Bacteria can be categorized into ‘friendly’ and ‘unfriendly’. Most of the bacteria found in aquariums are harmless, but others are potentially harmful in high densities.

Friendly bacteria include the scavenging, decomposing bacteria digesting uneaten fish food, plant matter, dead algae, and basically everything that consist of organic matter. The nitrifiers also known as "beneficial" bacteria convert ammonia (resulting from bacterial activity, fish waste etc.) into the less toxic compounds of nitrite and nitrate. On rare occasions, denitrifying bacteria can settle in oxygen free areas and transform nitrate into oxygen and nitrogen gas.

‘Unfriendly’ bacteria are summarized as pathogenic, disease causing bacteria.

Pathogenic bacteria are opportunistic, meaning as long as the fish is healthy, it will not be bothered. Some bacteria are present at all times and in a constant fight with the fishs' immune system. A strong immune system allows the survival of the bacteria strain without harming the fish.

Bacterial infections are secondary diseases, they can only prevail if the fish is weakened under stressful conditions (heat, ammonia, nitrite, high organics, low dissolved oxygen etc.), resulting in rapidly multiplying pathogens.

A stressed and weak fish with pathogenic bacteria present results in a bacterial infection, which will be fatal if left untreated. A bacterial infection can therefore be defined as by pathogens outgrowing the defending cells of the immune system.

Any time a bacterial disease occurs adjustments in the aquatic environment need to be made in order to lessen and to eliminate stress causing factors to the fish. Bacterial diseases should be treated with antibiotics, preferably in a quarantine/hospital tank.

Antibiotics function by slowing down the pathogens thus increasing the immune systems efficiency. Nevertheless, it is the immune system that cures the disease not the antibiotic.