Here is an interesting study. Using men from the intervention arm of the Ugandan RCT, the researchers studied the microbiological flora of the penis before and after circumcision.
The researchers found that there was a significant change in the types of bacteria found on the penis. In particular, the number of anaerobic bacteria fell significantly following circumcision.
The discovery that circumcision alters the penile flora is nothing new. Many studies have investigated this previously (for an overview see refs 12-22 in my letter here), and have come to similar conclusions.
The authors speculate that the presence of anaerobic bacteria on the uncircumcised penis might promote inflammatory conditions which activate immune cells that, in turn, act as a magnet for HIV.
It also, of course, helps to explain the fact that circumcised males enjoy reduced risk of urinary tract infections and local infections such as balanitis.