Microbiomics

The relationship between the microbiome and health is increasingly recognized and documented. Development of new technologies (therapeutics, actives and probiotics) targeting the microbiome to promote gut health and skin health is  now possible. 

Unlocking the microbiome potential using ~Omics

Complex communities of microbes – also known as microbiota– are found everywhere: in soil, (fermented) foods, and both on and inside the human body. Recently, more attention is given to the relation between the microbiota and health and immunity.

At NIZO, we have profound knowledge and experience in applying different techniques including 16S profiling, shotgun metagenomics, metabolomics, Single Locus Type Sequencing, to determine microbial diversity. Furthermore, we can identify key microbial players, genes that make up the microbiome or functions within the community related to not only human or animal health, but also food safety, crop development and fermentation.

Microbiome-based discovery and validation from in silico, to in vitro, to in vivo trials

The NIZO approach on Microbiomics covers microbiome-related services – from understanding the mechanisms of action via in vitro and in vivo validation of newly defined microbiome modulators to production and upscaling of modulators derived from human niches.  .

Recent development of next-generation sequencing technologies has increased the knowledge of the microbiome and its beneficial relation on skin and gut health. We have in place proprietary in silico predictive models and high-throughput in vitro micromodels systems that mimic the microbiome of different ecological human niches. This enables us to discover or validate microbiome modulators affecting metabolic activity, key community members, population structures and health-promoting metabolites. These candidate modulators are tested in human/animal proof-of-concept trials that are optimally designed based on in silico and in vitro data gathered. This integrative approachensures that solid conclusions can be drawn from the data generated from complex genomics projects. It also allows you to tackle spoilage issues in a product, identify new bio-stimulant organisms in soil or identify and validate intervention targets for gut health or skin health. Read more about our clinical trials.

Expert based, data driven biological interpretation of data

For the interpretation of the complex data (big data) throughout the discovery and validation pipeline we use various analysis and visualization tools designed for the analysis of genomics data. These tools can also be applied to other large, complex datasets . In addition, text-mining algorithms developed by our experts are used to complement the conclusions from microbiota and genomics studies with scientific literature or patent databases. Coupled with the knowledge of NIZO experts in the field of fermentation, gut health and immunity and food safety this results in solid conclusions on the relation of the microbiota to a food product or human or animal health.

Our track record in skin health

  1. Zeeuwen PL, Boekhorst J, Ederveen TH, Kleerebezem M, Schalkwijk J, van Hijum SAFT, Timmerman HM. Reply to Meisel et al. J Invest Dermatol. 2017 137:961-962. Summary: underpinning choice 16S primer sets for skin microbiome profiling.
  2. Zeeuwen PL, Ederveen TH, van der Krieken DA, Niehues H, Boekhorst J, Kezic S, Hanssen DA, Otero ME, van Vlijmen-Willems IM, Rodijk-Olthuis D, Falcone D, van den Bogaard EH, Kamsteeg M, de Koning HD, Zeeuwen-Franssen ME, van Steensel MA, Kleerebezem M, Timmerman HM, van Hijum SAFT, Schalkwijk J. Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin. J Allergy Clin Immunol. 2017 139:1368-1371. Summary: linking host genotype –> disease -> microbial modulator -> microbes -> molecular pathways.
  3. van der Krieken DA, Ederveen TH, van Hijum SA, Jansen PA, Melchers WJ, Scheepers PT, Schalkwijk J, Zeeuwen PL. An In vitro Model for Bacterial Growth on Human Stratum Corneum. Acta Derm Venereol. 2016 96:873-879. Summary: the NIZO callus model has been optimized based on this publication.
  4. Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J, Timmerman HM. Microbiome dynamics of human epidermis following skin barrier disruption. Genome Biol. 2012 13:R101. Summary: timeseries 16S analysis of skin tape stripping experiments resulting in a model for microbial regrowth in superficial wounds.

Our track record in gut health

  1. Gerritsen J, Hornung B, Renckens B, van Hijum SAFT, Martins Dos Santos VAP, Rijkers GT, Schaap PJ, de Vos WM, Smidt H. Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PeerJ. 2017 Sep 11;5:e3698. doi: 10.7717/peerj.3698. eCollection 2017.
  2. de Vos P, Mujagic Z, de Haan BJ, Siezen RJ, Bron PA, Meijerink M, Wells JM, Masclee AAM, Boekschoten MV, Faas MM, Troost FJ. Lactobacillus plantarum Strains Can Enhance Human Mucosal and Systemic Immunity and Prevent Non-steroidal Anti-inflammatory Drug Induced Reduction in T Regulatory Cells. Front Immunol. 2017 Aug 23;8:1000. doi: 10.3389/fimmu.2017.01000. eCollection 2017.
  3. Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT, Arias Vasquez A. Gut microbiome in ADHD and its relation to neural reward anticipation.  PLoS One. 2017 Sep 1;12(9):e0183509. doi: 10.1371/journal.pone.0183509. eCollection 2017.
  4. Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev. 2017 Oct;30(4):1015-1063. doi: 10.1128/CMR.00016-17. Review.
  5. de Nijs M, Mulder PPJ, Klijnstra MD, Driehuis F, Hoogenboom RLAP. Fate of pyrrolizidine alkaloids during processing of milk of cows treated with ragwort.Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2017 Aug 25:1-8. doi: 10.1080/19440049.2017.1364432

Working together in consortia

  • Clospore
  • GenoBox: A GENOmic toolBOX for microbial genome analysis

Recent publications

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