In vitro short-term colonic screening of compounds for gut microbiome interaction

Commonly used acronym: Short-term SHIME

Scope of the method

The Method relates to
  • Animal health
  • Human health
The Method is situated in
  • Basic Research
Type of method
  • In vitro - Ex vivo
This method makes use of
  • Other (e.g. bacteria)
Faecal sample from donor organism


Method keywords
  • gut microbiota
  • metabolic profiling
  • metagenome
  • screening
  • gut health
  • short-term
  • human
Scientific area keywords
  • fibre
  • probiotic
  • prebiotic
  • postbiotic
  • api
  • stability
  • drug-bug interaction
  • host-microbiome interaction
  • inter-individual variability
  • IBD
  • pathogen
Method description

ProDigest's short-term colonic simulation is an in vitro model for rapid screening of the interaction between test products and the gut microbiome. The key microbial saccharolytic and proteolytic markers are analysed as well as evolution in the composition of the microbiome and other endpoints as desired by the customer. Ideally suited for cost-efficient investigation of many test products, combinations or formulations, inter-individual variability in effect, ... Model organisms:

  • - human: adult vs infant, healthy vs diseased
  • - dog
  • - cat
  • - pig
  • - poultry (caecum)
Method status
  • History of use
  • Internally validated
  • Published in peer reviewed journal

Pros, cons & Future potential

  • Representative of donor microbiome ;
  • Robust simulation ;
  • Enough sampling for multiple analyses and kinetic investigations.

This set-up considers short-term interactions between one dose of test product and the microbiome.

References, associated documents and other information


Van den Abbeele, P., et al., 2018. A combination of xylooligosaccharides and a polyphenol blend affect microbial composition and activity in the distal colon exerting immunomodulating properties on human cells. Journal of Functional Foods, Vol. 47, pp. 163-171.

Van den Abbeele, P., et al. 2018. Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro. ACS Omega, Vol. 3 (10), pp. 12446-12456.

Van den Abbeele, P., et al. 2018. Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells. J. Agric. Food Chem. Vol 66 (5), pp. 1121-1130.

Gross, G., et al., 2010. In Vitro Bioconversion of Polyphenols from Black Tea and Red Wine/Grape Juice by Human Intestinal Microbiota Displays Strong Interindividual Variability. J. Agric. Food Chem, Vol. 58, pp. 10236-10246.


Contract Research
Flemish Region


ProDigest, ProDigest