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ARS Home » Northeast Area » Wyndmoor, Pennsylvania » Eastern Regional Research Center » Dairy and Functional Foods Research » Research » Research Project #438902

Research Project: Developing an in Vitro Model of the Human Small Intestinal Microbiota

Location: Dairy and Functional Foods Research

Project Number: 8072-41000-108-09-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 10, 2020
End Date: Jul 31, 2021

1. To optimize the preliminary model of the in vitro human small intestinal microbial ecosystem; and 2. Use the improved model to characterize the effect of dietary components on the composition and metabolic profile on the small intestine microbiota.

The ileostomy sample will be cultured using two BioFlow 320 bioreactors to generate a microbial community. The cultured community will be characterized in terms of microbial composition by 16S tagged sequencing and bacterial biomass assessed by 16S copy number polymerase chain reaction (PCR). The function of the community will be characterized by analyzing bile acid conversion, quantifying short chain fatty acids, and detecting the amounts of free amino acids. ARS and University of Pennsylvania scientists hypothesize that culturing the ileostomy sample will be sufficient to reproduce the composition and function of the human distal small intestinal microbiota in vitro. This model will be further advanced by developing a 2-stage small intestine gut microbiota model. This will be accomplished by using both BioFlow 320 units, one to simulate the proximal small intestine and the second to simulate the distal small intestine community. The proximal model will be developed by testing the addition of pepsin, bile acids, and lactase. Following the development of proximal model, the distal model will be evaluated and optimized by studying the response of the microbial community to food components, included but not limited to milk, fat free and full fat, cheese, and fiber. The proximal model of the small intestine will be developed by testing the effect of different amounts of pepsin, bile acids, and lactase on digestion. The distal model will be developed by performing culturing experiments and analyzing the results. The proximal and distal small intestine models will then be combined into a single model and experiments will be run to test the effects of food components on the small intestine microbiota.