Mining microbiota to ferment foods for human health

The Micropia research group in the O2 lab building of the VU University Amsterdam investigates bacterial members of the human microbiota in order to ferment foods for the benefit of human health. The group is part of the Systems Biology Laboratory at the Vrije Universiteit Amsterdam. Head of the group is Remco Kort [who has been professor at the VU since 2010 and has been officially appointed to Micropia-professor on the 27th of October, 2017].

Fermentation is an ancient human practice transforming local substrates by controlled microbial growth into foods with favorable properties including flavor and texture improvement, vitamin enrichment, toxin reduction and extended shelf life. Many of the food fermenting microbial species are members of the human microbiota and microbial fermentation processes are intricately linked to human physiology. This provides an opportunity to use fermented foods as a vehicle to confer health benefits mediated by bacterial members of the human microbiota. Moreover, these innovative fermentations of local ingredients, including dairy products and vegetables, lead to value-added foods allowing benefits for health and wealth to underserved communities in challenging settings. At the Micropia research group we investigate bacterial members of the human microbiota in order to ferment foods for the benefit of human health. This applied microbiological research entails the following topics:

  1. Comparative genome analysis of bacterial probiotics of human origin to identify key functions for fermentation and health benefits, including Lactobacillus rhamnosus from the gut [1] and Lactobacillus crispatus from the vagina [2].
  2. Human microbiota analysis for the identification of factors shaping the microbiota [3], correlations with human health conditions [4], and isolation of beneficial bacterial species [5].
  3. Development an characterization of defined starter cultures and their metabolic dependencies allowing food fermentations with bacteria of human origin [6].
  4. Integration of human bacterial isolates in the process of indigenous fermented food production, including lait caille and thiakry from Senegal [7], mutandabota from Zimbabwe [8], obushera [9] and kwete [10] from Uganda, and gundruk from Nepal. 
  5. Systematic review on the efficacy of probiotics [11], health benefits of fermented foods [12], and  nutritional trials with innovative foods fermented with bacteria of human origin [13].
  6. Development and implementation of school feeding and education programs to help underserved communities with the introduction of innovative fermented foods [Currently active in Uganda, Tanzania, Kenya, Ivory Coast, and Nepal, see also  www.yoba4life.org] [14]


Key publications

[1] Sybesma W, Molenaar D, van IJcken W, Venema K, Kort R. (2013) Genome instability in Lactobacillus rhamnosus GG. Appl Environ Microbiol. 79:2233-9.

[2] van der Veer C, Hertzberger RY, Bruisten SM, Tytgat HLP, Swanenburg J, de Kat Angelino-Bart A, Schuren F, Molenaar D, Reid G, de Vries H, Kort R. (2019) Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome. 2019 7:49.

[3] Kort R, Caspers M, van de Graaf A, van Egmond W, Keijser B, Roeselers G. (2014)  Shaping the oral microbiota through intimate kissing. Microbiome. 2:41.

[4] Atukunda P, Muhoozi GKM, van den Broek TJ, Kort R, Diep LM, Kaaya AN, Iversen  PO, Westerberg AC. (2019) Child development, growth and microbiota: follow-up of a randomized education trial in Uganda. J Glob Health. 9:010431.

[5] Wacoo AP, Atukunda P, Muhoozi G, Braster M, Wagner M, Broek TJVD, Sybesma W, Westerberg AC, Iversen PO, Kort R. (2020) Aflatoxins: Occurrence, Exposure, and Binding to Lactobacillus Species from the Gut Microbiota of Rural Ugandan Children. Microorganisms 8 pii: E347.

[6] Kort R, Westerik N, Mariela Serrano L, Douillard FP, Gottstein W, Mukisa IM,  Tuijn CJ, Basten L, Hafkamp B, Meijer WC, Teusink B, de Vos WM, Reid G, Sybesma W. (2015) A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods. Microb Cell Fact. 14:195.

[7] Parker M, Zobrist S, Donahue C, Edick C, Mansen K, Hassan Zade Nadjari M, Heerikhuisen M, Sybesma W, Molenaar D, Diallo AM, Milani P, Kort R. (2018) Naturally Fermented Milk From Northern Senegal: Bacterial Community Composition and Probiotic Enrichment With Lactobacillus rhamnosus. Front Microbiol. 9:2218.

[8] Mpofu A, Linnemann AR, Sybesma W, Kort R, Nout MJ, Smid EJ. (2014) Development of a locally sustainable functional food based on mutandabota, a traditional food in southern Africa. J Dairy Sci. 97:2591-9.

[9] Mukisa, IM, Byakika, S, Meeme, R, Wacoo AP, Sybesma W, Kort R. (2019) Adopting traditional fermented foods as carriers for probiotics: The case of Obushera and Lactobacillus rhamnosus yoba. Nutrition and Food Science, 50: 841-852.

[10] Wacoo AP, Mukisa IM, Meeme R, Byakika S, Wendiro D, Sybesma W, Kort R. (2019) Probiotic Enrichment and Reduction of Aflatoxins in a Traditional African Maize-Based Fermented Food. Nutrients. 11. pii: E265.

[11] Agamennone V, Krul CAM, Rijkers G, Kort R. (2018) A practical guide for probiotics applied to the case of antibiotic associated diarrhea in The Netherlands. BMC Gastroenterol. 18:103.

[12] Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, Smid EJ, Hutkins R. (2017) Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol. 44:94-102.

[13] Westerik, N., Nelson, A, Wacoo, AP, Sybesma W., and Kort R (2020) A comparative interrupted times series on the health impact of probiotic yoghurt consumption among schoolchildren from three to six years old in Southwest Uganda. Frontiers in Nutrition. Submitted.

[14] Reid, G., Sybesma, W., Matovu, W., Onyango, A., Westerik, N., & Kort, R. (2020). Empowering women through probiotic fermented food in East Africa. Journal of global health 10: 1-5.