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Food Microbiology

  • Wine
  • Sake*
  • Beer
  • Vinegar
  • Cheese
  • Soy Sauce
  • Sauerkraut
  • Yogurt
  • Tempeh*
  • Oncom
  • Quorn
  • Kombucha *


Microbial Husbandry (Preferential Selection and Management of Beneficial Micro-Organisms):

  • Yeast – Saccharomyces, Brettanomyces, Candida
  • Bacteria – Acetobacter, Lactobacillus, Leuconostoc
  • Mold – Penicillium, Aspergillus, and Rhizopus






Microbial Husbandry is all about supplying a beneficial energy source (Sugars and Organic Acids) and managing Oxygen, pH, acidity and osmotic balance.









Microbial Husbandry is all about supplying a beneficial energy source (Sugars and Organic Acids) and managing Oxygen, pH, acidity and osmotic balance.

  1. Description of the Food, Microbes used, and important steps in its production
  2. Important and/or interesting biochemical transformations facilitated by microbes.
  3. Brief History and/or Health Claims
  4. Miscellaneous (only if something seems compelling) 


 Wine  Sake*
 Beer  Vinegar
 Cheese  Soy Sauce
 Tempeh*  Oncom
 Quorn  Kombucha*
 Yogurt  Sauerkraut










“…the occurrence of ethanol in ripe and decaying fruit and the substantial heritability of alcoholism in humans suggest an important historical association between primate frugivory and alcohol consumption. “

(from: The Quarterly Review of Biology, 2000).


“Survival and reproductive success hinge on the perception of environmental stimuli. In this regard, foraging efficiency depends on discerning predictive signals in food. A widespread occurrence of ethanol in fruits indicates a sustained historical exposure of frugivores to this compound. Accordingly, Dudley (2000, Quart. Rev. Biol. 75:3–15) proposed that ethanol could represent a prominent sensory cue to primates because of direct and indirectly associated caloric and physiological rewards. …Ethanol has likely played a significant and underestimated role in the regulation of primate foraging behavior.“             

(from: INTEGR. COMP. BIOL., 44:295–303 (2004)).




“The ancient chemical evidence now enables the later beverages to be traced back as far as 7000 B.C. and reveals how Chinese beverage-making developed over the millennia. “

(from: PNAS, 2003)







Steps in Wine Making: (Simple Overview), (In the Vineyard) and (Detailed Outline)


  • Supplying the Microbes with the "Goods" (Fermentation Substrate and more).











Primary Fermentation:

Tiny Bubbles Diagram







Secondary Fermentation / Malolactic Fermentation:









Spoilage / Undesirable Fermentation:

  • Metabolic Oxidation of Ethanol by Acetobacter = Vinegar


  • Accentuated by chemical oxygenation of Ethanol into Acetaldehyde








Molds found on grapes:

  • Aspergillus
  • Penicillium
  • Rhizopus (Bread, Fruit Mold)








Yeast found on grapes:

  • Saccharomyces
  • Brettanomyces
  • Schizosaccharomyces








Good, pleasant, helpful Microbes in Wine:

  • Saccharomyces
  • Botrytis (Noble Rot)
  • Pediococcus cerevisiae, Leuconostoc, Lactobacillus (both in highly controlled conditions)







Bad, unpleasant, unhelpful Microbes in Wine:

  • Pediococcus cerevisiae, Leuconostoc, Lactobacillus (in uncontrolled conditions)
  • Acetobacter = Vinegar
  • Brettanomyces (and basically all yeast other than Saccharomyces cerevisiae) = off flavors








The Good, the Bad and the Ugly – It’s all about aromatic esters and phenols from secondary metabolites:


  • A condensation between an acetic acid and an alcohol yields the ester ethyl acetate. Small amounts smell and taste fruity, but quickly becomes vinegary and nail polish.

  • 4-ethyl phenol formed by Brettanomyces     Smell and taste of barnyard, rancidity and sweaty horse.



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