Expertise Group Leader Microbiomics

Interpretation of complex (microbiota) data requires understanding of both the biology and the relevant data analysis tools. Without the correct analyses you cannot prove significance, without biology you cannot judge relevance.

Microbial communities are present in numerous different environments, whether these are related to humans, animals, plants or food products. The nature of these communities is closely linked to health, food production and safety, and studying them is of vital importance to control and steer the efficacy and quality of food and health products. With the development of genomics techniques and methods to analyse the flood of data that comes from these experiments it is now possible to study a complete microbial community in reasonable time and at reasonable cost.

During my PhD studies at Wageningen University I combined classical microbiology with genomics techniques to create a complete overview of how a single microbial strain would respond to its environment. Within NIZO, these techniques have been developed towards studying complete collections of bacterial strains and eventually complete bacterial communities using 16S microbiota profiling. Currently we are developing new tools to obtain higher levels of detail by applying shotgun metagenomics.

We apply these methods to many diverse microbial communities such as different human body sites and animals, but also plant (leaf/soil) and food products. Do you want to study a complex bacterial community using genomics techniques? Feel free to contact me.

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Publications by Michiel Wels

Alkema W, Boekhorst J, Wels M, van Hijum SA. Microbial bioinformatics for food safety and production. Brief Bioinform. 2016 Mar;17(2):283-92. doi: 10.1093/bib/bbv034. Epub 2015 Jun 16. PubMed PMID: 26082168; PubMed Central PMCID: PMC4793891.

Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JE, Siezen RJ. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One. 2013 Jul 19;8(7):e68731. doi: 10.1371/journal.pone.0068731. Print 2013. PubMed PMID: 23894338; PubMed Central PMCID: PMC3716772.

van Bokhorst-van de Veen H, Lee IC, Marco ML, Wels M, Bron PA, Kleerebezem M. Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers. PLoS One. 2012;7(7):e39053. doi: 10.1371/journal.pone.0039053. Epub 2012 Jul 3. PubMed PMID: 22802934; PubMed Central PMCID: PMC3389004.

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 2012 Jul;6(7):1415-26. doi: 10.1038/ismej.2011.212. Epub 2012 Jan 19. PubMed PMID: 22258098; PubMed Central PMCID: PMC3379644.

Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ. Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. Microb Biotechnol. 2011 May;4(3):333-44. doi: 10.1111/j.1751-7915.2010.00217.x. Epub 2010 Oct 26. PubMed PMID: 21375715; PubMed Central PMCID: PMC3818992.

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