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Prebiotics and probiotics are both aimed at maintaining healthy colonies of beneficial bacteria in our gastrointestinal (GI) tracts. Our bodies are veritable smorgasbords for a vast range of bacteria, helminths, protozoa, viruses and yeasts. But it is not all bad. Our relationship with many of the bacteria that colonize the GI tract of our digestive system is a type of symbiosis called mutualism. This means that both sides benefit and prosper from the interaction. These are the "good bacteria" we hear about a lot these days, particularly in advertisements for prebiotic and probiotic products; they are often referred to as intestinal flora.

Although the ultimate goal is the same, the approach taken by prebiotics and probiotics is completely different, but not exclusive. In many situations they will be most effective used in conjunction with each other.

Prebiotics might be thought of as dietary supplements for bacteria. They contain carbohydrates that these bacteria need but our bodies generally do not. Such substances may be limited in our normal diets, although they are found in high fiber foods like bananas, onions, tomatoes and whole wheat. When they are in short supply it limits the growth rate and functionality of bacterial colonies, reducing the benefits they can supply our bodies. By supplying these resources, prebiotic products remove those limitations, so a bacterial colony can flourish and function to its full capabilities.

Probiotic products, on the other hand, supply the bacteria. Instead of feeding the bacterial colonies already present in the GI tract, they bring in more good bacteria to boost the numbers. These products are often yoghurts for this reason, as yoghurts are very good transport mediums for bacteria.

In exchange for what to them is a nice environment to live in, usually with ample food, these beneficial bacteria perform two main services: digestive and protective. To get their own energy and nutrients they break up organic molecules into smaller ones. Often our bodies do not produce enzymes or digestive juices capable of doing this, especially for some of the plant organic molecules in our food. But we can digest the derivatives left after bacteriological action or those might already be small enough to be absorbed through our intestinal walls. Plant materials can be particularly tough on animal digestive systems, which is why ruminant herbivores such as cows are completely dependent on the bacteria providing this service

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