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Vorländer D, Schultz G, Hoffmann K, Rasch D, Dohnt K. PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions. Biotechnol Bioeng 2024; 121:1118-1143. [PMID: 38151924 DOI: 10.1002/bit.28636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023]
Abstract
A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.
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Affiliation(s)
- David Vorländer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Gábor Schultz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristin Hoffmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Detlev Rasch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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Mathur H, Mechoud MA, Matthews C, Lordan C, FitzGerald JA, Beresford T, Cotter PD. Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-Matrix bioreactor fermentation system. MethodsX 2023; 11:102393. [PMID: 37846356 PMCID: PMC10577065 DOI: 10.1016/j.mex.2023.102393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, food ingredients and dietary supplements. A number of useful models already exist; however, they tend to be relatively low in terms of throughput (3-4 samples per experiment) with a long experiment duration of one to a number of weeks. Therefore, a need for a high-throughput system with a short duration time is required to enable screening of large numbers of samples. Therefore, we report here on the development of a system based on the Applikon micro-Matrix bioreactor which has the capacity to run 24 samples with an experiment duration of 48 h. However, Escherichia coli blooms are a common problem encountered in this model. Here, we describe the factors that contribute to such blooms and provide approaches to address them, providing:•Step by step optimisation of processes involved in conducting ex vivo distal colon experiments using the micro-Matrix bioreactor fermentation platform•Recommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments.
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Affiliation(s)
- Harsh Mathur
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Monica A. Mechoud
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Chloe Matthews
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Cathy Lordan
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Jamie A. FitzGerald
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Tom Beresford
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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