Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-Matrix bioreactor fermentation system
Harsh Mathur,
Monica A. Mechoud,
Chloe Matthews,
Cathy Lordan,
Jamie A. FitzGerald,
Tom Beresford,
Paul D. Cotter
Affiliations
Harsh Mathur
Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; Food for Health Ireland, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; Corresponding author.
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
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.