Microbial Ecology of Foods

This lecture is based on Chapter 2 and 3 of the text book

 Microbial Ecology of Foods
Microbial ecology of foods - study of:
• Contamination
• The microbial growth response
• Factors affecting survival, growth and death
of microorganisms
• How does microbial activity affect food
quality - chemistry and biochemistry?
Read: Fleet G.H. (1999). Microorganisms in food Ecosystems.
Int. J. Food Microbiology 50: 101-117
 Contamination
• What is the contamination load (cfu/g or
ml)?
• What are the main contaminating species/
strains?
• Where do microbial contaminants come
from? (source of contamination)
Prevention of contamination is the most
effective measure for controlling the
microbiological quality and safety of foods
 Origins of Contamination
• Plant and animal products have natural
microflora
• Air, dust; microbial spores
• Soil, water
• Processing equipment (poor cleaning and
sanitation)
• Ingredients, recycled products
• Insects, birds, vermin, animals
• Humans
 Prevention of Contamination

• Understanding of environmental
microbiology
• Consideration of total food chain
• Effective cleaning and sanitation
• Good hygienic practices during production
and service chain
• DESIGN – equipment, process, materials
 Microbial Growth Response

• Bacteria - binary fission

• Filamentous fungi - hyphal extension
• Yeasts - budding
• Human viruses - no growth
• Bacterial viruses (bacteriophage)-lytic/lysogenic
• Protozoans - no growth
• Algae - no growth
Microbial Growth Curve
Important properties

1.Length of lag phase

(hours)
2.Growth rate/
doubling time
(minutes)
3.Maximum cell
population (cells/cfu
per ml)
Microbial Growth Properties

Responses to:
• Temperature
• pH, acidity
• Water activity, moisture content
• Oxygen content, redox potential
Microbial Growth—Temperature
(Jay, J M 2000. Modern Food Microbiology, 6th edition, Aspen Publ)

Response varies with species

Psychrophiles: min less than
5 C; opt 12-15 C; max 20 C
Psychrotrophs: min less than
5 C; opt 20-30 C; max 35 C
Mesophiles: min 5 C; opt 30-
40 C; max 40-45 C
Thermophiles: min 40 C; opt
55-75; max 90+ C
 Microbial Growth - pH
see Jay (2000)

Different organisms in different media have different responses to pH

 Microbial Growth - Water Activity
(Aw)
• Microorganisms require
free water for growth
• In foods, it is present as
both free and bound forms
(eg. due to solutes)
• Water activity measures the
amount of free and available
water for microbial growth.
Pure water has an Aw of 1.0
• The amount of water
required for growth and
survival varies with the
microbial species
Minimum Aw needs for
different microbial groups:
Gram - ve bacteria; 0.97
Gram + ve bacteria; 0.90
Halophilic bacteria; 0.75
Most yeasts; 0.85
Osmotolerant yeasts; 0.60
Most fungi; 0.80
Xerophilic fungi; 0.60
(there are exceptions in
groups- eg. Staph.aureus,
0.85)
What Factors Affect Water Activity??

• Moisture or water content

• Concentration of solute
• Type of solute (eg. sucrose, NaCl, glycerol)
• Humidity of surrounding environment-
concept of equilibration (adsorb or desorb
water)
 Microbial Growth – Oxygen (O2)
Microorganisms differ in oxygen requirement
and response to redox potential
Aerobes
Anaerobes
Facultative anaerobes
Microaerophilic or microaerobic
 Oxidation - Reduction Potential
(Redox; Eh)
• Measure of tendency to gain electrons (be
reduced) or lose electrons (be oxidized)
• Different organisms have a redox range in
which they grow (high ranges being aerobic
and low ranges being anaerobic)

What factors affect the redox

potential of a food ?
Growth Options for Contaminants
• Death - environment unfavourable
• Survives in dormant state
• Growth after a short lag phase
• Growth after a long lag phase
• Sequential growth of several species
• Symbiotic growth
• Synergistic growth (commensalism)
• Antagonistic growth
 Microbial Growth Profile in a
Product
• Multiple species and strains
• Long “farm to fork” time frame
• Changing environmental factors throughout
time frame
• Environment in the product is heterogeneous
- aqueous and solid phases; differential
chemistry (eg. fat, protein components);
inner and outer sections
 Complex Microbial Ecology

• Heterogeneous distribution of populations and

species within the product
• Mix of bacteria, yeast, fungi, bacteriophages
• Mixtures of microbial cells in different stages of
growth or division cycle
• Cells - growing, dead, autolysing, sublethally
injured, viable but non culturable
• Growth as microbial biofilms
• Quorum sensing concepts
 Some Important Concepts
• Sublethal injury
• Biofilms
• Quorum sensing
 Sublethal Injury
• When microbial cells are exposed to physical and
chemical stresses they may not be killed but may be
physiologically or metabolically damaged or injured
(sublethal injury) - they may have damaged
membranes or ribosomes, inactivated enzymes.
Such damage is not lethal and can be repaired if the
cells are exposed to a suitable, nutritious
environment
• Sublethally injured cells will grow and form colonies
on normal non-selective media, but NOT on
selective media where the selective conditions
present an added stress that prevents cell growth
 Sublethal Injury
Mackey B (2000) Injured bacteria. In The Microbiological Safety and Quality of Food. Eds Lund et al. Aspen
Publisher, Maryland
 Sublethal Injury
• Injured cells are still dangerous - they can recover
and grow in the food over time, recover in the
consumer - lead to food spoilage and food
poisoning outbreaks

• In food microbiology, it is common practice to use

selective enrichment and plating media where
injured cells will not grow. Consequently, they will
not be detected and the microbiological risk of the
product can be grossly underestimated
 Sublethal Injury
• For detection, injured cells must be given a period
to repair and recover by a resuscitation step
• Resuscitation is done by incubating the food sample
in a nutrient medium at about 25oC for 2-4 hours.
• If resuscitation goes for too long, the repaired cells
and any non-injured cells will multiply, giving an
overestimation of the risk - careful control needed
 Sublethal Injury and Repair
Mackey B (2000) Injured bacteria. In The Microbiological Safety and Quality of Food, Eds Lund B et al Aspen
Publishers , Maryland
 Sublethal Injury
• Many food processes induce sublethal injury-
heating, refrigeration, freezing, drying,
addition of salt, sugar, preservatives
• Sometimes as great as 99% or more of the
population of a species in a product may be
sublethally injured. This is very significant if
pathogens such as Salmonella or Listeria are
present
 Question?

• For a given microbial species, a food may

contain a mixture of normal healthy cells,
dead cells and sublethally injured cells.
• How would you determine the populations of
each of these different cell types?
 Microbial Biofilms
• Most foods occur as a solid /semi-solid
matrix
• At the air/liquid interface with solids,

SEM images of biofilms

microorganisms grow as a biofilm
• The biofilm consists of a dense biomass
of microcolonies and excreted matrix of http://www.bacteriainphotos.
com/bacterial-biofilm.html
proteins, lipids, polysaccharides and
nucleic acids that bind the biomass into
a structured network
• Microbial cells occur in very high
density, with altered physiological and
biochemical properties
 Microbial Biofilms
Cells in biofilms:
• firmly attached to surface,

CLSM images of biofilms

harder to wash off
• more resistant to
temperature, chemicals,
sanitizers and destruction
• constant source of
contamination as cells
slough off

https://journals.plos.org/plosone/article/fi
gures?id=10.1371/journal.pone.0005822
 Biofilm Formation
Stages

• Initial reversible attachment of cells to surface by

electrostatic charge
• Microcolony formation by growth and excretion of
extracellular polymers that irreversibly bind cells to
surface
• Maturation of biomass into structured network of
channels for water and nutrient transport
• Progressive release and dispersion of cells from
biomass
 Biofilm Formation
Stages 4
Dispersal

3
2 Maturation
1
Microcolony
Attachment
formation
 Quorum sensing
Bacteria can sense the cell density of the population they are part of and change their
behavior by accordingly. This is call quorum sensing. They use chemical signals to sense
changes in cell density and use gene transcription to change behavior.

(See Annous B et al. 2009. Quorum sensing in biofilms. J Food Sci . 74, R 24-R37)
 Public good production and exploitation
For example, extracellular enzyme production

Chitin

Chitinase enzyme

Ineffectual individual behaviour

 Public good production and exploitation
For example, extracellular enzyme production

Chitin

Chitinase enzyme

Ineffectual individual behaviour

Public good production and exploitation

Effective group behaviour

Public good production and exploitation

Acetylglucosamine
(food)

Effective group behaviour. Liberation

of communal food supply
 Public good production and exploitation

Acetylglucosamine
(food)

x
Chitinase enzyme
x

Emergence of cheats
A genetic mutation rendering a cell incapable of contributing
 Public good production and exploitation

Emergence of cheats
Exploitation of group behaviour. The cheaters win!
 Public good production and exploitation

Resource limitation Proliferation

Bad guys win locally. Good guys win globally.

 Biochemistry of Microbial Growth in Foods

• Microorganisms use food components as substrates

for growth and release their metabolic end products
into the food.
• These reactions cause changes in the physical and
chemical properties of the food,
• These changes vary with the species and strains that
have grown and with the extent of their growth.
• These changes can increase or decrease food quality
and safety.
 Biochemistry of Microbial Growth in Foods
• Metabolism of sugars: fermentation, oxidation
(EMP, HMP, PK, TCA-pathways).
• Metabolism of amino acids (decarboxylation,
deamination, transamination)
• Utilization of organic acids
• Degradation of macromolecules (eg. proteins by
proteases; lipids by lipases; polysaccharides by
amylases, pectinases; nucleic acids by RNAases,
DNAases
• Metabolism of sulphur containing compounds
• Metabolism of inorganic substances (ammonium,
nitrites, nitrates)
 Impact of Microorganisms on Food Properties

• Appearance: colour, turbidity, sediment,

ropiness
• Texture: loss of structure; sliminess; gassy,
foaming; swollen
• Odour: sweet, estery, fruity, solventy,
putrefaction, sulphury
• Flavour: sour, bitter, ethanolic, medicinal

What populations are needed before we can detect these changes?

Enables us to predict shelf-life.
 Factors Affecting Microbial Growth and
Survival

• Properties of the food (intrinsic factors)

• Environmental, processing conditions
(extrinsic factors)
• Properties of the microorganism
(implicit factors)
 Properties of the Food
Nutrients for microbial growth
Energy source
Carbon source
Nitrogen source
Vitamins
Trace elements
Water
 Nutrients - Carbohydrates
• Monosaccharides - hexoses, pentoses
• Disaccharides - sucrose, lactose, maltose
• Oligosaccharides - raffinose, stachyose
• Polysaccharides - starch, glycogen, pectin,
cellulose, hemicelluloses, inulin, dextrans
(glucans, mannans)

Can all microbes utilize these nutrients??

 Nutrients - Nitrogen compounds
• Amino acids
• Peptides
• Proteins
• Urea
• Ammonium compounds
• Nitrites and nitrates
 Nutrients - Lipids
• Tri, - di, - mono- glycerides
• Phospholipids
• Fatty acids
• Waxes
• Sterols
 Nutrients - Others

• Minerals and vitamins

• Organic acids (citric, malic, lactic,
tartaric, acetic)
• Nucleic acids (RNA , DNA)
• Phenolic compounds
 Water Activity of Some Foods
Christian J (2000) Drying and reduction of water activity. In The Microbiological Safety and Quality of Foods.
Eds Lund B et al Aspen Publishers, Maryland
Minimum Water Activity Values for Microbial Growth
Jay J ( 2000) Modern Food Microbiology 6th ed Aspen Publishers, Maryland
Food Acidity and pH

https://www.vitafountain.com/ph-food-chart/
Natural Antimicrobial Constituents of Foods

Many examples
• Lysozyme in egg white
• Inhibine in honey
• Essential oils in herbs and spices (eugenol in
cloves, allicin in garlic, thymol in thyme)
• Lactoferrin, agglutinin, lactoperoxidase in
milk
• Benzoic acid in cranberries
 Biological Structure

• Solid/ liquid
• Shell, skin
• Surface texture
• Inner and outer tissues
• Minced, macerated, blended products
• Damaged foods, cut surfaces
Environmental and Processing Factors
• Storage temperature (refrigeration, hot store)
• Gaseous atmosphere - oxygen, CO2, nitrogen,
vacuum (packaging)
• Heat processing: pasteurization, retorting (time/
temperature combination); freezing (rate,
minimum temperature, matrix)
• Moisture content and water activity - drying
(time/temperature), freeze drying, atmospheric
humidity
• Addition of preservatives, antimicrobials (weak
organic acids, sugar, salt, nisin etc)
 Environmental and Processing Factors

• Irradiation
• Centrifugation
• Filtration
• Fermentation
• High pressure processing
• Pulsed field electricity
• Microwave processing
• Ohmic and inductive heating
• Ultrasound
 Properties of the Microorganism

Determined by the genome

• Maximum growth rate; growth limits
• Biochemical, metabolic properties (eg.
pathways, production of extracellular
enzymes)
• Production of antagonistic substances (eg.
bacteriocins, yeast killer toxins)
• Quorum sensing molecules
 Summary - Microbial Ecology
of Foods
• Contamination - sources, mechanisms, loads, diversity,
prevention; “farm to fork” concept
• Microbial growth options in foods
• Factors affecting survival, growth and death of
microbes - intrinsic, extrinsic, implicit factors;
interactions of the factors
• Important concepts - sublethal injury, biofilms, QS
• Impact of microbial activity on food quality - physical,
chemical and sensory aspects