Center for Microbiome Analyses and Therapeutics

The LUMC’s Center for Microbiome Analyses and Therapeutics (CMAT) facilitates all aspects of Microbiome research; from study design, sampling, DNA extraction and sequencing to data analysis and interpretation.

About CMAT

A core group of microbiome researchers and researchers from the Leiden Genome Technology Center (LGTC), has been formed focusing on the theme “microbiome”. The department of Medical Microbiology of theLUMC also hosts the Netherlands Donor Feces Bank (NDFB) which can offer “Fecal Microbiota Transplantations (FMTs)” for treatment of patients (for more information: www.ndfb.nl). CMAT collaborates with important service providers, such as GenomeScan and research support initiatives such as the Sequence Analysis Support Core, and Technical Focus Area; Data Analytics and Bioinformatics Center of Expertise. CMAT closely collaborates with the Medical Statistics Department in terms of study design, sample sizes and the required statistics for microbiome analysis.

Offered services

Advice on study design, subject/sample sizes, sampling method and storage conditions
Sample processing: DNA extraction and quality control
Microbiome analysis: 16S rRNA gene amplicon sequencing, Whole genome shotgun sequencing.
Other methodologies can be considered, including virome analysis, culturomics, metatranscriptomics, metaproteomics, metabolomics.
Data analysis and interpretation for a selection of services (16S, whole genome sequencing). Other analysis can be discussed.  

Scientific output

Therapeutische mogelijkheden van het microbioom volop in ontwikkeling. Zwittink RD, Hornung BVH, Ducarmon QR, Bloem MN, Terveer EM and Kuijper EJ. Bijblijven, 26 April 2019 https://doi.org/10.1007/s12414-019-0027-5

Issues and current standards of controls in microbiome research. Hornung BVH, Zwittink RD and Kuijper EJ. FEMS Microbiol. Ecol., 9 April 2019 https://doi.org/10.1093/femsec/fiz045

The preterm gut microbiota: an inconspicuous challenge in nutritional neonatal care. Henderickx JG, Zwittink RD, van Lingen RA, Knol J and Belzer C. Front Cell Infect Microbiol., 12 March 2019 https://doi.org/10.3389/fcimb.2019.00085

Dynamics of the gut microbiota in children receiving selective or total gut decontamination treatment during hematopoietic stem cell transplantation. Bekker V*, Zwittink RD*, Knetsch CW, Sanders IMJG, Berghuis D, Heidt PJ, Vossen JMJJ, de Vos WM, Belzer C, Bredius RGM, van ’t Hof PJ, Lankester AC* and Kuijper EJ*. Biol Blood Marrow Transplant., 5 Feb 2019 https://doi.org/10.1016/j.bbmt.2019.01.037

Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections. Baktash A, Terveer EM, Zwittink RD, Hornung BVH, Corver J, Kuijper EJ and Smits WK. Front. Microbiol., 12 June 2018 https://doi.org/10.3389/fmicb.2018.01242

Fecal Microbiota Transfer for Multidrug-Resistant Gram-Negatives: A Clinical Success Combined With Microbiological Failure. Stalenhoef JE, Terveer EM, Knetsch CW, Van't Hof PJ, Vlasveld IN, Keller JJ, Visser LG, Kuijper EJ. Open Forum Infect Dis. 2017 Mar 13;4(2)

Contact

For more information, please contact cmat@lumc.nl
The Center for Microbiome Analyses and Therapeutics is supported by the expertise of:

Microbiome platform working group

  • Liz Terveer
    Medical microbiologist (Medical Microbiology)
  • Romy Zwittink
    Molecular Microbiologist (Medical Microbiology)
  • Quinten Ducarmon
    PhD candidate, thesis: microbiome research (Medical Microbiology)
  • Anoe Geelen
    Research technician (Medical Microbiology)
  • Bastian Hornung
    Bioinformatician (Medical Microbiology)
  • Jeroen Corver
    Senior researcher experimental bacteriology (Medical Microbiology)
  • Jeroen Laros
    Bioinformatic scientist (LGTC, Human Genetics)
  • Eric Claas
    Medical molecular biologist (Medical Microbiology)
  • Ed Kuijper
    Medical Microbiologist (Medical Microbiology)