Bacteria are the most common cause of contamination for mushroom cultures. These one-celled microorganisms are a continuous danger for the mushroom. They compete with the mycelium for the nutrient soil. Surely in its early stage the mycelium is very weak and often not resistant to aggressive bacteria. This is why sterilizing is so important, so that all the bacteria are killed.
If the substrate is totally colonized, it's a little less vulnerable to the bacteria. The mycelium is then strong enough to mosly dominate the bacteria. This is however no reason to be less careful with the hygienic rules.
Bacteria in the substrate may apear in all sorts of colors. The most common colors are yellow, orange, black and green.