MBRA set-up, inoculation, and sample collection

MBRAs were prepared as previously described [18] and as presented in Figure S1. Briefly, this system, housed in an anaerobic chamber, consisted of 24 individual chambers containing 15 mL of Bioreactor Medium (BRM), as described in [18], except that polysorbate 80 (P80) was removed in order to have an emulsifier-free medium, and the 1 g/L of taurocholic acid was replaced with 0.5 g/L of bovine bile added prior to autoclaving. MBRA chambers were held on a magnetic stand for continual homogenization and were connected to two 24-channel peristaltic pumps with low flow-rate capabilities (205S peristaltic pump with 24-channel drive, Watson-Marlow). After autoclaving of the MBRA chambers and tubing, the system was put in place and left in the anaerobic chamber for at least 48 h. Chambers were filled with BRM and subsequently inoculated. For MBRA inoculation, fecal samples were resuspended at 25% w/v in anaerobic phosphate-buffered saline in the anaerobic chamber, vortexed for 5 min, and centrifuged at 200g for 5 min. The supernatant was subsequently collected in the anaerobic chamber and filtered through a 100-μm filter to remove any particles. 3.8 mL of this fecal slurry was used to inoculate each MBRA chamber. After inoculation, fecal bacteria were allowed to equilibrate for 16 h prior to initial sample collection (time 0 sample, Figure S1C) and flow initiation at 1.875 mL/h (8-h retention time). Four hundred microliters of samples was then collected as presented in Figure S1C (0 h, 24 h, 48 h, 72 h, 74 h, 77 h, 80 h, 96 h, 108 h, 120 h, 144 h, 168 h, 192 h, 216 h, 240 h, 264 h, and 274 h), with emulsifier treatment occurring between 72 and 216 h post-inoculation, as described below. Samples were stored at − 80 °C until further processed.