SHIME experiments are typically coupled with a wide set of analyses to investigate the microbial community structure and composition as well as chemical analyses to estimate the microbial community activity and the intestinal fate of active compounds. This allows to evaluate in great detail modifications of the product’s structure, its biological activity and the effect of the administration on the microbial community composition and host health.
Complimentary analyses include but are not limited to:
- Bacterial quantification: plate counts, quantitative PCR (qPCR), flow cytometry
- Next generation sequencing and specific gene arrays
- Fingerprinting techniques (qualitative changes): Denaturing Gradient Gel Elecrophoresis (DGGE), Terminal restriction fragment length polymorphism (tRFLP), Length Heterogeneity PCR (LH PCR), Automated Ribosomal Intergenic Spacer Analysis (ARISA)
- Determination of the concentration of SCFA, lactate, ammonium, phenol/p-cresol, specific bacterial enzymatic activities and wider metabolomic analyses
- Metabolite detection: HPLC, LC-MS, GC, specific metabolite detection kits, residual fiber concentration analysis, sugar content determination, micronutrients, protocol development and validation.