Sourdough bread is made by the fermentation of dough using naturally occurring lactobacilli and yeast. Sourdough bread has a more sour taste and better inherent keeping qualities than breads made with baker's yeast, due to the lactic acid produced by the lactobacilli. 
Sourdough is a dough containing a Lactobacillus culture in symbiotic combination with yeasts. It is one of the principal means of biological leavening in bread baking, the others using cultivated forms of yeast.
In the Encyclopedia of Food Microbiology, Michael Gaenzle writes: "The origins of bread-making are so ancient that everything said about them must be pure speculation. One of the oldest sourdough breads dates from 3700 BCE and was excavated in Switzerland, but the origin of sourdough fermentation likely relates to the origin of agriculture in the Fertile Crescent several thousand years earlier ... Bread production relied on the use of sourdough as a leavening agent for most of human history; the use of baker's yeast as a leavening agent dates back less than 150 years." 
Generally however they do not heat it up at all, but only use the dough kept over from the day before; manifestly it is natural for sourness to make the dough ferment... (Nat. His. 18:26 §104) 
Bread made from 100% rye flour, popular in the northern half of Europe, is usually leavened with sourdough. Baker's yeast is not useful as a leavening agent for rye bread, as rye does not contain enough gluten. The structure of rye bread is based primarily on the starch in the flour, as well as other carbohydrates known as pentosans; however, rye amylase is active at substantially higher temperatures than wheat amylase, causing the structure of the bread to disintegrate as the starches are broken down during cooking. The lowered pH of a sourdough starter, therefore, inactivates the amylases when heat cannot, allowing the carbohydrates in the bread to gel and set properly.  In the southern part of Europe, where panettone was originally made with sourdough,  sourdough has become less common in recent times; it has been replaced by the faster-growing baker's yeast, sometimes supplemented with longer fermentation rests to allow for some bacterial activity to build flavor.
French bakers brought sourdough techniques to Northern California during the California Gold Rush, and it remains a part of the culture of San Francisco today. (The nickname remains in " Sourdough Sam", the mascot of the San Francisco 49ers.) Sourdough has long been associated with the 1849 gold prospectors, though they were more likely to make bread with commercial yeast or baking soda.  The "celebrated"  San Francisco sourdough is a white bread characterized by a pronounced sourness, and indeed the strain of Lactobacillus in sourdough starters is named Lactobacillus sanfranciscensis, alongside the sourdough yeast Candida milleri found in the same cultures. 
The sourdough tradition was carried into Alaska and the western Canadian territories during the Klondike Gold Rush of 1898. Conventional leavenings such as yeast and baking soda were much less reliable in the conditions faced by the prospectors. Experienced miners and other settlers frequently carried a pouch of starter either around their neck or on a belt; these were fiercely guarded to keep from freezing. However, freezing does not kill a sourdough starter; excessive heat does. Old hands came to be called "sourdoughs", a term that is still applied to any Alaskan or Klondike old-timer.  The significance of the nickname's association with Yukon culture was immortalized in the writings of Robert Service, particularly his collection of " Songs of a Sourdough".
In English-speaking countries, where wheat-based breads predominate, sourdough is no longer the standard method for bread leavening. It was gradually replaced, first by the use of barm from beer making , then, after the confirmation of germ theory by Louis Pasteur, by cultured yeasts.  Although sourdough bread was superseded in commercial bakeries in the 20th century, it has undergone a revival among artisan bakers. 
The preparation of sourdough begins with a pre-ferment (the "starter" or "leaven", also known as the "chief", "chef", "head", "mother" or "sponge"), a fermented mixture of flour and water, containing a colony of microorganisms including wild yeast and lactobacilli.  The purpose of the starter is to produce a vigorous leaven and to develop the flavour of the bread. In practice there are several kinds of starters, as the ratio of water to flour in the starter (hydration) varies. A starter may be a liquid batter or a stiff dough.
Flour naturally contains a variety of yeasts and bacterial spores.   When wheat flour comes into contact with water, the naturally occurring enzyme amylase breaks down the starch into the sugars glucose and maltose, which sourdough's natural yeast can metabolize.  With sufficient time, temperature, and refreshments with new or fresh dough, the mixture develops a stable culture.   This culture will cause a dough to rise if the gluten has been developed sufficiently.  The bacteria ferment starches that the yeast cannot metabolise, and the byproducts, chiefly maltose, are metabolised by the yeast which produces carbon dioxide gas, leavening the dough.      [note 1]
Obtaining a satisfactory rise from sourdough takes longer than a dough leavened with baker's yeast because the yeast in a sourdough is less vigorous.   In the presence of lactic acid bacteria, however, some sourdough yeasts have been observed to produce twice the gas of baker's yeast.  The acidic conditions in sourdough, along with the bacteria also producing enzymes that break down proteins, result in weaker gluten and may produce a denser finished product. 
As it ferments, sometimes for several days, the volume of the starter is increased by periodic additions of flour and water, called "refreshments".  As long as this starter culture is fed flour and water regularly it will remain active.   
The ratio of fermented starter to fresh flour and water is critical in the development and maintenance of a starter. This ratio is called the refreshment ratio.   Higher refreshment ratios are associated with greater microbial stability in the sourdough. In San Francisco sourdough, the ratio  is 40% of the total weight, which is roughly equivalent to 67% of the new-dough's weight. A high refreshment ratio keeps acidity of the refreshed dough relatively low.  Acidity levels of below pH 4.0 inhibit lactobacilli and favour acid-tolerant yeasts.
A starter prepared from scratch with a salted wheat-rye dough takes about 54 hours at 27 °C (81 °F) to stabilise at a pH between 4.4 and 4.6.  4% salt inhibits L. sanfranciscensis, while C. milleri can withstand 8%. 
A drier and cooler starter has less bacterial activity and more yeast growth, which results in the bacterial production of more acetic acid relative to lactic acid. Conversely, a wetter and warmer starter has more bacterial activity and less yeast growth, with more lactic acid relative to acetic acid.  The yeasts produce mainly CO2 and ethanol.  High amounts of lactic acid are desired in rye and mixed-rye fermentations, while relatively higher amounts of acetic acid are desired in wheat fermentations.  A dry, cool starter produces a sourer loaf than a wet, warm one.  Firm starters (such as the Flemish Desem starter, which may be buried in a large container of flour to prevent drying out) tend to be more resource-intensive than wet ones.
A stable culture in which L. sanfranciscensis is the dominant bacterium requires a temperature between 25–30 °C (77–86 °F) and refreshments every 24 hours for about two weeks. Refreshment intervals of longer than three days acidify the dough and may change the microbial ecosystem. 
The intervals between refreshments of the starter may be reduced in order to increase the rate of gas (CO2) production, a process described as "acceleration."  In this process, the ratio of yeasts to lactobacilli may be altered.  Generally, if once-daily refreshment-intervals have not been reduced to several hours, the percentage amount of starter in the final dough should be reduced to obtain a satisfactory rise during proof. 
Faster starter processes, requiring fewer refreshments, have been devised, sometimes using commercial sourdough starters as inoculants.  These starters generally fall into two types. One is made from traditionally maintained and stable starter doughs, often dried, in which the ratios of microorganisms are uncertain. Another is made from microorganisms carefully isolated from Petri dishes, grown into large, homogeneous populations in fermentors, and processed into combined baker's products with numerically defined ratios and known quantities of microorganisms well suited to particular bread styles.  
Bakers have devised several ways of encouraging a stable culture of micro-organisms in the starter. Unbleached, unbromated flour contains more micro-organisms than more processed flours. Bran-containing (wholemeal) flour provides the greatest variety of organisms and additional minerals, though some cultures use an initial mixture of white flour and rye or whole wheat flour or "seed" the culture using unwashed organic grapes (for the wild yeasts on their skins). Grapes and grape must are also sources of lactic acid bacteria,   as are many other edible plants.   Basil leaves are soaked in room-temperature water for an hour to seed traditional Greek sourdough.  Using water from boiled potatoes is said to increase the activity of the bacteria by providing additional starch.
The piped drinking water supplied in most urban areas is treated by chlorination or chloramination, adding small amounts of substances that inhibit potentially dangerous micro-organisms but are harmless to animals. Some bakers recommend unchlorinated water for feeding cultures. :353 Because a sourdough fermentation relies on microorganisms, using water without these agents may produce better results. Bottled drinking water is suitable; chlorine, but not chloramines, can be removed from tap water by boiling it for a time, or simply by leaving it uncovered for at least 24 hours. Chlorine and chloramines can both be removed by activated carbon filters  and other methods. 
Bakers often make loaves with fermented dough from a previous batch (which they call "mother dough", [note 2] "mother sponge", "chef", or "seed sour") rather than making a new starter every time they bake. The original starter culture may be many years old. Because of their pH level and the presence of antibacterial agents, such cultures are stable and able to prevent colonization by unwanted yeasts and bacteria. For this reason, sourdough products inherently keep fresh for a longer time than other breads, and are good at resisting spoilage and mold without the additives required to retard spoiling of other types of bread. 
The flavour of sourdough bread varies from place to place according to the method used, the hydration of the starter and the final dough, the refreshment ratio, the length of the fermentation periods, ambient temperature, humidity, and elevation, all of which contribute to the microbiology of the sourdough.
The starter must be fed 4 to 12 hours prior to being added to dough, by mixing flour and water to the starter. This creates an active leaven, which should grow in size and is ready to use when it is bubbly and floats in water. The leaven is mixed with flour and water to make a final dough of the desired consistency. The starter weight is usually 13% to 25% of the total flour weight, though formulas may vary.    The dough is shaped into loaves, left to rise, and then baked. A number of 'no knead' methods are available for sourdough bread. Due to the length of time sourdough bread takes to proof, many bakers may refrigerate their loaves prior to baking. This process is known as 'retardation' to slow down the proofing process. This process has the added benefit of developing a richer flavoured bread.
Because the rise time of most sourdough starters is longer than that of breads made with baker's yeasts, sourdough starters are generally unsuitable for use in a bread machine. However, sourdough that has been proved over many hours, using a sourdough starter or mother dough, can then be transferred to the machine, utilizing only the baking segment of the bread-making program, bypassing timed mechanical kneading by the machine's paddle. This may be convenient for single loaf production, but the complex blistered and slashed crust characteristics of oven-baked sourdough bread cannot be achieved in a bread making machine, as this usually requires the use of a baking stone in the oven and misting of the dough to produce steam. Furthermore, ideal crust development requires loaves of shapes not achievable in a machine's loaf tin.
Sourdough is a stable culture of lactic acid bacteria and yeast in a mixture of flour and water. Broadly speaking, the yeast produces gas ( carbon dioxide) which leavens the dough, and the lactic acid bacteria produce lactic acid, which contributes flavor in the form of sourness. The lactic acid bacteria metabolize sugars that the yeast cannot, while the yeast metabolizes the byproducts of lactic acid fermentation.
Lactic acid bacteria are aerotolerant anaerobes, which means that though they are anaerobes, they can multiply in the presence of oxygen. Hammes and Vogel in 1995 distinguished three metabolic groups of lactic acid bacteria:  
- Group A. Obligately homofermentative. They metabolise hexoses via the Embden–Meyerhof–Parnas (EMP) pathway to produce two molecules of lactic acid (C3H6O3), (>85%)   but no carbon dioxide. They cannot tolerate oxygen. "They grow at 45 °C but not at 15 °C."  "They are represented by L. delbrueckii and L. acidophilus." 
- Group B. Facultatively heterofermentative. They metabolise hexoses to lactic acid,  and pentoses to lactic and acetic acids.   They can use oxygen and will "produce more oxidized fermentations (e.g. acetate) if O2 is present."  They "grow at 15 °C and show variable growth at 45 °C."  They are "represented by L. casei and L. plantarum." 
- Group C. Obligately heterofermentative. They metabolise hexoses via the EMP pathway to produce lactic acid, acetic acid, and CO2;  and pentoses via the phosphogluconate pathway to lactic and acetic acids.    They are represented by L. fermentum, L. brevis, L. kefiri, and L. sanfranciscensis.  
The phylogenetic groupings of Lactobacillus species have been undergoing reclassification, first being studied in 1991 by Collins, et al.  In 1995, Hammes and Vogel phylogenetically grouped L. sanfranciscensis to L. casei-Pediococcus.  In 2003, Hammes and Hertel grouped it to L. buchneri. In 2007, Dellaglio and Felis grouped it to L. fructivorans. 
Traditional San Francisco sourdough is a Type I sourdough.  Type I sourdoughs are generally firm doughs,  have a pH range of 3.8 to 4.5, and are fermented in a temperature range of 20 to 30 °C (68 to 86 °F). Lactobacillus sanfranciscensis was named for its discovery in San Francisco sourdough starters, though it is not endemic to San Francisco. Lactobacillus sanfranciscensis and L. pontis often highlight a lactic-acid bacterial flora that includes L. fermentum, L. fructivorans, L. brevis, and L. paralimentarius.    The yeasts Saccharomyces exiguus, Candida milleri, or Candida holmii  usually populate sourdough cultures symbiotically with Lactobacillus sanfranciscensis.  The perfect yeast S. exiguus is related to the imperfect yeasts C. milleri and C. holmii. Torulopsis holmii, Torula holmii, and S. rosei are synonyms used prior to 1978. C. milleri and C. holmii are physiologically similar, but DNA testing established them as distinct. Other yeasts reported found include C. humilis, C. krusei, Pichia anomaola, C. peliculosa, P. membranifaciens, and C. valida.   There have been changes in the taxonomy of yeasts in recent decades.   L. sanfranciscensis requires maltose,  while C. milleri is maltase negative and thus cannot consume maltose.      C. milleri can grow under conditions of low pH and relatively high acetate levels, a factor contributing to sourdough flora's stability. 
In order to produce acetic acid, L. sanfrancisensis needs maltose and fructose.  Wheat dough contains abundant starch and some polyfructosanes, which enzymes degrade to "maltose, fructose and little glucose."  The terms "fructosan, glucofructan, sucrosyl fructan, polyfructan, and polyfructosan" are all used to describe a class of compounds that are "structurally and metabolically" related to sucrose, where "carbon is stored as sucrose and polymers of fructose ( fructans)."  Yeasts have the ability to free fructose from glucofructans which compose about 1–2% of the dough. Glucofructans are long strings of fructose molecules attached to a single glucose molecule. Sucrose can be considered the shortest glucofructan, with only a single fructose molecule attached.  When L. sanfrancisensis reduces all available fructose, it stops producing acetic acid and begins producing ethanol. If the fermenting dough gets too warm, the yeasts slow down, producing less fructose. Fructose depletion is more of a concern in doughs with lower enzymatic activities. 
A Belgian study of wheat and spelt doughs refreshed once every 24 hours and fermented at 30 °C (86 °F) in a laboratory environment provides insight into the three-phase evolution of first-generation-to-stable sourdough ecosystems. In the first two days of refreshment, atypical genera Enterococcus and Lactococcus bacteria highlighted the doughs. During days 2–5, sourdough-specific bacteria belonging to the genera Lactobacillus, Pediococcus, and Weissella outcompete earlier strains. Yeasts grew more slowly and reached population peaks near days 4–5. By days 5–7, "well-adapted" Lactobacillus strains such as L. fermentum and L. plantarum had emerged. At their peaks, yeast populations were in the range of about 1–10% of the lactobacilli populations or 1:10–1:100. One characteristic of a stable dough is that the heterofermentative have outcompeted homofermentative lactobacilli. 
Investigations of wheat sourdough found that S. cerevisiae died off after two refreshment cycles.  S. cerevisiae has less tolerance to acetic acid than other sourdough yeasts.  Continuously maintained, stable sourdough cannot be unintentionally contaminated by S. cerevisiae. 
In Type II sourdoughs, baker's yeast or Saccharomyces cerevisiae  is added to leaven the dough; L. pontis and L. panis highlight the flora.    They have a pH less than 3.5, and are fermented within a temperature range of 30 to 50 °C (86 to 122 °F) for several days without feedings, which reduces the flora's activity.  This process was adopted by some in industry, in part, due to simplification of the multiple-step build typical of Type I sourdoughs. 
In Type II sourdoughs, yeast growth is slowed or stopped due to higher fermentation temperatures. These doughs are more liquid and once fermented may be chilled and stored for up to a week. They are pumpable and used in continuous bread production systems. 
Type III sourdoughs are Type II sourdoughs subjected to a drying process, usually either spray or drum drying, and are mainly used at an industrial level as flavoring agents. They are dominated by "drying-resistant [lactic acid bacteria] such as Pediococcus pentosaceus, Lactobacillus plantarum, and L. brevis." The drying conditions, time and heat applied, may be varied in order to influence caramelization and produce desired characteristics in the baked product. 
There are many breads that use techniques similar to that used in the making of sourdough bread. Danish rugbrød (rye bread) is a dense, dark bread best known from its use in the Danish smørrebrød (open-faced sandwiches).   The Mexican birote salado started out in the city of Guadalajara as a short French baguette that replaces the yeast with a sourdough fermentation process, yielding a bread that is crunchy outside but soft and savory inside.  Amish friendship bread uses a sourdough starter that includes sugar and milk. It is also leavened with baking powder and baking soda. An Amish sourdough is fed with sugar and potato flakes every 3–5 days. German pumpernickel is traditionally made from a sourdough starter,  although modern pumpernickel loaves often use commercial yeasts, sometimes spiked with citric acid or lactic acid to inactivate the amylases in the rye flour. Flemish desem bread (the word means 'starter') is a whole-wheat sourdough.  In Azerbaijan, whole-wheat sourdough flatbreads are traditionally eaten.  In Ethiopia, teff flour is fermented to make injera.  A similar variant is eaten in Somalia, Djibouti, and Yemen (where it is known as lahoh).  In India, idlis and dosa are made from a sourdough fermentation of rice and Vigna mungo. 
Sourdough fermentation and lactic acid bacteria may be useful to improve the quality of gluten-free breads, such as by enhancing texture, aroma, and shelf life, which can be extended by inhibition of mycotoxins associated with fungal contamination.  
Sourdough bread has a relatively low glycemic index compared with other types of bread.   The acidity of sourdough bread during fermentation may inhibit formation of phytates which affect the absorption of some dietary minerals.  In one review, sourdough bread made from whole grains was recommended as a key daily food in the Italian Mediterranean diet. 
- Michael Gänzle has said Markus Brandt estimated that, in a properly maintained sourdough of sufficient age, the yeasts and lactobacilli each contribute roughly 50% of the total CO2. Gänzle pointed out that while there are fewer yeasts, they are larger. 
- The term mother dough sometimes refers to a yeast sponge,   so one must look at the ingredients and process to understand if it is a multi-refreshment sourdough or instead a sponge made from only fresh ingredients.
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