Link to USGS home page.
Michigan Water Science Center


Fecal Indicator Bacteria and Sanitary Water Quality

A Little Information About Microorganisms

Microorganisms are found everywhere in our environment. They are common in the air, soil, water and in the habitats of our daily lives. The vast majority of microorganisms do not cause disease. Instead, they maintain the fertility of soil, they degrade wastes in our landfills and compost piles, and they cleanse water of the pollutants we add. We purposefully use some microorganisms to make food (cheese, beer, sauerkraut), we put microorganisms to work in sewage treatment plants, and we use them in biotechnology to produce chemicals.

Naturally some microorganisms have learned to live on or in the human body. Many of these microorganisms do no harm, and are even beneficial because they compete with other microorganisms that might cause disease if they could become established in or on our bodies. The fecal indicator bacteria are such microorganisms; they are normal inhabitants of the gastrointestinal tract of humans and many other warm-blooded animals and in general, they cause no harm.

A few microorganisms (called pathogens) can cause disease in humans. In order to cause disease, a pathogen must successfully invade some part of the body and either produce more of itself or produce a chemical (usually called a toxin) which interferes with normal body processes. Whether or not a pathogen is successful in causing disease is related to the health of the individual and the state of his or her immune system, as well as to the number of pathogen cells required to make the person ill. Some pathogens can cause disease when only a few cells are present. In other cases, many cells are required to make a person ill. Children and elderly persons are more susceptible to many pathogens than are young or middle-aged adults.

Some pathogens live out their lives in the soil and water and only cause disease under unusual circumstances. The microorganism that causes tetanus is an example. This microorganism (a bacterium named Clostridium tetani) lives normally in the soil. Clostridium tetani grows in the body only in deep puncture wounds where air cannot penetrate (termed anaerobic). In this environment it produces a toxin which spreads throughout the body and may cause paralysis. Other pathogens are more closely associated with humans and other warm-blooded animals. These pathogens are transmitted from one organism to another by direct contact, or by contamination of food or water. Many of the pathogens which cause gastrointestinal disease are in this category. Several human gastrointestinal pathogens produce toxins which act on the small intestine, causing secretion of fluid which results in diarrhea. In severe cases, such as cholera, the afflicted person may die from loss of body fluids and severe dehydration. Cells of the pathogen are shed in the feces, and if these cells contaminate food or water which is then consumed by another person, the disease spreads.

It is not unusual to find some fecal indicator bacteria and even some pathogens in natural environments. The organism called Giardia lamblia (a protozoan) is an example. This organism is found in the gastrointestinal system of some wild mammals, and may enter water through the feces of these mammals. The organism causes severe diarrhea in humans. Persons who backpack or hike in wilderness areas are advised to treat all water before drinking, even if it comes from a pristine, clear, cold mountain stream. Therefore, the risk of disease is not uniquely a result of the presence of human wastes in the environment.

Nevertheless, in natural environments, organisms are relatively dispersed, therefore wastes are also relatively dispersed. In addition, natural wastes are composed of compounds natural to that environment and microorganisms in the soil and water can degrade those wastes and recycle them into usable forms. When the quantity or type of waste exceeds the capacity of the microorganisms in soil and water to degrade it, we call the waste pollution. The degradation capacity of microorganisms in soil and water is challenged by extreme amounts of wastes, as well as by unusual (often man- made) or toxic compounds. It is difficult to live in an industrialized and urbanized world and not produce localized concentrations of wastes. When human fecal wastes are concentrated in the environment, we assume, for our own protection, that the risk of transmission of pathogens may increase, even though we may have no direct evidence of the presence of a specific pathogen. It is for this reason that we monitor the quality of our food and water, and establish personal hygiene and public policies that attempt to prevent contamination in the first place.

Answers to Some Common Questions About Bacteria and Water Quality.

How do we monitor the sanitary quality of water?

The fecal indicator bacteria are used to measure the sanitary quality of water for recreational, industrial, agricultural and water supply purposes. The fecal indicator bacteria, as noted above, are natural inhabitants of the gastrointestinal tracts of humans and other warm-blooded animals. These bacteria in general cause no harm. They are released into the environment with feces, and are then exposed to a variety of environmental conditions that eventually cause their death. In general, it is believed that the fecal indicator cannot grow in natural environments, since they are adapted to live in the gastrointestinal tract. Sunlight, temperature, competition with bacteria found naturally in the water, predation by protozoa and other small organisms, and toxic industrial wastes are all believed to influence the survival of fecal indicator bacteria in the water. In addition, some wastes are specifically treated to inhibit the survival of fecal bacteria and pathogens. Studies have shown that fecal indicator bacteria survive from a few hours up to several days in water, but may survive for days or months in sediments, where they may be protected from sunlight and predators. The survival time of fecal indicator bacteria in water is a function of many environmental influences and there is no number that applies to all water bodies, or even to all times of the year for a single body of water. We assume that pathogens die at the same rate as fecal indicator bacteria. Therefore, if we find relatively high numbers of fecal indicator bacteria in the environment, we assume that there is an increased likelihood of pathogens being present as well.

How is the fecal indicator test performed?

The fecal indicator bacteria are cultivated in the laboratory under conditions which encourage their growth, prohibit the growth of non-fecal indicator bacteria, and sometimes, provide special indications of their identity. With current tests, a specific amount of water is passed through a filter, which is then placed on a dish which contains the growth medium hardened into a gel. The test dish (called a Petri dish or Petri plate) is incubated for a specified amount of time at a specified temperature. At the end of the test, each single cell of a fecal indicator bacterium present in the original water will have reproduced sufficiently to produce a visible "colony" of bacteria. To improve the accuracy of the test results, dyes or special compounds may be included in the test growth medium which will result in the fecal indicator bacteria being a different color than any non-fecal indicator bacteria which might grow under the same conditions. Several different tests may be conducted for total coliform bacteria, fecal coliform bacteria, Escherichia coli (E. coli for short), as well as fecal streptococci and enterococci. The total coliform bacteria are defined as "all organisms that produce colonies with a golden-green metallic sheen within 24+2 hours when incubated at 35.0+ 0.5 oC" on a specified growth medium. Fecal coliforms are a subgroup of total coliforms, and Escherichia coli is a particular genus and species of fecal coliform. The enterococci are a subgroup of the fecal streptococci. Slightly different interpretations of water quality may occur based on the test performed. For example, the fecal streptococci are believed to survive longer in water than some coliform bacteria, and may be more associated with animal wastes than with human wastes.

How were recreational water quality standards for fecal indicator bacteria established?

Current guidelines established by the U.S. Environmental Protection Agency (USEPA) result from studies conducted at marine and freshwater beaches in the late 1970's and early 1980's. In 1986, the USEPA recommended that E. coli be used as an indicator of fecal contamination in recreational waters. The standard was set at a geometric mean concentration of 126 colonies per 100 milliliters (mL) of water, which was estimated to be correlated with a gastrointestinal illness rate of about 8 individuals per 1,000 swimmers. How was this determined? Swimmers and non-swimmers were interviewed at freshwater bathing beaches on Lake Erie in Pennsylvania and on Keystone Lake near Tulsa, Oklahoma. Swimming was strictly defined as activity which resulted in all upper body openings being exposed to the water. The beaches had different levels of fecal indicator bacteria. After 8 to 10 days, the swimmers and non-swimmers were interviewed again with regard to symptoms of gastrointestinal or respiratory illness. The prevalence of gastrointestinal or respiratory illness was then compared to the concentrations of E. coli, enterococci and fecal coliforms on the day of swimming, as well as between swimmers and non-swimmers. The conclusion of this study was that E.coli and enterococci showed the strongest relationship with swimming-associated gastrointestinal illness, but fecal coliform densities showed little or no relation to gastrointestinal illness in swimmers. This study serves as a reminder that it is not a simple task to arrive at recreational water quality standards. No single test is infallible or correct for every situation. Individuals use recreational waters in different ways, and are not equally susceptible to disease due to their different behaviors and their prior health conditions. Not every swimmer in these studies suffered gastrointestinal illness.

Why don't we test for the pathogens themselves?

There are many kinds of pathogens that might be transmitted in water. These include bacteria, viruses and protozoa. Each type of bacterium, virus or protozoan requires a different test. Many of these tests are expensive because they require special materials or equipment or are time-consuming. It is impractical to monitor water quality for every pathogen on a routine basis.

What factors lead to high fecal indicator bacteria numbers in recreational waters?

The sources of fecal indicator bacteria include waste waters from sewage treatment plants; other types of sewage inputs such as combined sewer outfalls and drainage from septic tanks; runoff from agricultural fields or feedlots; effluents from food processing plants (especially meats and beverages); and stormwater runoff (which carries animal and bird droppings). The likelihood that fecal indicator bacteria added to the environment by these means will survive to be counted at a given water quality monitoring site is a function of the distance of the site from such sources, and also a function of the effect of all the environmental factors that influence bacterial survival.

An early study (Burm, R.J. and R.D. Vaughan, 1966, Journal of the Water Pollution Control Federation, Vol. 38, pp. 400-409) compared the bacteriological quality of the separate stormwater distribution of the city of Ann Arbor, MI with that of the combined sewer system (specifically Conner Creek drain) of Detroit. Samples were taken over several months. In April, fecal coliform counts were 10,000 per 100 mL in the separate system (Ann Arbor) but 890,000 per 100 mL for the Detroit combined system. By comparison, in August, counts were 350,000 fecal coliforms per 100 mL at the Ann Arbor site, and 4,400,000 per 100 mL at the Detroit site. Fecal streptococci numbers were more similar between the two sites.

The U. S. Geological Survey has conducted several recent studies of fecal indicator bacteria in recreational waters in Ohio, in cooperation with a variety of Ohio State agencies including the City of Columbus Division of Sewerage and Drainage, the City of Akron Public Utilities Bureau, the Summit County Department of Environmental Services, the Ohio Water Development Authority, the Ohio River Valley Water Sanitation Commission, the Northeast Ohio Regional Sewer District and the Cuyahoga River Community Planning Organization. These studies have provided data on fecal indicator bacteria concentrations in selected rivers with respect to concentration, relationship to recreational water-quality standards, and influence of environmental factors such as rainfall, runoff, and wastewater chlorination and dechlorination practices. These studies have determined that fecal indicator concentrations may be highly variable along urban rivers (for example, fecal coliform counts ranged from 20 colonies per 100 mL to 2,000,000 colonies per 100 mL for different sites and sampling dates on the Scioto River in Columbus Ohio), and may exceed recreational water quality criteria even in the absence of significant rainfall. In Ohio rivers, fecal coliform densities and densities of E. coli were highly correlated. Current studies involve the suspension of test bacteria in enclosed but permeable chambers at various sites to determine the influence of treatment practices and environmental factors on their survival. These studies should provide more information on why fecal indicator counts are so variable, and what factors influence this variability.

The U. S. Geological Survey has also collected and published water quality data for the Clinton River at Mt. Clemens since 1975. Both fecal coliform and fecal streptococci numbers were determined on a monthly or quarterly basis, along with data on the chemical quality of the water. As with the Ohio studies, densities varied greatly from one sampling time to another. These data are currently being analyzed to determine if any water chemistry variables may help to explain the bacterial densities.

What are the standards for drinking water?

The USEPA issued revised Primary Drinking Water Standards in mid-1994. These standards address the source water quality, and vary somewhat with the treatment technique used for preparation of the drinking water from the source water. The Primary Standards suggest a presence/absence test for total coliforms. If this test is used, and the sampling agency tests more than 40 samples, no more than 5% of those samples may test positive for total coliforms. If fewer than 40 samples are used, no more than 1 sample may test positive. In addition, maximum contaminant levels, which vary with treatment technique, are specified for Giardia lamblia, Legionella (the bacterium which causes Legionnaire's disease) and viruses. The USEPA Safe Drinking Water Hotline provides more information. That number is 1-800-426- 4791.

USGS Contact:

Sheridan Haack- Project Coordinator
US Geological Survey
6520 Mercantile Way, Suite 5
Lansing, MI, 48911
Phone: 517-887-8909


U.S. Department of the Interior, U.S. Geological Survey logo Water Resources Division, Michigan District
Maintainer: Webmaster (
Last Modified: Wednesday, 04-Jan-2017 10:04:33 EST
Privacy Statement || Disclaimer || FOIA || Accessibility
URL Address: