Agricultural Microbiology - MICR20010

Agricultural Microbiology - MICR20010

• Course code: MICR20010
• Course name: Agricultural Microbiology
• Lecturer: Dr. Tadhg Ó Cróinín

Course Schedule

• Lectures: Mondays, 2-3 pm (A-H2.18-SCH) and Fridays 2-3pm (B004 HEA)
• Practicals: Wednesdays, 11 am - 1 pm (E2.46, E2.47, E2.48) and Wednesdays, 3 pm - 5 pm (E2.46, E2.47, E2.48)
• Practical schedule available in document

Assessments

• Practical accounts: 30%
• Two practical reports (online after practicals, including write-ups): 15%
• Practical exam (online, Friday Nov 22nd, 2-3 pm): 15%
• End-of-term MCQ exam in RDS: 70%

Microbiology

• The study of microorganisms
• Bacteria and viruses that cause disease
• Bacteria helpful for antibiotics and probiotics
• Biotech industry

Importance of Microbiology

• Industrial microbiology: food and beverage, health industries
• Environmental microbiology: bacteria's role in ecosystems, pollution and bioremediation
• Clinical microbiology: vaccine development, antibiotic treatments, diagnostics

Remaining Lectures

• Lecture 10: Microorganisms and Disease
• Lecture 11: The Immune System
• Lecture 12: Pathogenic Bacteria
• Lecture 13: Pathogenic Fungi and Viruses
• Lecture 14: Antibiotic Resistant Microorganisms
• Lecture 15: Microbiology in the Food Industry - The Fungi
• Lecture 16: Microbiology in the Food Industry - Fermentations
• Lecture 17: The Nitrogen Cycle

Microorganisms and Disease

• Microorganisms have various roles in disease and complex relationships with humans.
• Mutualism: beneficial associations, e.g., bacteria providing vitamin precursors in the gut.
• Commensalism: passive associations, e.g., non-pathogenic Staphylococcus.
• Parasitism: microorganisms harm, e.g. pathogenic bacteria

Good vs. Bad Bacteria

• Probiotics (good bacteria): Clostridium butyricum (produces important fatty acids), Bifidobacteria (modulates immune responses), Lactobacilli (produces vitamins).
• Bad bacteria (make you sick): Clostridium difficile (causes diarrhoea), Campylobacter (food poisoning), Enterococcus faecalis (post-surgical infections).

Koch's Postulates

• Criteria to prove a microbe is a pathogen:
  • Microbe present in diseased but not healthy animals
  • Microbe isolated and cultured in pure form
  • Healthy animal inoculated with pure culture; develops disease
  • Same microbe is isolated and cultured from the inoculated animal.

Exceptions to Koch's Postulates

• Some pathogens are difficult to culture
• Some diseases are caused by combinations of pathogens/physical/environmental/genetic factors
• Ethics with animal models; cannot be fully applied to HIV

Virulence Factors

• Features that contribute to pathogenicity: Toxins (host-specific), Adhesins (specific receptors), Endotoxins (e.g., LPS).
• Virulence factors contribute to host specificity

Extracellular Enzymes

• Microorganisms secrete enzymes to alter their environment.
• Protect from the immune system: Coagulase formation of clots to hide from immune responses.
• Damage immune cells: Leukocidins, destroy white blood cells, Catalase protects from reactive oxygen species.

Toxins

• Exotoxins:
  • Cytotoxins: kill or affect the functions of host cells
  • Neurotoxins: interfere with nerve cells
  • Enterotoxins: Affect cells lining the gut tract (e.g., Clostridium, Staphylococcus aureus, E. coli strains).

How is Disease Transmitted?

• Microbes can be present and exploit changes in the environment
• Opportunistic pathogens; such as S. aureus and C. difficile.

Modes of Transmission

• Contact transmission (direct/indirect)
• Vehicles (air, water, food)
• Vectors (biological/mechanical)

Basic Protections from Infection

• Skin: barrier of tightly packed cells. Cuts; entry point
• Mucous membranes: line body cavities, exposed to the outside world (e.g., nose)
• Adherence required for establishment of colonies

Adaptive Immunity

• Develops as we encounter pathogens
• Antigens trigger specific response targeting bacterial cell walls, capsules, flagella, proteins and toxins.
• Food can contain antigens that cause allergic reactions.

Antigens

• Recognized by antigenic determinants (epitopes).
• Large antigens (5-100 kDa) better than smaller ones. Made of proteins, glycoproteins.
• Smaller molecules (haptens; <5 kDa); cannot induce immune response on their own but bind to larger molecules. Need larger carrier for recognition.

Types of Antigens

• Exogenous antigens: from outside the body (toxins, components of microbial cell walls).
• Endogenous antigens: from inside the body (produced by microorganisms inside host cells).
• Autoantigens: present on normal, uninfected cells, sometimes inappropriately targeted by the immune system.

How to Detect Antigens

• Correctly identifying antigens is crucial for immune responses.
• Some pathogens mimic host antigens
• Antibodies are used for detection. (e.g., IgM, IgA, IgD, IgG, IgE)

Antibodies

• 4 polypeptide chains (2 identical heavy chains, 2 identical light chains)
• Disulfide bonds link chains
• Y shape structure
• Antigen-binding site; for recognition

Next lecture:

• Monday Nov 4th: How the immune system helps defend against pathogens

This quiz covers key concepts in Agricultural Microbiology, including the role of microorganisms in agriculture and industry. It assesses your understanding of practical applications and fundamental microbiological theories relevant to the course. Brush up on important topics like industrial and environmental microbiology to ace the quiz!