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

  • Environmental biotechnology
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Abstract

The importance of the gut microbiota in human health and disease progression 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 ranging 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 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 (SCFAs) 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, particularly between families Enterobacteriaceae, Bacteroidaceae, Synergistaceae, and Fusobacteriaceae. Functionally, the single vessel community produced significantly less SCFAs compared to the 3-stage colon system. These results provide valuable information on how culturing technique effects gut microbial composition and function, which may impact studies relying on the application of an in vitro strategy. This data can be used to justify experimental strategy and provides insight on the application of a simplified versus complex study design.

Key points

• A mature gut microbiota community can be developed in vitro using different methods.

• Beta diversity metrics are affected by the in vitro culturing method applied.

• The type and amount of short-chain fatty acids differed between culturing methods.

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All data will be made available upon request.

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Funding

This work was supported by the in-house Project 8072-41000-102-00D, “In Vitro Human Intestinal Microbial Ecosystem: Effects of Diet.”

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Authors and Affiliations

  1. Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, USA

    Jenni Firrman, LinShu Liu, Karley Mahalak & Jamshed Bobokalonov

  2. Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Ceylan Tanes, Kyle Bittinger, Lisa Mattei & Huanjia Zhang

  3. Prodigest, Ghent, Belgium

    Pieter Van den Abbeele

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  1. Jenni Firrman
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  2. LinShu Liu
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Contributions

JF, KM, and LSL designed and performed the experiments; LM and HZ performed Next Gen DNA sequencing; CT and KB performed the bioinformatical and statistical analyses; JB performed metabolomics; PVA assisted in experimental design; JF, KM, LSL, LM, HZ, CT, KB, JB, and PVA contributed to writing and revising the manuscript and interpreting the results; and JF was responsible for compiling the data and coordinating the research efforts.

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Correspondence to Jenni Firrman.

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Firrman, J., Liu, L., Mahalak, K. et al. Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design. Appl Microbiol Biotechnol 105, 3353–3367 (2021). https://doi.org/10.1007/s00253-021-11241-x

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