Bacterial microcompartment utilisation in the human commensal Escherichia coli Nissle 1917

Bacterial microcompartments (BMCs) are self-assembled protein structures often utilised by bacteria as a modular metabolic unit, enabling the catalysis and utilisation of less common carbon and nitrogen sources within a self-contained compartment. The ethanolamine (EA) utilisation (eut) BMC has been widely demonstrated in enteropathogens, such as Salmonella enterica, and current research is exploring its activity in the commensal species that populate the human gut. Escherichia coli Nissle 1917 (EcN) is a strong coloniser and probiotic in gut microbial communities, and has been used extensively for microbiome engineering. In this study, the utilisation of ethanolamine as a sole carbon source and the formation of the eut BMC in EcN were demonstrated through growth assays and visualisation with transmission electron microscopy. Subsequently, flux balance analysis was used to further investigate the metabolic activity of this pathway. It was found that not only is the utilisation of the eut BMC for the degradation of EA as a carbon source in EcN comparable to that of Salmonella enterica, but also that ammonium is released into solution as a byproduct in EcN but not in S. enterica. Control of EA-dependent growth was demonstrated using different concentrations of the operon inducer, vitamin-B12. We show that vitamin B12-dependent EA utilisation as the sole carbon source enables growth in EcN, and demonstrate the concurrent formation of the BMC shell and inducible control of the eut operon.