CALS Farm and Industry Short Course Program: Farm Microbiology: Archived Lecture Notes

General Survey of Important Prokaryotes (Bacteria and Archae)

  1. Overview of some of the important groups: SEE TABLE on special page. 

  2. Some special notes (comments, additions, etc.) concerning the organisms on the table: 

    1. The Enteric Bacteria ("enterics").  Many live in the intestinal tracts of animals – hence the name "enteric" – but there are many with close genetic ties that are free-living in the environment. (This group consists of Escherichia coli and its relatives.)

    2. What are coliforms? 

      Lactose-fermenting (to
      acid & gas) strains of:
         Escherichia coli

      1. Definition of term.  These are defined as "gram-negative, facultatively anaerobic bacteria that can ferment lactose rapidly to acid and gas at 35°C." (The most precise definitions indicate that coliforms do this in media that select against gram-positive bacteria and include a Durham tube to indicate hydrogen gas production.)

      2. Detection – taking advantage of coliforms' gram-negativity and ability to ferment lactose.  This makes them somewhat easy to detect with the use of a broth medium designed to inhibit gram-positive bacteria and also to detect (with a Durham tube) insoluble gas from lactose fermentation. (Details of detection, isolation and identification can be gone over in lab.)

      3. Importance of coliforms. 

        1. Indicators of possible health hazards.  Coliforms are good indicator organisms that abound in intestinal waste and soil; it is easier to look for these bacteria than to spend time and money looking for all of the real individual problems – i.e., specific pathogens and other hazards associated with fecal pollution and environmental contamination – in food, water and other consumable items. Finding E. coli in a sample implicates that sample as having been fecally polluted, and there is a possibility of intestinal pathogens also being present which could be any number or combination of bacteria, viruses and protozoa. Other coliforms – if found in drinking water – can implicate surface soil runoff into the well which can carry various chemical and biological hazards.

        2. Importance in some food fermentations.  The first stage in the sauerkraut fermentation involves the activity of coliforms – usually a strain of Klebsiella or Enterobacter – that begins the fermentation of the sugar in the cabbage tissue, leading to production of acid which increases with subsequent, successive populations of certain species of lactic acid bacteria. There is more about food fermentations in Section 5.

        3. Importance in soil.  Klebsiella pneumoniae is a common inhabitant of soil and many (if not most) strains can fix nitrogen. (More about soil organisms in Section 4.)

        4. Pathogenicity.  Klebsiella pneumoniae is also one of the causes of bacterial pneumonia. Some strains of E. coli can cause severe intestinal disease. Many coliforms (and other enterics) can be opportunistic pathogens which cause a problem only when introduced into an area (not their usual habitat) where they could cause some damage – e.g., E. coli in eyes or urinary tract and Enterobacter in the blood stream. (More about infectious diseases in Section 6.)

    3. Escherichia coli (good old E. coli). 

      1. Habitat.  Regular inhabitant of the intestine of humans (and found in no environments that are not fecally-contaminated).

      2. Use as indicator organism.  Used by public health authorities as an indicator of fecal pollution of drinking water supplies, swimming beaches, foods, etc.

      3. Use as experimental organism.  The most studied of all organisms in biology because of its occurrence, and the ease and speed of growing the bacteria in the laboratory. It has been used in countless experiments in cell biology, physiology, and genetics.

      4. Close relationship to Shigella.  If E. coli and the four species of Shigella were to be discovered today – instead of having been studied more or less separately throughout the 20th century – they would undoubtedly be placed in one species due to the extreme similarity of their DNA. Some strains of E. coli are very Shigella-like in their capability of causing intestinal disease, and sometimes it is very difficult to identify a strain one way or the other.

      5. Pathogenicity of E. coli.  One serotype – O157:H7 – is notorious in that it keeps turning up in raw hamburger headed for fast-food restaurants. Most strains can be considered non-pathogenic unless they get into places where they are not normally found – e.g., infections of the urinary tract caused by E. coli are fairly common. Organisms such as this are termed opportunistic pathogens. (Serotypes are one way to divide up species as indicated below; this is important in defining specific kinds of Salmonella and E. coli. Strains are simply pure cultures derived from various natural sources – soil, water, food, infected patients, etc.)

    4. What is a serotype? 

      1. For precise identification and epidemiology.  This is a way in which an organism can be identified more precisely than as a species. It could be analogous to classifying humans according to blood type. Important in epidemiology in that the finding of the same serotype among persons suffering from a certain disease – as well as in other things such as food products – can help to define the epidemic and to assist in determining the common source of the infection.

      2. O and H antigens.  An antigen is something that – when injected into a human or higher animal – causes the production of a matching antibody. Enteric bacteria and many other bacteria have antigens associated with the cell wall (O antigens) which are made up of polysaccharides. Each different antigen that has been found is given a certain number. There are also antigens associated with the flagella (H antigens) that are made up of amino acids, and each different one is given a certain letter or number.

      3. Examples.  For the following table, the O antigens are in red and the H antigens are in blue. Many serotypes of Salmonella have been given convenience names which are often written out like genus and species; for example, organisms with the antigenic formula shown below are commonly called Salmonella typhimurium. However, modern convention tends to follow this form: Salmonella enterica ser. Typhimurium. (There is more about serotypes on our Salmonella page, and the genus and species concept is briefly reviewed here.)

      genus and species example of serotype designation
      (the "antigenic formula")
      Salmonella enterica 1,4,5,12:i:1,2
      Escherichia coli O157:H7

    5. The Lactic Acid Bacteria ("lactics").  Named after the fact that lactic acid is the main end product of fermentation. Important in various food fermentations (sausage, sauerkraut, cheese, yogurt, etc.)

    6. The Pseudomonads. 

      1. Application of name.  Name applied to the genus Pseudomonas and certain other genera that are much like Pseudomonas morphologically and physiologically.

      2. Importance in the environment.  Most pseudomonads are free-living organisms in soil and water; they play an important role in decomposition, biodegradation, and the carbon and nitrogen cycles. They are a very diverse group of Gram-negative rods with a strictly respiratory mode of metabolism.

      3. Pathogenic importance.  Pseudomonas aeruginosa is the quintessential opportunistic pathogen; it is a leading cause of hospital-aquired infections and is quite resistant to a variety of antibiotics. Pseudomonad-like pathogens include Brucella (cause of brucellosis in cattle, sheep and related animals) and Bordetella (B. pertussis is cause of whooping cough in humans).

    7. Antibiotic-producing bacteria. 

      1. Many species of Streptomyces.  One of the most common organisms in the soil and various species are responsible for most the the antibiotics in use today.

      2. Some species of Bacillus and other genera. 

      3. From isolation of organism to production of antibiotic. 

    8. A couple bioterrorism concerns (mentioned earlier). 

      1. Yersinia pestis.  Causes pneumonic plague and bubonic plague. Enough in an aerosol can infect many.

      2. Bacillus anthracis.  Causes anthrax. Aerosol of concentrated spores can get into lungs (causing pulmonary anthrax – usually fatal) or collect on food or objects (causing severe intestinal and skin infections). Spores can exist for considerable amount of time and can each readily germinate into a vegetative cell. Various devices to detect endospores and/or B. anthracis DNA are being worked on these days.

Archived Lecture Notes: Previous Section,  Next Section.
Farm Microbiology Home Page.
CALS Farm and Industry Short Course Home Page.
Bacteriology Department Web Site.

Page last modified on
3/14/05 at 3:45 PM, CST.
John Lindquist, Dept. of Bacteriology,
University of Wisconsin – Madison