© 2023 J. de Jong
Food Microbiology (FHM35806)
This summary contains all lecture notes from this course, combined with the provided literature, quiz
answers (incorporated in the text) and information from the preceding course Food Microbiology
(FHM20306). The book referenced to in this summary is: Food Microbiology 4th edition by Adams,
Moss and McClure.
Contents
Food Microbiology (FHM35806) ............................................................................................................. 1
Lecture 1: microbiological food safety .................................................................................................... 2
Lecture 2: biofilms................................................................................................................................... 5
Lecture 3: minimal processing ................................................................................................................ 9
Lecture 4: detection methods & enrichment ecology .......................................................................... 14
Lecture 5: pathogen survival strategies ................................................................................................ 20
Lecture 6: fungi ..................................................................................................................................... 23
Lecture 7: genome sequencing & biomarkers ...................................................................................... 31
Lecture 8: quantitative microbiology .................................................................................................... 36
Lecture 9: risk assessment .................................................................................................................... 42
Lecture 10: sampling and monitoring ................................................................................................... 45
Lecture 11: viruses ................................................................................................................................ 49
Lecture 12: GI-tract composition .......................................................................................................... 53
Lecture 13: probiotics, prebiotics and gut health ................................................................................. 57
Lecture 14: GI-tract functionality .......................................................................................................... 62
Lecture 15: probiotics, prebiotics and gut health ................................................................................. 65
Factsheet pathogenic bacteria .............................................................................................................. 70
Cheat sheet definitions ......................................................................................................................... 71
1
, © 2023 J. de Jong
Lecture 1: microbiological food safety
Introduction
In food microbiology we study the significance of microorganisms in food (chains).
• The good → fermentation
o Taste, shelf-life, health
• The bad → pathogens
o Bacteria, viruses, parasites, (myco)toxins
o Food safety
• The ugly → food quality
o Bacteria, yeasts, moulds
o Food quality
Food Safety = pathogens (bacteria, viruses)
Food Quality = spoilage (bacteria, yeasts, moulds)
Food Quality = fermentation (taste, shelf-life, health)
Food Functionality = (probiotics, prebiotics, microbiota)
Food Micro = Safety, spoilage, fermentation
Food Safety = Public health, legal, economic
Issues in food safety
Burden of disease
The global burden of foodborne diseases is estimated with
deaths, YLDS (=years lived with disability), YLLS (=years of life
lost) → together DALYS (=disability adjusted life years). There is
a probability of 1 in 10 to get a foodborne disease every year.
Every year, 420.000 deaths occur. Children account for 1/3 of
deaths. In developing countries, the probability to die is higher.
Important: relevant public health burden, not the biggest.
Products related to causing organisms
Product relation compare types from foods and humans.
Number of cases of type I (phage and sero-types) in food j:
Mass * prevalence * type factor * food factor
• total Mass consumed of food product
• “type factor”: “infectivity”/”survivability” of the types
• “food factor”: survival/growth, eaten raw/cooked
• estimate of number of cases per food
Eggs are the most important vehicle.
2
, © 2023 J. de Jong
Control
A good food safety culture is required to control foodborne diseases.
Food safety objectives
For a certain objective, food safety objectives (=norm set by government) are set. A food safety
objective is based on cfu/g or prevalence at consumption. based on ALOP: Appropriate level of
protection (illnesses per year). FSOs and POs are distinct levels of foodborne hazards that cannot be
exceeded at the point of consumption and earlier in the food chain.
ICMSF = International Commission on Microbiological Specifications for Foods.
In every stage of the food chain, this equation can be used. For example, food safety is controlled in
milk by set process/product criteria in HACCP.
3
, © 2023 J. de Jong
• Appropriate Level of Protection illnesses/year (ALOP) = the level of protection deemed
appropriate by the Member (country) establishing a sanitary or phytosanitary measure to
protect human, animal or plant life or health within its territory→ D/R, consumption, ethics,
“distribution” of product groups.
• Food Safety Objective (FSO) = the maximum frequency and/or concentration of a (microbial)
hazard in a food at the time of consumption that still provides the ALOP (cfu/g or prevalence
(%) at consumption) → “distribution” over the chain.
• Performance Objective (PO) = the maximum frequency and/or concentration of a (microbial)
hazard in a food at a specified step in the food chain before time of consumption that still
provides or contributes to the achievement of an FSO or ALOP, as applicable (cfu/g or
prevalence (%)) → “distribution” over phenomena (initial contamination, growth,
inactivation, recontamination).
• Performance Criterion (PC) = the effect of one or more control measure(s) needed to meet or
contribute to meeting a PO → >6D inactivation, <3 logs growth → quantitative microbiology,
experiments, literature.
o Process criterion 15s 71.5°C
o Product criterion pH<4.6
A Performance Objective is equivalent to a FSO, specifying hazard levels that are tolerable, but are
set at one or more specific steps earlier in the food chain.
Example questions
1) Explain the difference between an FSO and a performance objective
2) For organism X there exist two types X1 and X2. In two food products (most relevant vehicles) the
following prevalences (%) are found:
Product X1 X2 Consumption
Cheese 0 15 10.000
Salmon 50 25 100
165 people got ill in the population of organism X, 10 by X1 and 155 by X2. Estimate the relative
importance of the two vehicles for organism X. Use the equation Xij=Mjpijqiaj and set the organism
factors q both at 1.
Answer: cheese is 10 times as important as salmon, 150 get ill due to cheese and 15 due to salmon.
4
, © 2023 J. de Jong
Lecture 2: biofilms
Biofilm = any syntrophic consortium of microorganisms in which cells stick to each other and often
also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is
composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS
components, which are typically a polymeric conglomeration of extracellular polysaccharides,
proteins, lipids and DNA. Biofilms may form on living (biotic) or non-living (abiotic) surfaces.
Biofilms give bacteria protection against: chemicals, UV, desiccation, mechanical forces, predators
and invasion. Biofilms are usually part of big communities. Biofilms are the most dominant form of
bacteria. They can be found everywhere. They can be beneficial (e.g. water treatment, fermentation
like kombucha) or harmful (e.g. in the lungs, contamination in pipes). Biofilm formation is a survival
strategy. They are formed when circumstances are not optimal especially in dynamic flow conditions.
When the concentration of nutrients in a liquid is low, cells will attach to the wall of a pipeline, since
nutrients may have settled at the substratum and in addition there is a (constant) stream of nutrients
passing by.
Biofilm formation
Biofilms can be formed on a solid (submerged) surface. It is important to know about these steps,
because for each step the method of preventing/removing requires a different approach. Multiple
factors affect biofilm formation and growth:
• Chemical and physical properties of the surface.
• Which species, strains are present, microbial interactions.
• Nutrient type and availability.
• Environmental conditions.
The first stage is the initial attachment (which involves a series of attachment/detachment events) of
the bacterial cells to a surface. At the second stage, cells reduce flagellar rotation and produce
extracellular polymeric substances, leading to irreversible attachment. At the third stage,
microcolonies are formed by clonal growth or by attachment of other planktonic cells. During the
fourth stage, biofilm maturation, complex structures of cells embedded in the extracellular matrix
develop. In the final stage, single cells can disperse from the biofilm. This dispersal is caused either
by shear forces or because the biofilm has reached its critical mass and outer cells start generating
planktonic cells, which can colonize a surface somewhere else.
The rate of biofilm formation depends on microorganisms present, nutrients in bulk liquid,
substratum (type of material/roughness/cracks/charge) and factory design (dead ends/roughness
materials/seals). The temperature has effect on the microorganisms (i.e. growth rate) and therefore
also on biofilm formation.
5
, © 2023 J. de Jong
Surface properties affect attachment of bacteria to a surface:
• Bacteria can have a negative or positive surface charge. Most studied bacteria are negatively
charged, causing them to attach to positively charged surfaces.
• Attachment also depends on wettability → is the surface hydrophilic or hydrophobic?
• Roughness of the surface.
• Topography of the surface.
• Stiffness of the surface.
Species interactions may enhance biofilm formation and enhance protection.
Extracellular matrix components and interactions
Biofilms are made of slime. Extracellular matrix components
play a role in aggregation, protection and the architecture of
the biofilm. Next to e.g. polysaccharides, extracellular DNA can
also be a component in biofilms (e.g. in Listeria monocytogenes
biofilm formation). Components in biofilms also interact with
each other in biofilm formation.
Mechanical properties
Biofilms exhibit viscoelastic behaviour = the property of
materials that exhibit both viscous and elastic characteristics when undergoing deformation. Viscous
materials, like water, resist shear flow and strain linearly with time when a stress is applied. Elastic
materials strain when stretched and immediately return to their original state once the stress is
removed. When there is force, the biofilm can extend.
The composition of the EPS also affects mechanical properties.
During biofilm formation cells do not produce flagella since they are imbedded in the matrix and are
non-motile. However, in fully matured biofilms and dependent on conditions, certain signals will
activate flagella synthesis and induce motility in cells at the surface leading to dispersal of these cells
from the biofilm.
Evolution and diversification
Environmental heterogeneity and interactions in a biofilm contributes diversification. Research has
found that 2-60 times more mutations take place in a biofilm.
Horizontal gene transfer contributes to diversification as well. Donor bacteria = the bacteria that
supplies the DNA.
6
, © 2023 J. de Jong
Communication
Bacteria can communicate with each other through e.g. quorum sensing (QS) [ADD IMAGE FROM
SLIDES]. Bacterial cells produce autoinducers. When there are more and more bacteria, the
autoinducers reach a certain threshold and change their behaviour. QS affects biofilm architecture in
e.g. B. subtilis.
Under flow conditions, communication may be disrupted. Under flow, not every bacterial cell may
benefit from QS. However, disrupted surfaces protect QS-activated bacteria from flow.
Bacteria can communicate via electrical chemical signalling as well. Biofilm cells attract free cells
through electrical signalling (K+).
7
Food Microbiology (FHM35806)
This summary contains all lecture notes from this course, combined with the provided literature, quiz
answers (incorporated in the text) and information from the preceding course Food Microbiology
(FHM20306). The book referenced to in this summary is: Food Microbiology 4th edition by Adams,
Moss and McClure.
Contents
Food Microbiology (FHM35806) ............................................................................................................. 1
Lecture 1: microbiological food safety .................................................................................................... 2
Lecture 2: biofilms................................................................................................................................... 5
Lecture 3: minimal processing ................................................................................................................ 9
Lecture 4: detection methods & enrichment ecology .......................................................................... 14
Lecture 5: pathogen survival strategies ................................................................................................ 20
Lecture 6: fungi ..................................................................................................................................... 23
Lecture 7: genome sequencing & biomarkers ...................................................................................... 31
Lecture 8: quantitative microbiology .................................................................................................... 36
Lecture 9: risk assessment .................................................................................................................... 42
Lecture 10: sampling and monitoring ................................................................................................... 45
Lecture 11: viruses ................................................................................................................................ 49
Lecture 12: GI-tract composition .......................................................................................................... 53
Lecture 13: probiotics, prebiotics and gut health ................................................................................. 57
Lecture 14: GI-tract functionality .......................................................................................................... 62
Lecture 15: probiotics, prebiotics and gut health ................................................................................. 65
Factsheet pathogenic bacteria .............................................................................................................. 70
Cheat sheet definitions ......................................................................................................................... 71
1
, © 2023 J. de Jong
Lecture 1: microbiological food safety
Introduction
In food microbiology we study the significance of microorganisms in food (chains).
• The good → fermentation
o Taste, shelf-life, health
• The bad → pathogens
o Bacteria, viruses, parasites, (myco)toxins
o Food safety
• The ugly → food quality
o Bacteria, yeasts, moulds
o Food quality
Food Safety = pathogens (bacteria, viruses)
Food Quality = spoilage (bacteria, yeasts, moulds)
Food Quality = fermentation (taste, shelf-life, health)
Food Functionality = (probiotics, prebiotics, microbiota)
Food Micro = Safety, spoilage, fermentation
Food Safety = Public health, legal, economic
Issues in food safety
Burden of disease
The global burden of foodborne diseases is estimated with
deaths, YLDS (=years lived with disability), YLLS (=years of life
lost) → together DALYS (=disability adjusted life years). There is
a probability of 1 in 10 to get a foodborne disease every year.
Every year, 420.000 deaths occur. Children account for 1/3 of
deaths. In developing countries, the probability to die is higher.
Important: relevant public health burden, not the biggest.
Products related to causing organisms
Product relation compare types from foods and humans.
Number of cases of type I (phage and sero-types) in food j:
Mass * prevalence * type factor * food factor
• total Mass consumed of food product
• “type factor”: “infectivity”/”survivability” of the types
• “food factor”: survival/growth, eaten raw/cooked
• estimate of number of cases per food
Eggs are the most important vehicle.
2
, © 2023 J. de Jong
Control
A good food safety culture is required to control foodborne diseases.
Food safety objectives
For a certain objective, food safety objectives (=norm set by government) are set. A food safety
objective is based on cfu/g or prevalence at consumption. based on ALOP: Appropriate level of
protection (illnesses per year). FSOs and POs are distinct levels of foodborne hazards that cannot be
exceeded at the point of consumption and earlier in the food chain.
ICMSF = International Commission on Microbiological Specifications for Foods.
In every stage of the food chain, this equation can be used. For example, food safety is controlled in
milk by set process/product criteria in HACCP.
3
, © 2023 J. de Jong
• Appropriate Level of Protection illnesses/year (ALOP) = the level of protection deemed
appropriate by the Member (country) establishing a sanitary or phytosanitary measure to
protect human, animal or plant life or health within its territory→ D/R, consumption, ethics,
“distribution” of product groups.
• Food Safety Objective (FSO) = the maximum frequency and/or concentration of a (microbial)
hazard in a food at the time of consumption that still provides the ALOP (cfu/g or prevalence
(%) at consumption) → “distribution” over the chain.
• Performance Objective (PO) = the maximum frequency and/or concentration of a (microbial)
hazard in a food at a specified step in the food chain before time of consumption that still
provides or contributes to the achievement of an FSO or ALOP, as applicable (cfu/g or
prevalence (%)) → “distribution” over phenomena (initial contamination, growth,
inactivation, recontamination).
• Performance Criterion (PC) = the effect of one or more control measure(s) needed to meet or
contribute to meeting a PO → >6D inactivation, <3 logs growth → quantitative microbiology,
experiments, literature.
o Process criterion 15s 71.5°C
o Product criterion pH<4.6
A Performance Objective is equivalent to a FSO, specifying hazard levels that are tolerable, but are
set at one or more specific steps earlier in the food chain.
Example questions
1) Explain the difference between an FSO and a performance objective
2) For organism X there exist two types X1 and X2. In two food products (most relevant vehicles) the
following prevalences (%) are found:
Product X1 X2 Consumption
Cheese 0 15 10.000
Salmon 50 25 100
165 people got ill in the population of organism X, 10 by X1 and 155 by X2. Estimate the relative
importance of the two vehicles for organism X. Use the equation Xij=Mjpijqiaj and set the organism
factors q both at 1.
Answer: cheese is 10 times as important as salmon, 150 get ill due to cheese and 15 due to salmon.
4
, © 2023 J. de Jong
Lecture 2: biofilms
Biofilm = any syntrophic consortium of microorganisms in which cells stick to each other and often
also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is
composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS
components, which are typically a polymeric conglomeration of extracellular polysaccharides,
proteins, lipids and DNA. Biofilms may form on living (biotic) or non-living (abiotic) surfaces.
Biofilms give bacteria protection against: chemicals, UV, desiccation, mechanical forces, predators
and invasion. Biofilms are usually part of big communities. Biofilms are the most dominant form of
bacteria. They can be found everywhere. They can be beneficial (e.g. water treatment, fermentation
like kombucha) or harmful (e.g. in the lungs, contamination in pipes). Biofilm formation is a survival
strategy. They are formed when circumstances are not optimal especially in dynamic flow conditions.
When the concentration of nutrients in a liquid is low, cells will attach to the wall of a pipeline, since
nutrients may have settled at the substratum and in addition there is a (constant) stream of nutrients
passing by.
Biofilm formation
Biofilms can be formed on a solid (submerged) surface. It is important to know about these steps,
because for each step the method of preventing/removing requires a different approach. Multiple
factors affect biofilm formation and growth:
• Chemical and physical properties of the surface.
• Which species, strains are present, microbial interactions.
• Nutrient type and availability.
• Environmental conditions.
The first stage is the initial attachment (which involves a series of attachment/detachment events) of
the bacterial cells to a surface. At the second stage, cells reduce flagellar rotation and produce
extracellular polymeric substances, leading to irreversible attachment. At the third stage,
microcolonies are formed by clonal growth or by attachment of other planktonic cells. During the
fourth stage, biofilm maturation, complex structures of cells embedded in the extracellular matrix
develop. In the final stage, single cells can disperse from the biofilm. This dispersal is caused either
by shear forces or because the biofilm has reached its critical mass and outer cells start generating
planktonic cells, which can colonize a surface somewhere else.
The rate of biofilm formation depends on microorganisms present, nutrients in bulk liquid,
substratum (type of material/roughness/cracks/charge) and factory design (dead ends/roughness
materials/seals). The temperature has effect on the microorganisms (i.e. growth rate) and therefore
also on biofilm formation.
5
, © 2023 J. de Jong
Surface properties affect attachment of bacteria to a surface:
• Bacteria can have a negative or positive surface charge. Most studied bacteria are negatively
charged, causing them to attach to positively charged surfaces.
• Attachment also depends on wettability → is the surface hydrophilic or hydrophobic?
• Roughness of the surface.
• Topography of the surface.
• Stiffness of the surface.
Species interactions may enhance biofilm formation and enhance protection.
Extracellular matrix components and interactions
Biofilms are made of slime. Extracellular matrix components
play a role in aggregation, protection and the architecture of
the biofilm. Next to e.g. polysaccharides, extracellular DNA can
also be a component in biofilms (e.g. in Listeria monocytogenes
biofilm formation). Components in biofilms also interact with
each other in biofilm formation.
Mechanical properties
Biofilms exhibit viscoelastic behaviour = the property of
materials that exhibit both viscous and elastic characteristics when undergoing deformation. Viscous
materials, like water, resist shear flow and strain linearly with time when a stress is applied. Elastic
materials strain when stretched and immediately return to their original state once the stress is
removed. When there is force, the biofilm can extend.
The composition of the EPS also affects mechanical properties.
During biofilm formation cells do not produce flagella since they are imbedded in the matrix and are
non-motile. However, in fully matured biofilms and dependent on conditions, certain signals will
activate flagella synthesis and induce motility in cells at the surface leading to dispersal of these cells
from the biofilm.
Evolution and diversification
Environmental heterogeneity and interactions in a biofilm contributes diversification. Research has
found that 2-60 times more mutations take place in a biofilm.
Horizontal gene transfer contributes to diversification as well. Donor bacteria = the bacteria that
supplies the DNA.
6
, © 2023 J. de Jong
Communication
Bacteria can communicate with each other through e.g. quorum sensing (QS) [ADD IMAGE FROM
SLIDES]. Bacterial cells produce autoinducers. When there are more and more bacteria, the
autoinducers reach a certain threshold and change their behaviour. QS affects biofilm architecture in
e.g. B. subtilis.
Under flow conditions, communication may be disrupted. Under flow, not every bacterial cell may
benefit from QS. However, disrupted surfaces protect QS-activated bacteria from flow.
Bacteria can communicate via electrical chemical signalling as well. Biofilm cells attract free cells
through electrical signalling (K+).
7
