9.4: E. coli as a model system

Every surface of your body harbors a flourishing microbial ecosystem. This is particularly true of yourgastrointestinal system that runs from your mouth and esophagus (with a branch leading to your nose), through the stomach, into the small and large intestine and the colon (→).^[381] Each region supports its own unique microbial community, known as its microbiome. These environments differ in terms of a number of properties, including differences in pH and O₂ levels. Near the mouth and esophagus O₂ levels are high and microbes use aerobic (O₂ dependent) respiration to maximize the extraction of energy from food. Moving through the system O₂ levels decrease until anaerobic (without O₂) mechanisms are necessary. Microbes with different ecological preferences and adaptabilities are found at different positions along the length of the gastrointestinal track.^[382]

One challenge associated with characterizing the complexity of the microbiome present at various locations is that the organisms present are often dependent upon one another for growth and survival. When isolated from one another and their normal environment they do not grow. Since the standard way to count bacteria is to dilute samples so that single bacteria land in isolation from one another on an agar plate surface, this can be a problem. When they grow and divide, they form macroscopic (visible) colonies. We count the number of “colony forming units” (CFUs) per original sample volume; this number provides a measure of the number of bacteria capable of growing and dividing. If an organism cannot form a colony under the assay conditions, it will appear to be absent from the population. Many bacteria are dependent on others and do not grow in isolation. Recent studies, however, have found ways to culture more of such organisms.^[383] To avoid many issues, molecular methods use DNA sequence analyses to identify which organisms are present without having to grow them.^[384] The result of these molecular analyses reveal, for the first time, the true complexity of the microbial ecosystems living on and within us.^[385]

Much of the early work in molecular biology was carried out using a relatively minor component of this microbial community, E. coli, a member of the Enterobacteriaceae family of bacteria. E. coli is found in the colons of birds and mammals.^[386] E. coli is what is known as a facultative aerobe, it can survive in both anaerobic and an aerobic environments. This flexibility, as well as E. coli’s generally non-fastidious nutrient requirements make it easy to grow in the laboratory. Moreover, the commonly used laboratory strain of E. coli, known as K12, does not cause disease in humans. That said, there are strains of E. coli, such as E. coli O157:H7, that are pathogenic (disease-causing). E. coli O157:H7 contains 1,387 genes that are not found in E. coli K12 and it is estimated that the two strains diverged from a common ancestor ~4 million years ago. What makes E. coli O157:H7 pathogenic? Sorry, that is beyond our scope here.^[387]

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