Food and water can carry pathogenic microbes so water supplies and foods should be checked regularly for possible contamination. States have determined permissible limits; but the identification of all microbes on a routine basis is too costly and not practical. Therefore, microbiologists have identified certain organisms as indicator species.

The clarity of the water is an important factor in the growth of algae in the water. Microbiologists can determine much about the water by routine observation of the species of algae present in the water. In addition bacteria called coliforms (found in intestines of animals) are the most significant microbe related to declaring food and/or water contaminated and unsafe. Coliforms are described as aerobic gram-negative bacilli that lack endospores and are capable of fermenting lactose. Examples of coliforms include E. coli, Klebsiella, Enterobacter, Hafnia, Serratia, Citrobacter, and others. The presence of these coliforms in food indicates unsanitary processing, handling, or storage of the food. Other microbes in water that indicate unsafe water include bacteria like fecal Streptococcus and Vibrio; protozoans such as Giardia and Crytosporidium; and Norwalk viruses.

The methods for confirming the presence and number of indicator species in water are explained in the Standard methods for the Examination of Water and Wastewater. Sterile sampling bottles are used; and the water must be refrigerated and analyzed with 6-12 hours if possible. Procedures used to count or estimate the number of microbes (bacteria) include standard plate count (SPC), membrane filtering (MF), and most probable number method (MPN). Presumptive tests are completed and confirmatory tests used to verify the presence of pathogens. Differential broths and solid media are used in some of the determinations. The final observation of stained microbes may complete the identification process. It is desirable that the potable (drinking) water have less that 4 coliforms per 100 mls of city water and less than 200 per 100 mls of swimming and fishing waters; coliform counts over 1000 per 100 mls of water will require that the Health Department prevent any use of the water related to possible human consumption.