Our microbiota experts are ready to help you
What is your hypothesis, and how can you best set up your study in order to generate a set of microbiota analysis results, and what exactly should be analysed? Should you perhaps include fungi in your study, as well as bacteria? What does the resulting data tell us? These questions and more are answered by MiCA’s team of experts: all dedicated scientists at the forefront of microbiota research.
Molecular and microbiologists
Our senior researchers provide guidance and advice on your study set-up and listening to your requirements
Hilde Herrema’s knowledge on pathophysiology of (metabolic) disease and methodologies to (mechanistically) assess this, allows her to work on the interface of several skill sets of translational research and to ‘connect the dots’. Herrema’s role at MiCA is to advise on study design and data interpretation. Herrema: “The role of (gut) microbiota in health and disease is a textbook example of how a translational research approach, in which clinical studies go hand in hand with mechanistic studies and computational approaches, will provide crucial answers to treat and cure disease. MiCA can help with several aspects of this approach.”
Background
During her PhD (Laboratory of Pediatrics, University Medical Center Groningen), Herrema studied the interplay between glucose, fatty acid and bile salt metabolism in mouse models for fatty liver disease.
She subsequently focused on the role of hepatic endoplasmic reticulum (ER) stress in obesity in development of T2DM during her postdoc in the Division of Endocrinology of Boston Children’s Hospital (Harvard Medical School, Boston, USA). Alongside her work for MiCA, she holds a position in the Nieuwdorp group (Experimental Vascular Medicine, AMC Amsterdam), where she uses her expertise on physiology and molecular biology techniques to disentangle the role of the gut microbiota in development of obesity and related disease such as T2DM.
Wetlab (16S, ITS and metagenomics)
MiCA’s wet lab expertise prepares your samples for Illumina MiSeq sequencing of both bacterial and fungal microbiota or metagenomics
Jorn Hartman is the senior lead laboratory technician for the wet lab at MiCA. He is responsible for developing a track-and-trace system that follows each sample from the intake of the raw material at the start until the raw data from the sequence machines at the end. His work also involves giving unique ID to samples, helping calculate dilutions, library pools, library compositions, combining wet lab data with metadata.For wetlab work he does everything from weighing materials to preparing pools for sequence and the analysis.
Background
Hartman graduated in 2011 from HAN Nijmegen in the field of molecular technology. He is especially interested in molecular techniques such as DNA isolation from faecal material and PCR on specific characteristics of organisms and regions. Prior to joining MiCA four years as a microbiology technician at Wageningen University Research working on projects related to 16S.
Theo Hakvoort helped to set up the fungi ITS sequencing at MiCA. Recently, he has become increasingly interested in NextGen sequencing, ranging from RNAseq, T-cell clones, microbe compositions, almost all in relation to inflammatory bowel diseases.
Background
Hakvoort studied biochemistry at the BCP Jansen Institute, University of Amsterdam and earned his PhD on enzymology and protein structure related research at the same university in 1990. During the period 1988-90 (Northwestern University, Evanston, Illinois) and 1990-92 (University of Illinois, Chicago) he studied molecular biology on mitochondrial proteins. In 1992 he started research on whole body amino acids metabolisms at the AMC, Amsterdam.
Bioinformatics
These experts are at the leading edge of microbiota research and combine computer science, biology, mathematics, and engineering to analyse and interpret biological data
Mark Davids is an experienced next-gen microbiota data cruncher. In his work he places a clear emphasis on the methods rather than the biology and constantly strives to obtain the most reliable results. Davids has scientific interests which center around microbial physiology branching towards microbial genetics, ecology and evolution. He has a background in metabolic modelling and metatranscriptome analysis and he is now moving into the field of statistics related to ecology and microbiome research. Davids: “I am healthily skeptical about many claims derived from microbiota research due to my personal tendency to focus on methods rather than biology”.
Background
Davids has an MSc in bioprocess engineering with a focus on microbial metabolism. He was a PhD candidate at Wageningen University with focus on the technical aspects of microbiota metatranscriptome analysis. He implemented wet lab protocols and a data analysis platform for microbiota research at Nutreco/Trouw Nutrition.