The Big Four are Aeromonas, Pseudomonas, Flexibacter (Columnaris), and Bacterial Gill Disease.
These four bacteria's far exceed any other bacteria's or illness that fish succumb to. These bacteria can create havoc with your Koi because they are naturally occurring and are present in all waters. There are however, certain temperatures that these bacteria thrive at and multiply at an alarming rate. This time period is called Aeromonas Alley. In summary, within temperature ranges of 47°F to 62°F the aeromonas bacteria run rampant.

Every hobbyist knows that spring is a critical time for Koi. Often the Koi get sick, grow ulcers, develop fin rot and die. After a long winter of fasting, the fish are naturally weak and immunilogically stressed. As the temperature warms up, the fish are slowly adapting to their new environmental conditions. Preying parasites and aeromonas bacteria are growing rapidly, and the stressed fish become their helpless victims. Why then, don't the fish suffer the same consequences in the fall when they are exposed to the same temperature ranges? The reason is that the fish have been building up their immunity all summer and are at the peak of health so they are better conditioned to fight off diseases, besides, the biofilters are also at their optimum, and so the water conditions are at their highest quality.

The general health of the fish and whether or not the fish has been stressed play a big role in whether the bacteria becomes a problem. Highly stressed fish become targets and will come down with a bacterial infection before a less stressed, happier fish. Bacteria can enter the fish by openings made by parasites or when a fish is injured. It is possible for infected fish to also spread disease to others depending on the bacteria involved. Overcrowded ponds are at high risk for Ulcer Disease and the dreaded Bacterial Gill Disease.

When a fish is ill and it’s apparent that the illness is bacterial in nature we often refer to it as Aeromonas. We accuse this bad bacteria for a host of illnesses that other types of bacteria can also create. That's where the Big Four come into play.  Aeromonas and Flexibacter though, are by far the most commonly seen and causes dreaded holes in the skin. What they all have in common is that they all are deadly.  The trick to keeping your koi free of them is preventative measures and clean clean water. These four bacteria's far outweigh KHV or SVC virus's. Wage war on these bad bacteria's before they wage war on your fish!
For a complete article on Flexibacter (Columnaris) click here

Every pond owner with fish, at some time or another, will probably have to medicate their pond.
Though Koi are extremely hardy, it is very important to keep a watch on their environment to keep them at their healthiest. Attention should be paid to the quality of water and balance of the pond (i.e. pH levels etc.). However, if problems do occur, the first step is to remove the individual fish or decide whether to treat the entire pond. It is sometimes difficult to be aware of a problem with a fish until its too late. Be aware of your Koi's behavior patterns so changes can be detected early. A change in your Koi's behavior is usually the first sign that your Koi are stressed or ill.

     Bacteria problems are manifested in several ways. The fins and mouth of the fish may appear to be eaten away. We call this Mouth Rot and Fin Rot, the culprit being more than likely Flexibacter.  Flexibacter Columnaris is also called “Cotton Mouth Disease”. This appears as a cottony growth on the mouth of the fish. Although this may appear to be a fungus, it is not. It is a type of bacterial infection and must be treated as such. A True fungus growth can be, however, an indication that bacterial problems exist. Fungus feeds on dead tissue created by bacterial infection. You can treat for the fungus and still miss the culprit.