FIGURE A2.

Whole tissue digestion is required to isolate all bacteria. Two matched biopsies (~5 mm) were washed in PBS, after which DNA of the Biopsy wash and the Biopsy was isolated separately. For every DNA isolate, a duplicate was run, of which each value is plotted relative to the mock community (ΔCt). Paired t‐tests revealed that DNA from the biopsy isolates contained a similar bacterial fraction, albeit with fewer Bacteroidetes and more Actinobacteria. Hence, whole tissue digestion is required to analyze the complete bacterial component of the tissue