Researchers Document Impact of Coffee on Bowels [sciencedaily.com]:
Coffee has long been known to increase bowel movement, but researchers have not pinpointed the specific reason or mechanism. Researchers examined changes to bacteria when fecal matter was exposed to coffee in a petri dish, and by studying the composition of feces after rats ingested differing concentrations of coffee over three days. The study also documented changes to smooth muscles in the intestine and colon, and the response of those muscles when exposed directly to coffee.
The study found that growth of bacteria and other microbes in fecal matter in a petri dish was suppressed with a solution of 1.5 percent coffee, and growth of microbes was even lower with a 3 percent solution of coffee. Decaffeinated coffee had a similar effect on the microbiome.
After the rats were fed coffee for three days, the overall bacteria counts in their feces were decreased, but researchers said more research is needed to determine whether these changes favor firmicutes, considered "good" bacteria, or enterobacteria, which are regarded as negative.
Muscles in the lower intestines and colons of the rats showed increased ability to contract after a period of coffee ingestion, and coffee stimulated contractions of the small intestine and colon when muscle tissues were exposed to coffee directly in the lab.
NOTE: Original is at Digestive Disease Week [ddw.org], but Javascript is required to view it. Also available at EurekAlert [eurekalert.org].
Further avenues of research that immediately came to my mind:
Time to start conducting interviews of Starbucks' baristas.