Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design

Authors: Firrman, Jenni; Liu, Linshu; Mahalak, Karley; TANES, CEYLAN - Children'S Hospital - Philadelphia, Pennsylvania; BITTINGER, KYLE - Children'S Hospital - Philadelphia, Pennsylvania; BOBOKALONOV, JAMSHED - US Department Of Agriculture (USDA); VAN DEN ABBEELE, PIETER - Prodigest; MATTEI, LISA - Children'S Hospital - Philadelphia, Pennsylvania; ZHANG, HUANJIA - Children'S Hospital - Philadelphia, Pennsylvania

Submitted to: Applied Microbiology and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2021
Publication Date: 3/25/2021
Citation: Firrman, J., Liu, L.S., Mahalak, K.K., Tanes, C., Bittinger, K., Bobokalonov, J., Van Den Abbeele, P., Mattei, L., Zhang, H. 2021. Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design. Applied Microbiology and Biotechnology. volume 105, pages 3353–3367. https://link.springer.com/article/10.1007/s00253-021-11241-x.
DOI: https://doi.org/10.1007/s00253-021-11241-x

Interpretive Summary: The gut microbiota is a large community of microbes that lives in the intestinal tract and plays a very important role in human health; however, it is difficult to study because it located inside the human and interacts with human cells on a molecular basis. Due to these difficulties, studies on the gut microbiota alone are often performed in the laboratory using advanced systems that can recreate the environmental conditions of the intestinal tract. There are different types of systems that are available for these studies with a wide range of complexity, yet the benefits and drawbacks of choosing one system over the other remains unclear. Here, an analysis was performed looking at the similarities and differences between a gut microbiota community grown using a simple system compared to a more complex system by collecting the same data from each and then comparing the results. The data demonstrated that the gut microbiota community was affected by the system as was the type and amounts of byproducts released. The community grown in the more complex system was more similar to the starting material then the simple system. This is important to know when deciding which experimental system to use and the data provided valuable information on how experimental conditions can affect the gut microbiota.

Technical Abstract: The importance of the gut microbiota in human health, and its association with the progression of disease, makes it a target for research in both the biomedical and nutritional fields. To date, a number of in vitro systems have been designed to recapitulate the gut microbiota of the colon that range in complexity from the application of a single vessel to cultivate the community in its entirety, to multi-stage systems that mimic the distinct regional microbial communities that reside longitudinally through the colon. While these disparate types of in vitro designs have been employed previously, information regarding the similarities and differences between the communities that develop within was less defined. Here, a comparative analysis of the population dynamics and functional production of short chain fatty acids was performed using the gut microbiota of the same donor cultured using a single vessel and a 3-stage colon system. The results found that the single vessel communities maintained alpha diversity at a level comparable to the distal regions of the 3-stage colon system. Yet, there was a marked difference in the type and abundance of taxa, with the largest discrepancies occurring between families Enterobacteriaceae, Bacteroidaceae, Synergistaceae, and Fusobacteriaceae. Functionally, the single vessel community produced significantly less short-chain fatty acids compared to the 3-stage colon system. Taken together, these results provide valuable information on how culturing technique effects the gut microbiota composition and function, which may have an impact on studies relying on the application of an in vitro strategy. This data can be used to justify experimental designs for gut microbial studies and provides insight on the application of a simplified versus complex study design.