Good question, and no one really knows for sure. The ammonia produced by certain bacteria is likely to change the environment for other bacteria.
Keep in mind that our bodies are continually reingesting/recycling urea in the gut anyway.
The liver turns excess ammonia into urea, and some ends up released in sweat (moisturising, selecting agent for microbes that grow on skin); saliva (hold moisture); urine; and some is even released into our gut.
In the gut, certain microbes produce the enzymes needed to digest urea - and break it down into amino acids and ammonia. This gives us a source of amino acids like glycine and lysine, and is useful particularly for people on low protein diets. Glycine is necessary for the liver to detoxify the blood. The excess ammonia is absorbed back into the body, whereupon the liver once again converts it to urea.
Many of the bacteria that like urea are considered beneficial, and may prefer a high pH environment. One study (on renal failure patients) showed that treatment with lactulose (lowers pH in a segment of the colon) was able to stop bacteria from consuming urea. Pathogens like urea too e.g. helicobacter pylori (hence the urea breath test). The lactic acid bacteria don't consume urea, and like a lower pH (acidic) environment.
It does sound almost as though in doing urine therapy, one is supporting the urea-splitting bacteria over the lactic acid bacteria. There's not much research on how supplemental urea in humans alters the bacterial population; then again most research on bacterial population shows that it takes a long time to significantly alter things with diet alone.