Chapter 2: Apply knowledge of physiology, genetics, biochemistry and behavior of food microorganisms

Food microorganisms and parasites play a critical role in nutrition and dietetics, particularly in Kenya where food safety and public health are major concerns. Understanding the physiology, genetics, and biochemical behavior of these organisms helps nutrition professionals prevent foodborne diseases and improve dietary outcomes. This chapter examines the detailed anatomy and physiology of microorganisms and parasites relevant to food microbiology and parasitology, equipping students with the knowledge to identify, control, and manage these agents in food environments.

2.1 Microorganisms' anatomy and physiology

Anatomy describes what a microorganism is made of and how it is shaped. Physiology describes how those parts work: how the organism feeds, grows, copies its genes, responds to stress and passes genes on. For a dietitian the two cannot be separated, because food treatments act on structures and food conditions act on physiology. A sanitiser that damages a cell membrane, a salt solution that draws water out of a cell, and a cooking temperature that stops an enzyme are all explained by the topics below. This topic deals with microorganisms; the anatomy and physiology of parasites follow in the next topic.

2.1.1 Anatomy of microorganisms

Microorganisms have very different body plans. Some are cells with no nucleus, some are cells with a nucleus and organelles, and viruses are not cells at all. Their shape, arrangement and internal parts decide how they are identified under a microscope, how they survive heat and chemicals, and how they attach to food and to the gut.

2.1.1.1 Shapes and arrangement of microorganisms

Shape is the first feature used to describe a microorganism. It is fixed by the cell wall, so it stays the same under normal conditions, and it is seen on a stained smear or a wet mount.

Noroviruses, hepatitis A virus and rotavirus are many-sided particles. A bacteriophage, the virus that infects bacteria, has a many-sided head and a tail through which it injects its genes. In moulds, the hyphae of some species have cross-walls and in others, such as the bread mould Rhizopus, they have none. Moulds produce their spores at the tips of stalks or in a sac, and the colour of the spores gives the visible green, black or white colouring on spoiled food.

2.1.1.2 Cell cytology

Cytology is the study of cell structure. Two cell plans occur in food microorganisms. The bacterial cell is prokaryotic: it has no nucleus and no membrane-bound organelles. The cells of yeasts, moulds, algae and protozoa are eukaryotic: they have a nucleus and organelles. The basic division is taught in the topic Classification of food microorganisms. Here the parts are described.

A Gram-positive wall is a thick layer of peptidoglycan. A Gram-negative wall has a thin peptidoglycan layer under an outer membrane. This difference is the basis of the Gram stain, which is taught in the topic Gram staining method.

A virus has a different plan again: a core of DNA or RNA inside a protein coat called the capsid. Some viruses have an additional lipid envelope. A virus has no ribosomes, no membrane of its own to control transport and no metabolism. It becomes active only inside a living host cell.

2.1.1.3 Bacterial cell arrangement

Bacterial cells divide by splitting in two. Whether the new cells separate or stay together, and the direction in which they divide, produces the characteristic arrangement. Arrangement helps to identify bacteria on a smear, but it does not identify a species by itself, because arrangement can vary with the growth medium and the age of the culture.

Arrangement also affects counting. A chain or cluster of cells that starts a single colony on an agar plate is counted once, so the number of colony-forming units is lower than the number of cells in the sample.

Sporulation

Sporulation is the formation of an endospore inside a bacterial cell. It is carried out by Bacillus and Clostridium and by a few related genera, and it is triggered when nutrients run short. One cell makes one spore, so sporulation is a way of surviving poor conditions and not a way of multiplying.

The process takes place in stages: the cell copies its chromosome, a wall forms to cut off a part of the cell as the forespore, a thick layer and a protein coat are built around it, and the parent cell breaks open to release the finished spore. The spore holds very little water, and its core contains calcium dipicolinate and small proteins that protect the DNA. These features make it tolerant of heat, drying, cold and many chemicals.

The place of the spore in the cell helps identification. In Bacillus cereus the spore is central and does not swell the cell. In Clostridium botulinum it lies off-centre near one end and swells the cell slightly. In Clostridium tetani it lies at the very end of the cell and gives a drumstick shape.

For food handling the point is that boiling at 100 °C does not destroy spores. Cooked rice, beans or stew that cools slowly allows surviving spores to germinate and grow, which is why cooked food is cooled quickly and refrigerated. Destroying spores in canned food needs heating under pressure at about 121 °C.

Cocci

Cocci are spherical or nearly spherical cells. The arrangement depends on how many planes the cells divide in and whether the daughter cells stay attached.

A Gram-positive coccus in clusters on a smear from a wound or a food-handler's swab suggests Staphylococcus, which is then confirmed by culture.

Bacilli

Bacilli are rod-shaped cells, and a bacillus divides across its short axis, so its arrangement is simpler than that of the cocci. The common patterns are single rods, pairs end to end (diplobacilli), chains (streptobacilli), and rods lying side by side or at angles like a fence or like Chinese letters (palisades). Bacillus cereus and Bacillus subtilis often form chains in culture. Corynebacterium forms palisades. Short rods that look almost like cocci are called coccobacilli, and Brucella, which can be found in raw milk, is an example.

Many of the food-poisoning bacteria that were named earlier in the unit, including Salmonella, Escherichia coli, Listeria and Clostridium, are bacilli, so the rod shape on a smear narrows the possibilities but does not name the organism.

Spiral chains

Spiral bacteria are curved or coiled rods. A comma-shaped cell is a vibrio, as in Vibrio cholerae. A rigid corkscrew is a spirillum. A flexible, tightly coiled cell that moves by twisting is a spirochaete. Spiral cells usually lie singly. When daughter cells stay joined end to end after division, they form short spiral chains. Campylobacter cells are curved or spiral, and in culture they are often seen in pairs that form S-shapes or gull-wing shapes and sometimes in short spiral chains.

Spiral bacteria are fragile when they leave the gut. Campylobacter dies quickly in dry air and in the presence of oxygen at room temperature, so its spread depends on moist, fresh contamination such as raw poultry juices on hands and boards.

2.1.2 Physiology

Physiology is the set of chemical and biological processes that keep a microorganism alive and let it multiply. The eight topics below move from energy and growth, through structure and adaptation, to genes and how they change.

2.1.2.1 Metabolic processes

Metabolism is the sum of all the chemical reactions in a cell. Catabolism breaks nutrients down to release energy, and anabolism uses that energy to build new cell parts. The energy is stored in a molecule called ATP, and every reaction is controlled by an enzyme.

Microorganisms are grouped by their source of energy and carbon. Almost all of the bacteria, yeasts and moulds in food are chemoheterotrophs: they get energy and carbon from the food itself, from sugars, proteins and fats. Algae and cyanobacteria are phototrophs: they use light energy and carbon dioxide.

The way energy is released differs by pathway:

• Aerobic respiration: glucose is broken down completely with oxygen to carbon dioxide and water, releasing a large amount of ATP. Moulds, Pseudomonas and many other spoilage organisms obtain their energy this way, so they grow on the surface of food exposed to air.
• Anaerobic respiration: some bacteria use another substance in place of oxygen, such as nitrate or sulphate.
• Fermentation: glucose is broken down only partly without oxygen, releasing a little ATP, about two molecules per molecule of glucose, and leaving products such as lactic acid, ethanol and carbon dioxide. The types of fermentation used in food are taught in the topic Fermentation processes.

A microorganism feeds by releasing exoenzymes, which are enzymes that work outside the cell and break large food molecules into small ones that can be absorbed. The enzyme explains the kind of spoilage:

Some metabolic products are directly harmful. Certain bacteria in fish that has been held warm convert the amino acid histidine into histamine, and histamine poisoning follows, with flushing, headache and rash soon after the meal. Histamine is not destroyed by cooking. Lactic acid bacteria use up lactose in milk when they make yoghurt, which is why the product has a lower lactose content than the milk it came from.

2.1.2.2 Growth and reproduction

In microbiology, growth means an increase in the number of cells, not in the size of one cell. Bacteria reproduce by binary fission: the cell enlarges, copies its chromosome, forms a dividing wall across the middle, and splits into two identical cells. The time needed for the population to double is the generation time. The number of cells after a period of growth is calculated from the starting number:

N = N₀ × 2ⁿ, where n = t ÷ g

N₀ is the starting number of cells, t is the time of growth, g is the generation time and n is the number of generations.

Example: a hypothetical bacterium has a generation time of 40 minutes, and a gram of cooked food starts with 500 cells.

After 4 hours (240 minutes):

n = 240 ÷ 40 = 6 generations

N = 500 × 2⁶ = 500 × 64 = 32,000 cells per gram

After 8 hours (480 minutes):

n = 480 ÷ 40 = 12 generations

N = 500 × 2¹² = 500 × 4,096 = 2,048,000 cells per gram

Doubling the time does not double the number of cells: it multiplies it by 64 in this example. The calculation assumes that conditions stay ideal. In real food the rate falls when nutrients, water or space become limited, and the full pattern of lag, rapid growth, steady state and decline is taught in the topic Growth pattern of microorganisms and parasites.

Other groups reproduce differently:

• Yeasts: a bud forms on the parent cell, receives a copy of the nucleus, and then separates.
• Moulds: the threads lengthen at their tips and branch, and the mould spreads by producing very large numbers of light spores, which are carried through the air to new food. Spores formed in this way are for dispersal, not for surviving heat.
• Viruses: a virus attaches to a host cell, injects or releases its genes, makes the host cell build new virus particles, and the new particles leave the cell. This happens in a living host and not in food.

2.1.2.3 Cell structure and function

Each cell structure has a job, and food treatments work by damaging one of those jobs. The table links the structure described under Cell cytology to what it does and to a point in food handling.

A dietitian uses this link to explain practical advice. Brushing and scrubbing, and not only rinsing, are needed to remove films that bacteria build on surfaces. Salting and sugaring work by drawing water out of cells. Cooking and sanitising work by damaging proteins and membranes.

2.1.2.4 Adaptation mechanism

Microorganisms can change how they behave in response to their surroundings, often within minutes. This is a change in which genes are switched on, not a change in the genes themselves. Adaptation explains why a population that survives one mild treatment is harder to kill by the next.

• Heat shock response: after a rise in temperature, cells make heat shock proteins that protect other proteins from damage, so a population heated gently may survive a later higher temperature.
• Cold shock response: when the temperature falls, cells make proteins that keep their membranes fluid and their enzymes working. This lets psychrotrophic bacteria such as Pseudomonas and Listeria grow in refrigerators.
• Acid tolerance response: exposure to a mild acid switches on genes that raise the cell's tolerance, so Escherichia coli and Salmonella that have grown in a mildly acid food survive better in a stronger acid, including stomach acid.
• Osmotic adaptation: in salty or sugary surroundings, cells build up small protective molecules inside to hold water, so Staphylococcus aureus can grow in some salted foods.
• Starvation survival: when nutrients are short, cells shrink, slow down and become more resistant. Some stay alive but cannot be grown in the laboratory, a state called viable but non-culturable, so a negative culture result does not always mean the food is free of living cells.
• Biofilm formation: cells attach to a surface and surround themselves with a layer of slime. They signal each other by chemicals in a process called quorum sensing. Cells in a film are far more resistant to cleaning agents than free-floating cells.
• Sporulation: the formation of an endospore is an extreme adaptation to poor conditions.
• Movement towards food: cells with flagella sense chemicals and swim towards nutrients, a behaviour called chemotaxis.

A practical result is that treatments such as cooking, chilling, acidifying and sanitising are applied at the full strength and time specified. A weak or short treatment can select for tougher survivors instead of killing them.

2.1.2.5 Genome structure and function

The genome is the complete set of genetic material of an organism. In many bacteria it is a single circular chromosome of DNA lying in the nucleoid, often with plasmids. Escherichia coli, for example, has a genome of about 4.6 million base pairs holding about 4,300 genes. In yeast the genome is about 12 million base pairs spread over 16 linear chromosomes in the nucleus. In a virus the genome is DNA or RNA, single-stranded or double-stranded, and often only a few thousand bases long.

A gene is a section of the genome that carries the instructions for one protein or RNA. The cell makes a copy of the gene as messenger RNA (transcription) and ribosomes read that copy to build the protein (translation). Genes are grouped and switched on or off according to need. In the lac operon of Escherichia coli, the genes for digesting lactose are expressed only when lactose is present and glucose is not, which saves the cell the energy of making enzymes it does not need.

Genes decide the traits that matter in food: the enzymes that cause spoilage, the ability to ferment, the production of toxins, and resistance to antibiotics and to heat. Some toxin genes are carried by viruses that infect bacteria. The Shiga toxin of pathogenic Escherichia coli and the cholera toxin of Vibrio cholerae are encoded by genes brought into the bacterium by a bacteriophage. Neurotoxin genes of Clostridium botulinum can lie on a phage, a plasmid or the chromosome, depending on the strain.

2.1.2.6 Horizontal gene transfer

Vertical gene transfer is the passing of genes from parent to daughter cell at division. Horizontal gene transfer is the passing of genes between cells that are not parent and offspring, often between different species. It happens in three ways:

1. Transformation: a cell takes up free DNA released from a dead cell and may build it into its own chromosome.
2. Transduction: a bacteriophage carries a piece of DNA from one bacterium to another when it infects the second cell.
3. Conjugation: two cells join through a pilus, and a copy of a plasmid passes from one to the other.

Horizontal transfer is important in food and health because a trait can spread through a population in a single generation. Genes for antibiotic resistance carried on plasmids pass between harmless gut bacteria and pathogens such as Salmonella, and this can happen in the gut of an animal or a person and on food. Toxin genes carried by phages can turn a harmless strain into a toxin producer. The same mechanism is useful in dairy starter bacteria, where the ability to use lactose and resistance to phages are often carried on plasmids that can be passed between strains.

The dietitian's role is to understand why antimicrobial resistance is a nutrition and food safety issue: infections in malnourished children are harder to treat when the organisms are resistant. Good hygiene lowers the number of infections and so the chances of transfer, antibiotics are used only on the advice of a clinician and for the full course, and food of animal origin is cooked thoroughly.

2.1.2.7 Mutation and evolution

A mutation is a permanent change in the sequence of a cell's DNA or RNA. It arises from a mistake when the genome is copied, or from damage by ultraviolet light, radiation or chemicals. A mutation can replace one base by another, add one or more bases or delete them. Many mutations make no difference, some harm the cell and a few give an advantage in the conditions it meets.

A mutation in a single cell is rare, but food and the gut can hold millions of cells in a gram, and a population can double every hour or less, so useful mutants appear regularly. RNA viruses, such as norovirus, make more copying errors than DNA organisms, which is one reason new strains appear and a person can be infected more than once.

Evolution is the change in the genetic make-up of a population over generations. It works through selection: when a treatment kills the susceptible cells, the survivors, which may carry a mutation that helps them, multiply and become the population. An example is a sanitiser used below the strength on the label. It kills the weaker cells and leaves the more tolerant to multiply. The same process produces antibiotic-resistant bacteria and strains that tolerate acid or preservatives.

Evolution also has a positive side in food: starter cultures and baking yeasts have been improved over time by selecting strains with useful traits, such as faster acid production or tolerance to alcohol.

2.1.2.8 Genetic manipulation

Genetic manipulation is the deliberate change of an organism's genes to give it a wanted trait. The simplest form is old: cultures are selected for the best performance, or a culture is exposed to a mutagen such as ultraviolet light and the improved mutants are picked out. Genetic engineering is a more precise form. In recombinant DNA technology a gene is cut out with a restriction enzyme, joined to a plasmid vector by a ligase enzyme, and introduced into a host microorganism, which then makes the protein. Genome editing tools such as CRISPR change a chosen site in the genome directly. The CRISPR system is a defence that bacteria use against phages, and it was shown to work as one in Streptococcus thermophilus, the bacterium used in yoghurt.

Applications relevant to food and nutrition include:

• Enzymes: chymosin, the enzyme that clots milk in cheese-making, is now made by engineered microorganisms instead of being taken from calf stomachs. Amylases and lactase used in food processing are also made by selected or engineered moulds and bacteria.
• Vitamins: riboflavin and cobalamin (vitamin B12) used in fortified foods and supplements are produced in industrial fermentation using selected or engineered microbes.
• Starter cultures: strains of lactic acid bacteria are selected or modified to resist phages and give consistent results.
• Detection: genetic tests, based on copying a short piece of the pathogen's DNA, identify Salmonella, Listeria and other pathogens in food faster than culture.

Genetic modification raises questions of safety, allergens, labelling and environmental release. In Kenya, work with genetically modified organisms is regulated under the Biosafety Act, 2009, which established the National Biosafety Authority. A dietitian does not need to settle these debates. The task is to give clients accurate, balanced information about what a product is and how it is regulated.

Chapter Summary

This chapter explored the anatomy and physiology of microorganisms, detailing their shapes, arrangements, cell cytology, and specific structures such as sporulation and cell arrangements like cocci, bacillus, and spiral chains. It also examined physiological aspects including metabolic processes, growth and reproduction, cell structure and function, adaptation mechanisms, genome structure, horizontal gene transfer, mutation, evolution, and genetic manipulation. The anatomy and physiology of parasites were similarly covered, focusing on their shapes, arrangements, metabolic activities, growth patterns, cell functions, and adaptation strategies. Factors influencing the growth and activity of food microorganisms and parasites were analyzed, distinguishing between intrinsic factors like nutrient content, water activity, pH, antimicrobial substances, and biological structures, and extrinsic factors such as temperature, oxygen concentration, and relative humidity. The chapter further explained the growth patterns of microorganisms and parasites through the stages of microbial growth and the microbial growth curve. Finally, the Gram staining method was discussed as a key technique for identifying and understanding microorganisms involved in food fermentation processes.