Mitigating E. coli blooms on the microMatrix fermentation platform

Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, including food ingredients and dietary supplements, fermented foods, prebiotics as well as other test substrates such as antimicrobials. Combined with the capacity to perform such assays at a relatively high throughput, thereby facilitating screening programmes, such systems are valuable as the samples generated can be the focus of downstream metagenomics, transcriptomics, metabolomics, proteomics, culturomics and other such approaches to assess various aspects of microbiome responses to the foods tested. However, a relatively common problem encountered in ex vivo distal colon model experiments is the undesired phenomenon of blooms of certain genera, especially Escherichia, during the course of such experiments. Here, we describe the variety of factors that can contribute to such Escherichia coli blooms and provide approaches to address this issue. We also briefly outline the merits as well as limitations of utilising the micro-Matrix bioreactor fermentaton system (Applikon) for ex vivo modelling of the distal colon microbiome.