Quantitative RT-PCR detection of the in vivo effect of coffee on the total microbiota and different groups of microbes in the ileum. Coffee (Coff) or decaffeinated coffee (Dec) (250 mg in 2 mL water) was administered by oral gavage daily for 3 days. Sham rats were treated similarly, but with 2 mL of saline. Rats were euthanized 3 days later. The intraluminal contents from the ileum were collected. The total microbiota (A) and compositions of different groups (B) of microbes (Enterobacteria, Gammaproteobacteria, Lactobacillus, and Firmicutes) relative to overall microbiota (universal) were determined by real time PCR assays. N = 6 or 5 rats in each group. Sham (Sh). Coff, regular coffee; Dec, decaffeinated coffee.