7.20 Microbes, Food, and Nutrition

Describe roles microbes play in every part of food production

Food chain: Soil/Farm → Processing → Distribution → Retail → Kitchen → Consumer

Beneficial roles	Harmful roles
Nitrogen fixation and nutrient recycling	Plant and animal pathogens
Mycorrhizal fungi improve crop growth	Contaminated water spreads disease
Rumen microbes digest cellulose	Food spoilage (~20% food loss)
Fermentation preserves food	Poor hygiene causes food-borne illness
Gut microbiome supports digestion and immunity	Microbiome disruption linked to disease

Plant and animal pathogens

• Plant pathogens: ~30% of global crop yield lost annually (~$1 trillion).

  • Banana Sigatoka fungus: threatens genetically identical Cavendish bananas. Fungicide overuse selects for resistance, similar to antibiotic resistance.

  • Tobacco mosaic virus (TMV): first virus discovered (1892); 3 genes; infects multiple plant species (e.g. tomato, tobacco, potato).

  • Monoculture: genetically identical crops → high disease vulnerability; genetic diversity increases resistance.

• Animal pathogens: ~20% of livestock production lost annually.

  • Foot-and-mouth disease virus (FMDV): infects cattle, pigs, sheep and goats; not humans.

  • UK 2001: ~10 million animals culled, £8 billion cost.

  • Indonesia 2022 outbreak → Australian biosecurity concerns.

  • Australian outbreak could cost ~$80 billion over 10 years → importance of quarantine.

Zoonosis — transmission from animals to humans

Type	Definition	Example
1	Pathogenic to both animal and human	Rabies virus — transmitted by bites; affects brain
2	Normal flora in animal, pathogenic in human	Salmonella — chicken gut flora; causes human gastroenteritis
3	Animal acts as a vector (carrier)	Lyme disease — ticks transmit Borrelia bacteria

COVID-19: Possible zoonotic origin involving bats and intermediate hosts; exact transmission pathway remains uncertain in the lecture.

Explain how microbes support plant and animal health in agriculture

Soil microbes

• Nitrogen fixation: atmospheric N₂ → NH₄⁺ (ammonium), making nitrogen accessible to plants.

• Decomposition: organic waste → inorganic nutrients recycled into soil.

• Pathogen suppression: competition limits harmful microbes.

• Detoxification: breakdown of toxins, including pesticides.

Plant–microbe mutualism

Mutualism = both organisms benefit.

	Mycorrhizal fungi	Rhizobium bacteria
Association	~90% of land plants	Legumes (peas, beans, soybeans)
Location	Plant roots	Root nodules
Plant benefits	Increased water and nutrient absorption (N, P)	N₂ fixation → NH₄⁺
Microbial benefits	Sugars from photosynthesis	Sugars from photosynthesis
Significance	Helped plants colonise land ~460 million years ago	Reduces synthetic fertiliser requirements

Microbes in herbivores

• Cellulose: abundant plant sugar polymer; animals cannot readily digest it themselves.

• Rumen microbes produce cellulase, breaking cellulose into sugars → organic acids, CO₂ and CH₄.

• Animals absorb organic acids (including butyrate) and digest microbial cells for nutrients.

• Disadvantage: methane (CH₄) is a greenhouse gas → contributes to climate change.

Describe how fermentation preserves food and adds value

Preventing food spoilage

~20% of food lost through microbial spoilage, mainly from bacteria and moulds secreting degradative enzymes.

Preservation method	Mechanism
Refrigeration	Slows microbial growth; does not stop it
High salt/sugar	Water leaves microbial cells by osmosis → inhibits growth
Acids	Lower pH → inhibit growth
Fermentation	Produces acids/alcohol → inhibits spoilage microbes

Fermentation

• Biochemical definition: anaerobic metabolism of sugars → alcohols, organic acids and/or CO₂ (pyruvate acts as an electron acceptor).

• Food science definition: microbial transformation of food to improve preservation, flavour and value.

Food	Microorganism	Process/product
Beer/wine	Saccharomyces cerevisiae	Sugar → ethanol + CO₂
Bread	S. cerevisiae + lactic acid bacteria	CO₂ causes rising
Yoghurt/cheese	Lactobacillus spp.	Lactose → lactic acid
Kimchi	Lactic acid bacteria	Acid production preserves food
Kombucha	Bacteria + yeast (SCOBY)	Sugars → acids + CO₂

Key concept: fermentation preserves food by creating conditions unfavourable for spoilage microbes while improving flavour.

Distinguish food-borne infection from food-borne intoxication

Spoilage ≠ food poisoning: spoiled food is not necessarily contaminated with pathogens, while fresh-looking food may be unsafe.

	Food-borne infection	Food-borne intoxication
Mechanism	Live pathogens ingested → survive and grow in gut	Pre-formed microbial toxins ingested
Onset (lecture comparison)	6–48 hours	Often 1–6 hours
Example	Salmonella enterica	Clostridium botulinum
Action	Infects intestinal lining	Produces potent botulinum neurotoxin under anaerobic conditions
Management	Rehydration ± antibiotics	Toxin-specific urgent treatment

Food safety risk factors

• Food origin: poultry → Salmonella; canned food → C. botulinum; seafood → Vibrio/norovirus.

• Temperature: danger zone 5–60°C; holding food for over 2 hours increases risk.

• Cross-contamination: raw chicken utensils contacting cooked food.

• Hygiene: Staphylococcus aureus from skin/hands can contaminate food and cause intoxication → handwashing is essential.

One Health connection: healthy soil → healthy animals/plants → safe processing → hygienic handling → human health.

Explain how diet and other factors shape the gut microbiome

Gut microbiome

• ~40 trillion bacteria, over 1,000 identified species; ~2 kg microbial mass (lecture estimates).

• Considered a functional organ due to its roles in health.

• Culture-independent DNA sequencing: identifies microbes without culturing them.

• 16S rRNA sequencing: PCR amplification and sequencing of bacterial ribosomal genes to identify microbial groups.

Factors affecting gut microbiome

Factor	Effect
High-fibre diet	↑ Bacteroidetes
High-fat/protein diet	↑ Firmicutes
Western diet	↓ Microbial diversity
Vaginal birth	Initial colonisation by maternal microbes
Caesarean birth	Initial colonisation by skin/hospital flora; potentially lower diversity
Antibiotics	May reduce diversity by 25–50%; recovery takes weeks–months
Probiotics	Live beneficial microorganisms (e.g. yoghurt, kefir); benefits strain-specific
Prebiotics	Dietary fibre that feeds beneficial microbes

Birth-mode effects and the long-term benefits of probiotic products remain areas of ongoing research.

Gut microbiome and health

Healthy microbiome	Disrupted microbiome
Digestion: ferments fibre → short-chain fatty acids (SCFAs), fuelling gut cells	Type 2 diabetes: altered carbohydrate fermentation and reduced SCFAs
Pathogen resistance: competitive exclusion prevents harmful microbial overgrowth	Clostridium difficile overgrowth
Immune regulation: trains immune system	Allergies/asthma: associated with reduced early microbial exposure (hygiene hypothesis)
Gut–brain axis: associated with mental health regulation	Anxiety/depression: correlations under investigation
Supports normal nutrient metabolism	Obesity: altered Firmicutes/Bacteroidetes ratio associated with energy extraction

Important: Many gut microbiome–disease associations are still being investigated; association does not necessarily establish causation.