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STUDY GUIDE CHAPTER 1

Microorganisms and human health

  • Microorganism vs microbiome

    • Microorganisms: tiny living organisms (bacteria, archaea, fungi, protozoa, algae, viruses) that may inhabit humans and the environment.
    • Microbiome: the collective genome and community of microorganisms living in a defined environment (e.g., human gut, skin, oral cavity).
    • Health relevance: a balanced microbiome supports digestion, immune development, barrier function; dysbiosis can contribute to metabolic, inflammatory, and infectious diseases; some microbes provide essential functions (e.g., vitamin synthesis, competition with pathogens).

  • Normal flora

    • Resident microorganisms that colonize surfaces (skin, mucosa) without causing disease in healthy individuals.
    • Provide protection via niche occupation, antagonism to pathogens, and immune system education.

Key concepts in infectious disease biology

  • Infectious disease vs disease

    • Infectious disease: illness caused by a pathogenic organism (bacteria, virus, fungus, parasite) that can be transmitted between hosts.
    • Disease: impairment of normal function; not all diseases are infectious.

  • Epidemic, Endemic, Pandemic

    • Epidemic: a sudden increase in cases above the expected level in a specific population or region.
    • Endemic: disease consistently present at a baseline level within a population or area.
    • Pandemic: epidemic that spreads across multiple countries or continents.

  • Newly emerging vs reemerging infectious diseases

    • Emerging: diseases that are newly identified or rapidly increasing in incidence or geographic range.
    • Reemerging: diseases that were under control or declining but later increase again due to factors like waning immunity, pathogen evolution, or changes in surveillance.

  • Newly emerging/reemerging disease framework

    • Causative organism: the pathogen responsible (bacteria, virus, fungus, parasite).
    • Mode of transmission: how the pathogen spreads (airborne, droplet, contact, vector-borne, fecal-oral, etc.).
    • Control: strategies to prevent or reduce transmission (vaccination, hygiene, vector control, antimicrobial stewardship, public health interventions).

  • Diseases listed (examples of infectious diseases to know for exam)

    • Measles
    • Causative organism: measles virus (a paramyxovirus).
    • Mode of transmission: airborne/respiratory droplets.
    • Control: vaccination (MCV); isolation; herd immunity.
    • Influenza
    • Causative organism: influenza virus (A/B/C strains).
    • Mode of transmission: respiratory droplets and aerosols.
    • Control: annual vaccination; antiviral treatment; infection control measures.
    • Pertussis (Whooping Cough)
    • Causative organism: Bordetella pertussis.
    • Mode of transmission: respiratory droplets.
    • Control: vaccination (DTaP/Tdap); antibiotics for cases;
      public health surveillance.
    • MRSA (Staphylococcus aureus infection)
    • Causative organism: Staphylococcus aureus (methicillin-resistant strains).
    • Mode of transmission: direct/indirect contact; fomites.
    • Control: hygiene, contact precautions, antimicrobial stewardship, decolonization in outbreaks.
    • Lyme disease
    • Causative organism: Borrelia burgdorferi.
    • Mode of transmission: tick vectors (Ixodes spp.).
    • Control: tick avoidance, environmental management, antibiotics for early infection.

Historical development in medical microbiology

  • Anton van Leeuwenhoek

    • Contributions: first to observe and describe microorganisms using powerful single-lens microscopes; coined observations of "animalcules".

  • Robert Hooke

    • Contributions: described cells in cork and early microscopy; foundational to modern cell theory.

  • Holmes and Semmelweis

    • Oliver Wendell Holmes Sr.: proposed transmission of puerperal fever via contaminated hands; emphasized antisepsis.
    • Ignaz Semmelweis: introduced handwashing with chlorinated lime solution to reduce maternal mortality from puerperal fever.

  • Carl Linnaeus

    • Contributions: system of nomenclature (binomial nomenclature) and taxonomy for organizing living organisms.

  • Louis Pasteur

    • Contributions: germ theory of disease; pasteurization; vaccines (anthrax, rabies); fermentation science.

  • Robert Koch

    • Contributions: Koch's postulates establishing a causal link between specific microbes and diseases; techniques for isolation and visualization.

  • Joseph Lister

    • Contributions: antiseptic surgery using carbolic acid (phenol); promoted aseptic techniques.

  • Paul Ehrlich

    • Contributions: concept of chemotherapy and synthetic drugs; “magic bullet” approach; arsenic-based therapy (e.g., Salvarsan for syphilis).

  • Alexander Fleming

    • Contributions: discovery of penicillin; foundation of antibiotic therapy.

  • Edward Jenner

    • Contributions: smallpox vaccination; early immunology principles.

  • Exam note: For influenza, be prepared to match the scientist to the contribution (e.g., Pasteur and vaccines, Fleming and antibiotics, Jenner and vaccination, Koch and postulates, Semmelweis and hand hygiene).

New branches in microbiology (definitions)

  • Immunology
    • Study of the immune system, host-pathogen interactions, innate and adaptive responses, vaccines, immunopathology.
  • Virology
    • Study of viruses: structure, replication, host interaction, viral diseases, antiviral strategies.
  • Clinical microbiology
    • Diagnosis and management of infectious diseases in clinical settings; culture, identification, susceptibility testing, infection control.
  • Mycology
    • Study of fungi: yeasts and molds, fungal infections, taxonomy, antifungal therapies.
  • Industrial microbiology
    • Use of microorganisms for industrial processes: fermentation, production of enzymes, biofuels, bioremediation, bioproducts.
  • Recombinant DNA technology
    • Genetic engineering to modify organisms for research, medicine, and industry; techniques include cloning, plasmids, gene editing, expression systems.

System of nomenclature and basic taxonomy (Linnaean framework)

  • Naming and classification basics (Linnaeus)
    • Genus: a group of related species.
    • Species: basic unit of classification; organisms that can interbreed and produce fertile offspring (conceptually applied to microbes with distinct characteristics).
    • Example: Escherichia coli (Genus: Escherichia; Species: coli).
  • Three domains and four (traditional) kingdoms
    • Three domains: Bacteria, Archaea, Eukarya.
    • Four kingdoms within Eukarya (traditional): Protista, Fungi, Plantae, Animalia.
    • Note: Modern taxonomy is more nuanced, but these categories are commonly tested on exams.
  • Diversity of microorganisms (types to know)
    • Bacteria
    • Archaea
    • Fungi
    • Protozoa
    • Algae
    • Viruses

Diversity and characterizations of microorganisms

  • Unicellular vs multicellular
    • Bacteria: unicellular
    • Archaea: unicellular
    • Fungi: both unicellular (yeasts) and multicellular (molds, mushrooms)
    • Protozoa: mostly unicellular
    • Algae: can be unicellular or multicellular
    • Viruses: acellular (not cells)
  • Prokaryotic vs eukaryotic
    • Prokaryotic: Bacteria, Archaea (no true nucleus; no membrane-bound organelles)
    • Eukaryotic: Fungi, Protozoa, Algae, Animals, Plants
    • Viruses: non-cellular; require host cells to replicate
  • Nutrition (general patterns)
    • Bacteria/Archaea: autotrophs or heterotrophs; photoautotrophs, chemolithoautotrophs, chemoheterotrophs, photoheterotrophs.
    • Fungi: heterotrophic; absorb nutrients from environment.
    • Protozoa: heterotrophic; ingest or absorb nutrients.
    • Algae: photoautotrophic (photosynthetic).
    • Viruses: no metabolism of their own; rely on host metabolism.
  • Locomotion (general)
    • Bacteria: flagella, pili; some glide.
    • Archaea: flagella-like structures; varied motility.
    • Fungi: most non-motile; spores may disperse passively.
    • Protozoa: cilia, flagella, amoeboid motion.
    • Algae: some motile with flagella; others non-motive.
    • Viruses: no locomotion of their own; movement via host cell entry.
  • Reproduction (general)
    • Bacteria/Archaea: asexual binary fission; some horizontal gene transfer (transformation, conjugation, transduction).
    • Fungi: asexual (budding, spore formation) and sexual reproduction; complex life cycles.
    • Protozoa: sexual and asexual reproduction; diverse life cycles.
    • Algae: sexual and asexual reproduction; varied lifecycles.
    • Viruses: replication via host cellular machinery; assembly and release depend on virus family.

Beneficial activities of microorganisms

  • Roles in ecosystems and health

    • Important part of the food chain: producers, decomposers, and nutrient recyclers.
    • Recycling of chemical elements: part of nitrogen, carbon, and oxygen cycles.
    • Nitrogen cycle: ext{N}2 ightarrow ext{NH}3
      ightarrow ext{NO}2^- ightarrow ext{NO}3^-
    • Carbon cycle: ext{CO}2 ightarrow ext{organic matter} ightarrow ext{CO}2
    • Oxygen cycle: photosynthesis by algae and plants; respiration and decay release CO2 and water; microbes participate in oxidation-reduction processes.
    • Photosynthesis: microbes (e.g., cyanobacteria, algae) convert light energy into chemical energy, producing organic matter and O2.
    • Synthesis of vitamins: gut microbiota synthesize vitamin K and several B vitamins essential for host metabolism.

  • Commercial and environmental applications

    • Synthesis of chemical products: enzymes, biofuels, organic acids, solvents.
    • Food industry: fermentation (bread, yogurt, cheese, beer), flavor and texture development.
    • Sewage treatment: microbial communities degrade organic waste and remove nutrients.
    • Clean up of toxic dumps: bioremediation using microbes to degrade pollutants.
    • Insect pest control: microbial pesticides (e.g., Bacillus thuringiensis) used to manage pests in agriculture.

Exam-oriented notes and connections

  • Expect multiple-choice or matching questions on:

    • Names and contributions of key historical figures (Pasteur, Koch, Lister, Fleming, Jenner, Semmelweis, Leeuwenhoek, Hooke, Ehrlich, Linnaeus).
    • Classification schemes (three domains, four kingdoms, genus vs species).
    • Types of microorganisms, their characteristics, and whether they are prokaryotic or eukaryotic, unicellular or multicellular, and their nutrition modes.
    • Definitions and examples of infectious diseases, epidemics, endemics, and pandemics.
    • Benefits of microorganisms and their roles in cycles, health, and industry.

  • Conceptual connections to foundational principles

    • Germ theory of disease (Pasteur, Koch) linked microbes to disease causation and hygiene practices (Lister).
    • Taxonomy and nomenclature (Linnaeus) provide a framework for communicating about organisms.
    • Immunology and vaccination advances (Jenner; later developments) underpin modern public health.
    • Antibiotics and antimicrobial stewardship (Fleming; Ehrlich) transformed clinical treatment, with ongoing concerns about resistance (MRSA as an example).

  • Ethical, philosophical, and practical implications

    • Antibiotic resistance and responsible use of antimicrobials.
    • Vaccination ethics and public health policy (herd immunity, access, misinformation).
    • Safety in handling microorganisms in labs and clinical settings; importance of asepsis and biosafety.

  • Numerical, statistical, or mathematical references

    • Nitrogen, carbon, and oxygen cycles involve fluxes and rates; representative simplified pathways shown above.
    • Quantitative assessment of disease spread (epidemics/pandemics) relies on reproduction number (R0), incubation period, case fatality rate, and surveillance data. While not provided in the transcript, these are foundational concepts in exam questions.

  • Examples and hypothetical scenarios you might encounter

    • Scenario: A region experiences a measles outbreak despite vaccine availability. Analyze causes (vaccine hesitancy, waning immunity, importation) and propose control measures (catch-up vaccination, public health messaging, isolation of cases).
    • Scenario: An outbreak of MRSA in a hospital. Propose infection-control strategies, including hand hygiene, contact precautions, and antimicrobial stewardship.
    • Scenario: A farmer wants to use a microbial-based biopesticide. Explain how Bt toxins work and regulatory/eco-safety considerations.

  • Quick-reference links to the core topics

    • Definitions: infectious disease, epidemic, endemic, pandemic, normal flora.
    • Emerging/reemerging diseases: causative organisms, transmission, control.
    • Historical contributions: Leeuwenhoek, Hooke, Holmes, Semmelweis, Linnaeus, Pasteur, Koch, Lister, Ehrlich, Fleming, Jenner.
    • Branches of microbiology: immunology, virology, clinical microbiology, mycology, industrial microbiology, recombinant DNA technology.
    • Taxonomy basics: genus, species, three domains, four kingdoms.
    • Diversity and types of microorganisms: bacteria, archaea, fungi, protozoa, algae, viruses.
    • Beneficial roles: nutrient cycles, photosynthesis, vitamin synthesis, fermentation, bioremediation, pest control.