pests and fungi?
Digestion and the primate microbiome
Gorillas in zoos die of cardiometabolic disease. Together with the University of Minnesota and the Institute of Vertebrate Biology CAS we looked for the trace in gut fermentation.
People
Assoc. Prof. Jaroslav Havlík, Ph.D.
group leader
NMR metabolomics, polyphenols, gut microbiome | Anna Mascellani Bergo, Ph.D.
postdoctoral researcher
NMR and LC-MS metabolomics, chemometrics, plant metabolomics |
Saetbyeol Lee, Ph.D.
postdoctoral researcher
honey bee metabolomics, insect biochemistry | Veronika Jarošová, Ph.D.
postdoctoral researcher – on parental leave
in vitro models of digestion, cell cultures |
Chandrama Roy Chowdhury, MSc.
Ph.D. student
faecal metabolomics, dietary biomarkers | Buse Dengiz, MSc.
Ph.D. student
probiotics for honey bees, pathogen inhibition |
Eliška Jeníčková, MSc.
Ph.D. student
faecal metabolomics in clinical studies | Kateřina Tomisová, MSc.
Ph.D. student
microbial catabolism of polyphenols, in vitro fermentation |
Completed doctoral theses
Veronika Jarošová, Ph.D. (2023) – Mutual interactions of stilbenoids, colon microbiota and the intestinal epithelium
Lucie Kejdová Rysová, Ph.D. (2023) – Innovative approaches to the assessment of milk quality and safety
Collaborations
Most of our work is done within long-standing consortia – clinical data come from our partners, the chemistry from us.
- University of Glasgow – Prof. Konstantinos Gerasimidis: Crohn's disease, exclusive enteral nutrition, micronutrients
- Tampere University – Prof. Heikki Hyöty: type 1 diabetes, dietary and viral exposures in cohort studies
- Motol University Hospital and 2nd Faculty of Medicine, Charles University – O. Cinek, J. Bronský, Z. Šumník: paediatric gastroenterology and diabetology, microbiota sequencing
- Wageningen University & Research – Dr. Kirsten Leiss: plant metabolomics, defence metabolites and resistance to pathogens
- University of Minnesota – Dr. Andrés Gómez and the Institute of Vertebrate Biology CAS – Dr. Klára Petrželková: metabolomics of digestion and the primate microbiome
- Honey bee consortium – Masaryk University Brno, Bee Research Institute Dol, Institute of Animal Physiology and Genetics CAS: P. Hyršl, P. Dobeš, M. Kamler, J. Killer – bee physiology, immunity and probiotics
What's new with us: follow us on LinkedIn.
Interested in a thesis or a Ph.D.?
We take on students interested in analytical chemistry, the microbiome and data. Write to us about what interests you – we will work out a specific topic together.
Interested in research collaboration?
We would be glad to collaborate on a research project. NMR gives insight into the stress of cells, organisms and soil, and it may hold the answers to your questions.
Contact: havlik@af.czu.cz, home.czu.cz/havlik, +420 777 558 468
