Applying in vitro culturing technology to establish and evaluate the human gut microbiota

Authors: Firrman, Jenni; Liu, Linshu; VAN DEN ABBEELE, PIETER - Prodigest; TANES, CEYLAN - Children'S Hospital - Philadelphia, Pennsylvania; BITTINGER, KYLE - Children'S Hospital - Philadelphia, Pennsylvania; Tomasula, Peggy

Submitted to: Journal of Visualized Experiments
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2018
Publication Date: 2/15/2019
Citation: Firrman, J., Liu, L.S., Van Den Abbeele, P., Tanes, C., Bittinger, K., Tomasula, P.M. 2019. Applying in vitro culturing technology to establish and evaluate the human gut microbiota. Journal of Visualized Experiments. 144:1-12. https://doi.org/10.3791/59054.
DOI: https://doi.org/10.3791/59054

Interpretive Summary: The human colon is home to large amounts of many different types of bacteria, collectively referred to as the gut microbiota. The gut microbiota plays an important role in human health by doing things such as making vitamins, breaking down foods that were not digested in the small intestine, and producing many helpful products that can be used by the human cells. There is a lot of interest in studying the gut microbiota to understand even more about its function in the human body; however, studying the gut microbiota is not an easy task. Animals can be used, such as mice, but their digestive tracts are different from humans, and it is hard to distinguish between what the gut microbiota is doing, and what the animal’s cells themselves are doing. An alternate way to study the gut microbiota is to use an artificial system, one that is designed to mimic the human digestive tract. This system is made of glass vessels, with one glass vessel representing each region of the digestive tract (the stomach, small intestine, ascending colon, transverse colon, and descending colon). Each vessel has environmental controls for temperature and pH, and is oxygen free. Each glass vessel also has a surface added, to mimic the intestinal surface that is found inside the human colon. Research has demonstrated that an artificial system can be used to grow and study the gut microbiota. Using this system, the important functions of the gut microbiota can be further evaluated, and the effects that different foods, food components or pharmaceuticals may have on the gut microbiota can be studied.

Technical Abstract: The human gut microbiota plays a vital role in both human health and disease. Studying the gut microbiota using an in vivo model is difficult due to its complex nature, and its diverse association with mammalian components. The application of in vitro methods allows for the study of the gut microbiota dynamics without having to consider the contribution of the mammalian milieu. Advancements in in vitro culturing technology make it possible to mimic the physiological conditions of the gastrointestinal tract, simulating the human conditions with inclusion of parameters such as pH, temperature, anaerobiosis, and transit time. The intestinal surface of the colon can be simulated by adding mucin-coated carriers, creating a mucosal phase and adding further dimension. The gut microbiota can be cultured by inoculating with human fecal material. Upon inoculation with this complex mixture of bacteria, specific microbes are enriched in the different longitudinal (ascending, transverse and descending colons) and transversal (luminal and mucosal) environments of the in vitro model. It is crucial to allow the system to reach a steady state, in which the community and the metabolites produced remain stable. Once steady state is achieved, the system can be used to analyze bacterial interactions and community functions, or to test the effects of any additives on the gut microbiota, such as food, food components, or pharmaceuticals.