There are a few published articles. From these and from in house studies it is clear that Caffeine consumption impacts the gut micro biome. A general increase in Bifidobacteria has been found in some studies but some of the results are conflicting,

try the following for starters -also there is some information to be found in the diabetes literature.

Cowan TE, et al J Nutr Biochem. 2014 Apr;25(4):489-95.doi: 10.1016/j.jnutbio.2013.12.009.

Ludwig IA, et al Biofactors. 2013;39(6):623-32. doi: 10.1002/biof.1124.

Jaquet M,Ret al Int J Food Microbiol. 2009 Mar 31;130(2):117-21. doi: 10.1016/j.ijfoodmicro.2009.01.011.

Thanks a lot Doctor Elaine Holmes.

Maybe the following papers will help you:

The answer is Yes! Higher caffeine consumption is associated with increased richness and evenness of the mucosa-associated gut microbiota, and higher relative abundance of anti-inflammatory bacteria, such as Faecalibacterium and Roseburia and lower levels of potentially harmful Erysipelatoclostridium.

Article Caffeine Consumption and the Colonic Mucosa-Associated Gut M...