SIFR - predictive ex vivo gut microbiome simulation

Commonly used acronym: SIFR

Scope of the method

The Method relates to
  • Animal health
  • Human health
The Method is situated in
  • Basic Research
  • Translational - Applied Research
Type of method
  • In vitro - Ex vivo
This method makes use of
  • Animal derived cells / tissues / organs


Method keywords
  • gut microbiota
  • metabolomics
  • metagenomics
  • screening
  • mechanism of action
  • gut health
  • predictivity
  • humans
Scientific area keywords
  • fibre
  • probiotic
  • prebiotic
  • postbiotic
  • api
  • drug-bug interaction
  • host-microbiome interaction
  • inter-individual variability
  • IBD
  • pathogen
  • digestion
  • colonic fermentation
  • kinetics
Method description

The Systemic Intestinal Fermentation Research technology, SIFR in short, is a uniquely validated simulation of gut microbial ecosystems, shown to be predictive for clinical outcomes. The SIFR can simulate a wide variety of gut microbiota from humans (infants, adults, elderly; healthy, diseased) to animals (pig, poultry, cat & dog). Working ex vivo (maintaining the integrity of the gut microbiome during the investigation) and integrating robotics for a high throughput, this versatile technology can address early and late preclinical needs: screening and in-depth mechanistic characterisation. Each study addresses interindividual variability in the target population.

Method status
  • History of use
  • Internally validated
  • Published in peer reviewed journal

Pros, cons & Future potential

  • - Validated to be predictive for clinical outcomes
  • - Can address simultaneously a wide array of analytics: compositional, metabolic, host-microbiome interactions, fingerprinting...
  • - Gets rid of in vitro bias
  • - Embraces biological variation
  • - High-throughput and technically robust thanks to automation

The SIFR is modular: pre-digestion, mucosal simulation, host-microbiome module.

References, associated documents and other information

  • Van den Abbeele P, Deyaert S, Thabuis C, Perreau C, Bajic D, Wintergerst E, Joossens M, Firrman J, Walsh D and Baudot A (2023) Bridging preclinical and clinical gut microbiota research using the ex vivo SIFR® technology. Front. Microbiol. 14:1131662. doi: 10.3389/fmicb.2023.1131662
  • Van den Abbeele, P.; Deyaert, S.; Albers, R.; Baudot, A.; Mercenier, A. Carrot RG-I Reduces Interindividual Differences between 24 Adults through Consistent Effects on Gut Microbiota Composition and Function Ex Vivo. Nutrients 2023, 15, 2090.
  • Bajic, D.; Wiens, F.; Wintergerst, E.; Deyaert, S.; Baudot, A.; Van den Abbeele, P. HMOs Exert Marked Bifidogenic Effects on Children’s Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition. Nutrients 2023, 15, 1701.
  • Van den Abbeele, P.; Goggans, M.; Deyaert, S.; Baudot, A.; Van de Vliet, M.; Calatayud Arroyo, M.; Lelah, M. Lacticaseibacillus rhamnosus ATCC 53103 and Limosilactobacillus reuteri ATCC 53608 Synergistically Boost Butyrate Levels upon Tributyrin Administration Ex Vivo. Int. J. Mol. Sci. 2023, 24, 5859.
  • Van den Abbeele, P.; Detzel, C.; Rose, A.; Deyaert, S.; Baudot, A.; Warner, C. Serum-Derived Bovine Immunoglobulin Stimulates SCFA Production by Specific Microbes in the Ex Vivo SIFR® Technology. Microorganisms 2023, 11, 659.
Associated documents
2023 - SIFR validation.pdf

Contact person

Aurélien Baudot