Supplemental Figure 4.

Bacterial 16S quantification and bacterial viability in extracts. A) Quantification of 16s rRNA concentration using broad range 16S qPCR in bacterial extracts derived from lower SI segments from conventionalized (Conv) mice harbouring a complex microbiota or germ-free (GF) mice (n = 2–6). B) Colony Forming Unit (CFU) counts from viable bacteria present in sonicated and non-sonicated lower SI extracts cultivated in BHI agar. C) CFU counts of viable bacteria obtained from sonicated or non-sonicated SI extracts that underwent spore germination with ethanol shock and were cultivated in BHI supplemented with rumen fluid. Identification of bacterial colonies was done using MALDI-TOF spectrometry.