C57BL/6J mice (8 weeks, female) and ApoE KO mice with a C57BL/6 genetic background (8-weeks old, female) were purchased from Vital River Laboratory Animal Technology Co., Ltd (Beijing, China), and maintained at 22 ± 2 °C, 55 ± 5% relative humidity, with a 12-h light/dark period. In the experiments, mice were fed a standard chow diet (containing 0.1% choline) or choline diet (chow diet with 1% additional choline) with or without additional BBR (Deze biotechnology, Nanjing, China) and libitum access to water. A mixture of Abs (200 mg/kg vancomycin, 400 mg/kg neomycin sulfate, 400 mg/kg metronidazole, 400 mg/kg ampicillin; Sigma-Aldrich, St. Louis, MO, USA) were given by gavage. During the experiment, C57BL/6J mice and ApoE KO mice were fed for 6 weeks and 16 weeks before sacrificed respectively. Mice were weighed every week. At the end of the experiment, mice were anesthetized with pentobarbital sodium anesthesia (50 mg/kg of body weight) to surgical procedures to minimize suffering, then the heart was perfused with PBS. At euthanasia, tissues and cecal content were harvested and stored at −80 °C. All animal experiments were carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Authority for Laboratory Animal Care of Institute of Medicinal Biotechnology.

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