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Background Host microbiota are thought to play a role in atherosclerotic cardiovascular disease (ACVD), a leading cause of morbidity worldwide. Western-style diet can be metabolised by some intestinal microbiota harbouring CutC , e.g. E. fergusonii, to produce trimethylamine (TMA), which is metabolised by the liver to trimethylamine-n-oxide (TMAO). TMAO has been linked with ACVD through human association studies and gnotobiotic in vivo experimental models.Hypothesis Introduction of a humanised synthetic intestinal core community (HuSICC) with modification of a TMAO-producing bacterial species will ameliorate experimental atherosclerosis.Aims To successfully deplete murine intestinal microbiota and establish a HuSICC, within a murine model of experimental atherosclerosis. To create E. fergusonii ∆cutC for use in this experimental model.Methods DNA of murine intestinal commensals was extracted from murine faecal pellets and identified using Oxford Nanopore Technology (ONT). Broad-spectrum antibiotics and a HuSICC were administered to C57BL/6 female mice fed a high-fat western-style diet. Classical cloning techniques were utilised for mutant creation.Results Murine gut microbiota composition, depletion and repletion with a HuSICC was determined by in-house ONT sequencing. Twice daily gavage of broad-spectrum antibiotics for three days was sufficient to deplete the murine gut microbiome. Gavaged HuSICC bacteria were detectable by ONT sequencing following a two-week repletion regime. Anaerobic growth curves and ONT sequencing provide evidence for creation of E. fergusonii ∆cutC.Conclusion These data provide a proof of principle for our in-house use of ONT sequencing of murine faecal pellets in monitoring our engineering of murine intestinal microbiota. Future studies will further optimise the colonisation of a HuSICC containing E. fergusonii wild-type or E. fergusonii ∆cutC and determine effect on atherosclerotic plaque development.