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Fermentations of Importance to Humans

©2000 Timothy Paustian, University of Wisconsin-Madison

For millenia humans have taken advantage of the fermentations microbes perform. Over the years we have learned to control and optimize theses fermentations through trial and error. It was only in the last 100 years that the biochemistry behind fermentation has become clear.

In this section we take a little time off from the serious study of metabolism to look at the production of products we're all familiar with.

Several of the fermented products we consume depend upon yeast fermentation of glucose to ethanol as we just discussed in the section of fermentation.

Brewing Beer

Beer is a fermentation of barley and hops by yeast. The starch in barley is broken down into glucose and then fermented to ethanol by yeast. The finish product is aged and then packaged for distribution and consumption. It is an involved six stage process, beginning with the formation of malt from barley.

  1. Malt - Barley is first soaked in water for 5 to 7 days. At this time the grain germinates and produces amylases (enzymes that degrade starch to glucose) and proteases (enzymes that break down proteins). These enzymes are essential to the brewing process. Amylase provides sugar for the yeast fermentation and the proteases solubilize compounds in the grain and hops important for the quality of the beer. The germinated malt is then dried and crushed.

  2. Mash - Mashing solubilizes the starch and other flavors in the grain and extracts flavors and preservatives for the beer. The prepared malt is suspended in water mixed with boiled malt adjuncts (other grains, carbohydrates and sugars that provide a source of starch to be converted to sugar). This mash is then incubated at 65-70°C for a short time to allow the amylase to break down the starch to glucose. The temperature is raised to 75°C to inactive the enzymes and then allowed to settle. Insoluble matter sinks to the bottom and serves as a filter as the liquid (now called wort) is taken from the container.

  3. Boiling with Hops - Hops and wort are combined and boiled for 2.5 hours. The liquid is removed and ready for fermentation. Boiling with hops serves several purposes -

    • Concentration

    • Sterilization, killing many microbes that might spoil the beer

    • Further inactivation of enzymes in the mash.

    • Solubilization of important compounds in the hops and mash. Some of these add to the flavor of the beer while others, especially from the hops, have antiseptic qualities and help preserve the beer.

  4. Fermentation - Fermentation begins by adding the brewers yeast Saccharomyces carlsbergensis to the wort. The starter culture is usually obtained from a previous batch of beer and is added at a very high concentration (500 grams per 120 liters). Fermentation is at a low temperature between 3.3 and 14°C for 8 to 14 days. At this time the glucose in wort is converted to ethanol and CO2. Other compounds in the wort are also fermented to add to the characteristic flavor of beer.

  5. Aging - The fermented wort (green beer) is aged at 0 °C for a period of weeks or months depending on the brewer. At this time the yeast settle to the bottom of the vessel, bitter flavors are mellowed and other compounds are formed that enhance flavor.

  6. Finishing - The beer is now prepped for packaging. This can involve filtering, pasteurization, carbonation to 0.45 to 0.52% CO2, and clarification. All of these processes depend upon the beer being made and each brewery will specialize the fermentation, aging and finishing of their beer. This is often the inspiration for various advertising done by the brewery.

The beer is then put in containers and distributed to customers. Beer normally has a shelf life of about 6 months and after that starts to take on undesirable flavors.


Bread is a simple fermentation of sugar to CO2 and alcohol. The baker first combines flour, sugar, milk and other ingredients with a microorganism, usually a bread yeast such as Saccharomyces cerevisiae, but not always. The ingredients are mixed and then allowed to incubate at 27°C for a few hours. During this time the yeast convert the sugar present to ethanol and CO2. Most incubations are for less than 4 hours not leaving enough time for the yeast to increase in number. The CO2 produced causes the bread to rise (leaven) and become porous. The success of leavening is dependent upon the rate of gas production. This can be increased by adding more yeast, more sugar, or dough conditioners (various salts that the yeast need). Tweaking a recipe by manipulating these factors can speed CO2 production, within reasonable limits. Adding too much of anything can either kill the yeast or cause the bread to rise too quickly. The temperature of incubation is another critical consideration. Saccharomyces grows best at 26 to 28°C and deviations from that temperature will usually result in slow or complete lack of leavening. Failure as a baker can normally be attributed to either not adding the exact amounts of ingredients or inappropriate incubation temperatures during leavening.


Yogurt is a product of fermented milk. Lactic acid bacteria are the major microbes in many milk based fermented products. These bacteria are finicky having many growth requirements all of which can fortunately be satisfied by a milk mixture. Lactose in milk is fermented to lactic acid either via the homofermentative or heterofermentative pathway.

Production of yogurt starts by conditioning the milk. The water content of milk is first lowered 25% by vacuum evaporation and 5% milk solids are added. As a final conditioning step, the milk is heated to 86 to 93°C for 30-60 minutes. This causes some breakdown of proteins and other molecules and kills contaminating microbes that may compete with the starter culture. After cooling to 45°C a 1:1 mixture of Streptococcus thermophilus and Lactobacillus bulgaricus is added. Fermentation is at 45°C until the desired degree of acidity is reached. This usually occurs in 3-5 hours. The finished product may have other ingredients added (such as mold inhibitors or dye) and is packages with fruit. Yogurt is stored at 0-4°C until consumed to prevent spoilage.

There is some evidence that consumption of products containing active cultures of lactic acid bacteria can be beneficial. However, the health claims by proponents of this idea have yet to withstand serious scientific scrutiny. It is reasonable to assume that ingesting lactic acid bacteria may help deter other more sever pathogens such as E. coli or Salmonella typhimurium


Cheese is also a milk fermentation, but its production is more complex. Different bacteria come into play and production periods are much longer than yogurt. Despite there being 20 classes and hundreds of varieties of cheeses the initial manufacturing process is surprisingly similar.

  1. Curd Formation - Milk is first pasteurized and then fermented by a starter culture. This is usually a lactic acid bacteria with the specific species in use dependent upon the cheese being produced.

    Rennet (a protease) is added to the fermentation and along with the lactic acid made by the added starter, causes the milk to form curds.

  2. Curd Concentration - depending upon the cheese being made, the curds may be concentrated in some manner. The goal here is to remove the appropriate amount of whey (liquid left from curd formation). For fresh cheeses (cottage or mozzarella) no concentration takes place. For soft cheeses the curds are cut into large cubes and then ripened with a fungus or mold. Hard and semi-hard cheeses are cooked and then cut into small pieces to release more whey.

  3. Ripening - prepared curd is then pressed into molds, salted and ripened for weeks to years. This process if different for each cheese.

The finished product is sold either as a complete mold (a wheel of cheese) or cut into smaller pieces. Most cheeses are stored at refrigerator temperatures.

Other Products

We have only touched on a few foods that are made with the help of microbes, there are many more. To give you an idea of the array of products, here is a list of fermented foods and the microbes that are involved in their formation.

Table 1. Some of the many fermented foods produced around the world
Foods and ProductsRaw IngredientsFermenting OrganismsCountry Commonly Produced in
Dairy Products
KefirMilkStreptococcus lactis, Lactobacillus bulgaricus, Torula sp.Southwestern Asia
TaetteMilkS. lactis var. taetteScandinavian peninsula
TarhanaWheat meal and yogurtLacticsTurkey
Meat and fish products
Country-cured hamPork hamsAspergillus, Penicillium spp./Southern U. S.
Lebanon bolognaBeefPediococcus cerevisiaeEurope, U.S.
Fish saucesSmall fishhalophilic Bacillus spp.Southern U. S.
KatsuobushiSkipjack tunaAspergillus glaucusJapan
Nonbeverage plant products
Cocoa beansCacao fruitsCandida krusei, Geotrichum spp.Africa, South America
Coffee beansCoffee cherriesErwinia dissolvens, Saccharomyces spp.Brazil, Congo, Hawaii, India
KimchiCabbage and other vegetablesLactic acid bacteriaKorea
OlivesGreen OlivesLeuconostoc mesenteroides, Lactobacillus plantarumWorldwide
PicklesCucumbersPediococcus cerevisiae, Lactobacillus plantarumWorldwide
Bourbon whiskyCorn, ryeSaccharomyces cerevisiaeU. S.
CiderApples, other Saccharomyces spp.Worldwide
MezcalCentury plantYeastsMexico
SakeRiceSaccharomyces sakiJapan
VinegarCider, wineAcetobacter spp.Worldwide
WineGrapes, other fruitsSaccharomyces ellipsoideus strainsWorldwide

Fermentation of organic substrates is one way to make a living, but it is a poor choice. Energy yields are low and microbes have to ferment large amounts of substrate to get enough energy for cellular processes. Anaerobes were probably the first microbes to evolve billions of years ago, but once oxygen became prevalent in the atmosphere, a better method of catabolism evolved, respiration.

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