Journal
METHODSX
Volume 11, Issue -, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.mex.2023.102393
Keywords
Escherichia coli; Gut microbiome; Blooms; Metagenomics
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The development of a high-throughput system based on the Applikon micro-Matrix bioreactor for screening gut microbiome modulation is reported. However, Escherichia coli blooms are a common problem encountered in this system. The study provides optimization steps and approaches to attenuate E. coli blooms in such ex vivo colon model experiments.
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 platformRecommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments.
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