7 mm probe

At the appropriate time point, the colon was removed from euthanized animals and placed directly in 10 ml PBS in a 50 ml falcon tube. Samples were homogenized using the Tissue Master 125 Lab Homogenizer with 7 mm probe (Omni International, TM125-115) until no chunks of tissue were visible. The homogenizer was rinsed in the following sequential solutions: water, 70% ethanol, water. Adhered tissue was removed and the probe placed in 70% ethanol. The probe was rinsed one final time in water before homogenizing the next sample. One in 10 serial dilutions of the samples were made from 10⁻¹ to 10⁻⁵ and 100 μl of the original sample and its dilutions were plated on selective LB Congo red agar plates and placed at 37 °C. CFUs were counted the following day.

At the appropriate time point, the colon was removed from euthanized animals and placed directly in 6 ml of TRIzol (Thermo Fisher Scientific, 15596026) in a 50 ml falcon tube. Samples were homogenized in TRIzol using the Tissue Master 125 Lab Homogenizer with a 7 mm probe (Omni International, TM125-115). One milliliter of the TRIzol homogenate was placed into a 1.5 ml microfuge tube containing 200 μl of chloroform. Samples were vigorously shaken, incubated at room temperature for 2–3 min, and centrifuged at 12,000 rcf for 10 min. Five hundred microliters of the aqueous (top) phase was placed into a 2.0 ml microfuge tube that contained 500 μl isopropanol and 20 ng/μl glycogen, and mixed by inversion. Samples were stored as a mixture with isopropanol at −20 °C until further processing. The RNA samples in isopropanol were precipitated and washed with 75% ethanol following the TRIzol Reagent User Guide. Samples were resuspended in 100 μl of RNase-free water and stored in 10 μl aliquots at −80 °C.