week 9

• Learning Outcomes


  • List some of the common microbes which cause spoilage of food
  • Describe methods used to preserve food
  • Describe some of the processes where microbes are used in food and drink production
  • Describe some of the uses of microbes in industry
  • Describe primary and secondary metabolites
  • Illustrate the industrial fermentation process
  • Describe biocontrol and its uses
  • Describe bioremediation and how it is useful in oil spills
• Lecture Outline


  • Food microbiology
  • Food spoilage and preservation
  • Food and drinks produced with the aid of microbes
  • Industrial Microbiology
  • Microbial metabolites
  • Industrial fermentation
  • Environmental Microbiology
  • Biocontrol of pests
  • Bioremediation
• Food microbiology


  Microorganisms are usually seen in a negative way, but they are also useful as a food source, for preservation of foods, and for enhancing or changing flavour, texture or aroma. Many practices used for centuries, like beer and bread making, date back to the Egyptians.
• Food spoilage and preservation

  • Spoilage Microbes
  • Food Preservation methods
• Spoilage Microbes


  • Fruits & Vegetables: Bacteria - Erwinia, Pseudomonas, Corynebacterium; Fungi - Aspergillus, Botrytis, Geotrichum, Rhizopus, Penicillium, Cladoporium, Alternaria, Phytophthora, various yeasts
  • Meat, poultry & seafood: Bacteria - Acinetobacter, Aeromonas, Pseudomonas, Micrococcus, Achromobacter, Flavobacterium, Proteus, Salmonella, Escherichia, Campylobacter, Listeria; Fungi - Cladosporium, Mucor, Rhizopus, Penicillium, Geotrichium, Sporotrichium, Candida, Torula, Rhodotorula
  • Milk: Bacteria - Streptococcus, Leuconostoc, Lactococcus, Lactobacillus, Pseudomonas, Proteus
  • High sugar foods: Bacteria - Clostridium, Bacillus, Flavobacterium; Fungi - Saccharomyces, Torula, Penicillium
• Food Preservation methods


  • Cold storage
  • Pickling
  • Dehydration
  • Heating
  • Irradiation
  • Natural antimicrobial agents (e.g. Benzoic acid in cranberries)
• Cold storage and Freezing

  Lower temperatures slow microbial growth and food spoilage. Psychrotolerant bacteria can survive and grow at low temperatures. Freezing is required for longer term storage, but can change the physical properties of foods.
• Pickling


  Acidic conditions, often using vinegar or dilute acetic acid, prevent the growth of many spoilage organisms. pH 5 or less is required.
• Dehydration


  Reducing the water activity (aw) by adding solutes inhibits the growth of most bacteria, although moulds can still grow under low aw conditions. Other methods of lowering available water include drying and freeze drying.
• Heating


  Pasteurisation lowers the bacterial load without sterilising, maintaining flavour. Canning uses high heat to kill organisms including bacterial endospores.
• Irradiation


  Ionizing radiation, such as from Cobalt-60 or Cesium-137, damages the DNA of bacteria, fungi and insects, reducing contamination. Irradiated foods must be labelled with the Radura logo.
• Foods produced with Microbes

  • Breads (yeast based)
  • Dairy
  • Meat products
  • Vegetables
  • Soy sauce
  • Beer / wine
• Useful Microbes


  • Cheese, yoghurt: Lactococcus, Lactobacillus, Streptococcus thermophilus
  • Bread: Saccharomyces cerevisiae
  • Beer, wine: Saccharomyces, Zymomonas
  • Pepperoni, salami: Pediococcus, Lactococcus, Micrococcus, Staphylococcus
  • Sauerkraut: Leuconostoc, Lactobacillus
  • Soy Sauce: Aspergillus, Tetragenococcus halophillus, yeasts
  • Vinegar: Acetobacter, Gluconobacter
  • Quorn: Fusarium graminarum
  • Edible mushrooms: Basidiomycetes
• Bread making


  1. Anaerobic metabolism by Saccharomyces cerevisiae (bakers yeast)

  2. Sugars + grain carbohydrate -> CO2 + Ethanol

  3. CO2 causes the bread to rise, creating the holes and texture
• Cheese making


  1. Fermentation by lactic acid bacteria like Lactococcus, Lactobacillus, Streptococcus

  2. Lactose -> glucose + galactose -> lactic acid

  3. Decrease in pH from raw milk (~pH 7-8) to cheese (<pH 5.3)

  4. Some cheeses have secondary cultures added to provide characteristic textures or flavours, e.g. Propionibacterium in Swiss cheese, Penicillium in blue cheese
• Fermented Drinks


  1. Alcoholic fermentation of simple sugars by yeasts like Saccharomyces cerevisiae and Saccharomyces uvarum

  2. Glucose -> Ethanol + CO2

  3. Originally via surface yeasts, now using specially selected starter cultures
• Wine making


  1. Dry wine: all sugar fermented

  2. Sweet wine: not all sugar fermented

  3. Sparkling wine: 2nd fermentation in bottle to produce high CO2

  4. Malolactic fermentation: malic acid -> lactic acid, making wine less acidic and more palatable
• Industrial Microbiology


  Microorganisms are grown on a large scale to produce valuable products or carry out important chemical processes. Biotechnology uses gene manipulation techniques to yield products not naturally produced by microbes.
• Biocatalyst


  Term for reactions carried out by microbes, often using genetically engineered strains to increase yield.
• Examples of Industrial Products

  • Supplements (e.g. yeast extract)
  • Cells (e.g. baking/brewing)
  • Enzymes (e.g. glucose isomerase)
  • Antibiotics (e.g. penicillin)
  • Food additives (e.g. amino acids)
  • Alcohol (e.g. ethanol)
  • Chemicals (e.g. citric acid)
• Primary Metabolites


  Created during the growth phase, e.g. alcohol from yeast anaerobic metabolism. Involved in growth, development and reproduction.
• Secondary Metabolites


  Created near the end of the growth phase/approaching stationary phase. Do not play a role in growth, development and reproduction, but often have ecological functions like defence mechanisms (e.g. antibiotics).
• Industrial Fermentation


  1. Large enclosed vessels, varying in size from 5-10L (lab scale) to 500,000L (industry scale)

  2. Anaerobic fermenters need little specialist equipment, just a cooling jacket

  3. Aerobic fermenters require more elaborate equipment to ensure mixing and adequate aeration

  4. Most industrial fermentations are aerobic
• Scaling up from small-scale lab fermenters to large-scale commercial production can cause problems with mixing, aeration, and high oxygen demand from rich media and high biomass. Oxygen transfer is essential to avoid reduced product yield.
• Stages in Antibiotic Production

  1. Traditional approach: Isolate screening

  2. New approach: Computer modelling

  3. Organism producing a new antibiotic is discovered

  4. Structural analysis, toxicity and therapeutic tests

  5. Must be able to produce in large scale fermenters and purify the product efficiently (e.g. solvent solubility, adsorption, ion exchange, chemical precipitation)

  6. Goal is to obtain a crystalline product of high purity
• Isolated microorganisms rarely produce antibiotics in high enough concentrations, so high yielding strains must be sought through medium optimisation and genetic engineering.
• Fermentation Vessel


  • Little specialist equipment needed
  • Only cooling jacket
  • More elaborate equipment required
  • Ensure mixing and adequate aeration
• Most industrial fermentations are aerobic
• Scaling up


  1. Most processes first carried out in small-scale lab fermenters

  2. Allows optimisation

  3. Small scale ≠ large scale

  4. Most problems occur in mixing

  5. Aeration

  6. Rich media

  7. High biomass

  8. High O2 demand
• • Oxygen transfer is essential
  • Reduced aeration, even temporary, could lead to reduced product yield
  • Much easier to control in a small scale fermenter
• Stages in Antibiotic Production

  1. Isolate screening

  2. Computer modelling

  3. Structural analysis

  4. Toxicity and therapeutic tests

  5. Purification
• • To be commercially successful it must produce in large scale fermenters
  • Must be able to purify the product efficiently
• Solvent soluble


  Adsorption, ion exchange or chemical precipitation
• Goal is to obtain crystalline product of high purity
• Increasing Yield


  1. High yielding strain sought

  2. Medium used

  3. Mutagenesis

  4. Genetic engineering

  5. Alterations in regulation process
• Isolated microorganisms rarely produce antibiotic in high enough concentrations
• Amoxicillin


  Semi synthetic penicillin produced by removing the benzyl side chain of Pen G to produce 6-APA and adding a totally artificial side chain using an acylase, often done using immobilised enzymes
• Other products


  • Vitamins
  • Amino acids
  • Steroids
  • Enzymes
• Environmental Microbiology


  • Pest Control
  • Water Quality
  • Bioremediation
• Biocontrol of Insect pests

  • Muted as 'safer' than chemical pesticides
  • Biological insectocides
  • Exploiting natural disease
  • Baculovirus (Baculoviridae) viruses that attack insects and other arthropods
  • Majority used as biological control agents belong to the genus Nucleopolyhedrovirus
  • Species-specific, narrow spectrum insecticidal applications
  • No negative impacts on plants, mammals, birds, fish, or even on non-target insects