In vitro experiments using mouse intestinal epithelial cells (MODE-K cells)

Mouse intestinal epithelial cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM), with 2 mM L-glutamine and 1 mM sodium pyruvate. DMEM was supplemented with 10% FBS, 1% (v/v) glutamine, penicillin–streptomycin, and 1% HEPES. To determine if bacteria regulated gene expression, a confluent monolayer of cells was incubated with a 1:1 mixture of penicillin–streptomycin-free DMEM and CFS collected from either cultured Clostridia consortia or Desulfovibrio species for 4 hours. The media was then aspirated and cells were placed in 600 μL of RiboZol (VWR) for later analysis.