Without friendly probiotics, the final stage of digestion can't take place in the colon. Debris rots in there. Opportunistic bacteria and Candida albicans start taking over. Bernard Jensen , on the relation between the bad bacteria and the undigested food:

"...bacteria and viruses, which are cell scavengers, are not there for lack of something better to do. They're there because there is malnourished, enzyme-depleted, diseased, and necrotic tissue. Functioning as nature's biological sanitation department, they must break down and eliminate the sick tissue to prevent further poisoning of the body. If you stop their action, you allow continuous poisoning by the decaying tissue "
- Empty Harvest p 113

Jensen makes a point here that should not be missed. He's talking about rotting food in the colon as well as diseased living cells of the colon itself, both attracting bacteria. It's an identical situation in the two separate instances:

Undigested food in the colon


Bacterial infection in a diseased organ of the body (the colon)


In neither case are the bacteria causing illness. They are trying to prevent illness by breaking down the dying tissue. Whether it's rotting yogurt in a blocked colon, a dead coyote in the forest, or infected liver cells in the body of an alcoholic, bacteria are just doing what they do best: cleaning up. When the bacteria are "diagnosed" as the cause of the illness, rather than a sign of the illness, the medical approach is to try and kill them. But that's like killing the garbagemen. The garbage remains. Understanding such a simple concept is pivotal in arriving at a holistic outlook toward health.

Chronically undigested food is often present in quantities too great for any bacteria to scavenge. The debris then becomes plastered onto the inside lining of the colon, eventually making it smooth and shiny, like the inside of a new shotgun barrel. When this happens, absorption is blocked. (Rogers)

The Doctor Within