Simulator of Human Intestinal Microbial Ecosystem

Commonly used acronym: SHIME

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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
  • Other (e.g. bacteria)
Animal or human fecal material

Description

Method keywords
  • gut health
  • gut microbiota
  • colonic metabolism
  • dose response
  • metabolomics
  • metagenomics
  • long-term effects
  • repeated dosing
  • in vivo-like models
  • predictivity
  • humans
  • companion animals
  • farm animals
  • Compartmentalized
Scientific area keywords
  • fibre
  • prebiotics
  • probiotics
  • postbiotics
  • symbiotics
  • proteins
  • carbohydrates
  • nutraceuticals
  • plant extracts
  • drugs
  • api
  • formulations
  • polyphenols
  • minerals
  • HMO
  • vitamins
  • digestion
  • host-microbiome interaction
  • pathogen
  • Fermentation (kinetics)
  • kinetics
Method description

The SHIME® (Simulator of Human Intestinal Microbial Ecosystem) model is currently the most representative in vitro technology for the combined simulation of the physiological, chemical and microbiological properties of the gastrointestinal tract. The model enables study of the impact of long-term repeated dosing and of the modulation of the microbiota in function of the gut location. The SHIME® can be seen as a clinical trial in vitro, which can provide the spatiotemporal insight into the mechanism of action of a specific treatment, therefore providing complementary data to in vivo studies. The SHIME® simulates all the compartments of the GI tract, starting with the stomach followed by the small intestine, the proximal and the distal colon (with an option to include the mouth and a specific ileal compartment with ileal microbial community). To be as close as possible to the in vivo situation, the SHIME® model reproduces multiple physiological and microbial in vivo parameters, including body temperature, intestinal volumes, enzyme concentrations, feeding cycles, pH, microbial diversity across anatomical compartments… Due to its flexibility, interindividual variability as well as various specific population groups (babies, children, elderly, healthy and diseased humans, or adjusted to the research question) and even animal models (cats, dogs and pigs) can easily be studied.

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

Pros, cons & Future potential

Advantages
  • - Closest to the in vivo context
  • - Validated with in vivo data (IVIVC)
  • - Most accurate reproduction of the gut microbiota (composition and functionality) over a longer period of time
  • - Provides insights into the impact of repeated dosing and into the long-term effects
  • - Facilitates the understanding of the mechanism of action (MoA)
  • - Takes into account interindividual variability
  • - Predicts the impact of a product on the top of a normal diet
  • - Able to recreate the specific composition and functionalities of the microbiome in the specific parts of the gut.
  • - In its most extensive configuration: the microbiome in the ileum, the ascending, transverse and descending colon can be simulated.
  • - Enables the simulation of the ileal microbiome
  • - Representative of the microbiome of a specific donor.
  • - Complementary representation of the Luminal and Mucosal gut microbiota (M-SHIME)
  • - Adaptations of the conditions to mimic those of a specific population group: for example baby SHIME
  • - Incorporation of multiple treatment in a sequential manner, e.g., antibiotic treatment.
  • - Wash-out phase extension, to evaluate the long-term effects of a test product after stopping its administration, to establish the engraftment of probiotics, etc.
  • - Possibility to establish a dose-response relationship.
Modifications
  • - Dysbiotic SHIME: allows the representative simulation of a dysbiotic microbial community, e.g., IBD, IBS, etc.
  • - Screening SHIME: allows the screening of multiple colonic vessels in parallel (multiple test products/microbiomes)
  • - M-SHIME: allows the simulation of the mucosa-associated microbial community
  • - Upper GIT model: focuses on the single passage of a test product through the stomach and small intestine (duodenum, jejunum, ileum). The inclusion of a dialysis module enables the simulation of intestinal absorption.

References, associated documents and other information

References

Duysburgh, C., Govaert, M., Guillemet, D., & Marzorati, M. (2024). Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties. Nutrients, 16(11), 1570.

Kirby, T. O., Sapp, P. A., Townsend, J. R., Govaert, M., Duysburgh, C., Marzorati, M., ... & Esposito, R. (2024). Changes in the fecal polar metabolome due to AG1 supplementation in the SHIME® model: A proof of principle study. Journal of Functional Foods, 119, 106319.

Duysburgh, C., Miclotte, L., Green, J. B., Watts, K. T., Sardi, M. I., Chakrabarti, A., ... & Marzorati, M. (2024). Saccharomyces cerevisiae derived postbiotic alters gut microbiome metabolism in the human distal colon resulting in immunomodulatory potential in vitro. Frontiers in Microbiology, 15, 1358456.

Marsaux, B., Moens, F., Marzorati, M., & Van de Wiele, T. (2023). The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model. Journal of Fungi, 9(9), 877.

Kirby, T. O., Townsend, J. R., Sapp, P. A., Govaert, M., Duysburgh, C., Marshall, T. M., ... & Esposito, R. (2023). The Novel Synbiotic, AG1®, Increases Short-Chained Fatty Acid Production in the Simulator of Human Intestinal Microbial Ecosystem (SHIME) Model®. Nutraceuticals, 3(4), 489-498.

Arroyo, M. C., Laurie, I., Rotsaert, C., Marzorati, M., Risso, D., & Karnik, K. (2023). Age-dependent prebiotic effects of soluble corn fiber in M-SHIME® gut microbial ecosystems. Plant Foods for Human Nutrition, 78(1), 213-220. .......

Organisations

ProDigest
Gastrointestinal Expertise
Belgium
Flemish Region