Microbiology Lecture Flashcards

What is microbiology?

• Definition: microbiology is the study of small microorganisms that cannot be seen with the unaided eye; includes bacteria, fungi, molds, yeast, viruses, and parasites.
• Scope: encompasses all aspects of microbes; most are unicellular, but not all.
• Key takeaway: microbiology covers the biology, ecology, genetics, and interactions of microbes with humans and the environment.

Microbes are everywhere

• Microbes inhabit nearly every environment on earth; the world teems with microbes.
• The human gut contains more microbes than the human population on the planet: there are vastly more microbial cells in the intestinal tract than there are humans on Earth.
• Pathogens are microbes that cause disease; most microbes are non-pathogenic and harmless to humans.
• Distinction: pathogens cause disease; non-pathogenic microbes can be beneficial or neutral.

Importance of microbes

• Ecological roles:
  • Marine and freshwater microbes sit at the bottom of the aquatic food chain.
  • Soil microbes decompose waste and fix nitrogen, enriching soil for plants.
• Photosynthesis: many microbes perform photosynthesis, contributing to global primary production.
• Human health: intestinal microbes manufacture vitamins we cannot synthesize ourselves.
• Industrial relevance: microbes produce acids, alcohols, vitamins, and drugs; they are central to food production (e.g., cheeses, yogurt) and to controlling pathogens in foods.

Industrial microbes

• Applications: production of commercially important compounds via microbial metabolism (acids, alcohols, vitamins, drugs).
• Food industry: fermentation and preservation processes rely on microbial activity.
• Food safety: microbes are used to control pathogenic microbes in consumables and processed foods.

Nomenclature (binomial naming)

• All microorganisms have two names: genus and species; both are italicized when typed.
• Genus name: capitalized; species name: lowercase.
• When referring to a microbe, both genus and species names should be used.
• Abbreviation rules: the genus name may be abbreviated to its first letter after the full name has been used once (e.g., Escherichia coli → E. coli after the first mention).
• Exception: viruses do not always follow the same abbreviation rules.

Nomenclature cont.

• Example: Escherichia coli can be abbreviated as E. coli after it has appeared in full once; the abbreviation uses the first letter of the genus and the full species name.
• Viruses: do not strictly follow these abbreviation rules.

Nomenclature (shape and environment clues)

• Scientific names often reflect shape or living environment.
• Example: Staphylococcus aureus
  • Staphylo = clustering shape of cells
  • coccus = spherical shape of the bacterium
  • aureus = Latin for golden; refers to the color of many colonies

Types of microbes

• Major groups:
  • Bacteria
  • Archaea
  • Fungi
  • Protozoa
  • Algae
  • Multicellular Animal Parasites
  • Viruses

Bacteria

• Type: prokaryotic, unicellular organisms.
• Genetic material: not enclosed in a membrane-bound nucleus (no true membrane-bound organelles).
• Common shapes: bacillus (rod), coccus (spherical), spirillum/spirilla (spiral).

Bacteria (cell structure and metabolism)

• Cell wall: composed of peptidoglycan and carbohydrates; peptidoglycan is a protein–carbohydrate complex.
• Cell wall composition is used to classify bacteria as Gram-positive (Gram+) or Gram-negative (Gram-).
• Metabolism: bacteria obtain nutrients by metabolizing organic compounds from living/dead matter; some synthesize their own nutrients.

Bacteria (reproduction and motility)

• Reproduction: binary fission (asexual).
• Motility: some are motile via flagella; others use pili or fimbriae for attachment or movement.

Archaea

• Prokaryotes with cell walls that lack peptidoglycan.
• Includes extremophiles:
  • Methanogens
  • Halophiles
  • Thermophiles
• Pathogenicity: historically not known to cause human disease; one 2006 paper suggested possible involvement in dental disease, but evidence is inconclusive.

Fungi

• Eukaryotic organisms; can be unicellular or multicellular.
• Reproduction: both asexual and sexual modes.
• Major forms: yeasts (unicellular), molds and mushrooms (multicellular).
• Size comparison: even unicellular fungi are typically larger than bacteria.

Fungi (ecology and nutrition)

• Ecology: natural decomposers; essential for nutrient cycling.
• Nutrition: do not perform photosynthesis; obtain nourishment by absorbing nutrients from surroundings.
• Reproduction: prolific spore formers; fungal spores differ from bacterial spores and enable fungi to disperse widely.

Protozoa

• Eukaryotic, unicellular, motile organisms.
• Motility: pseudopods, cilia, or flagella; diverse morphologies.
• Ecology: most are free-living in the environment; some are disease-causing parasites.
• Reproduction: can be sexual or asexual.

Algae

• Photosynthetic, eukaryotic organisms.
• Size: can be unicellular or multicellular.
• Habitat: found in fresh and saltwater environments.
• Ecological role: produce oxygen and essential carbohydrates for other organisms; metabolism relies on photosynthesis using CO₂ and light.

Multicellular Animal Parasites

• Not technically microbes, but included due to medical importance.
• Helminths: two main categories are roundworms and tapeworms.
• Identification uses techniques similar to those used for microbes.

Viruses

• Acellular (non-living) infectious entities.
• Classifications: capsid-only viruses and enveloped viruses.
• Capsid viruses: DNA or RNA core surrounded by a protein coat.
• Enveloped viruses: capsid enclosed in a lipid membrane derived from a host.
• Metabolism: viruses do not carry out metabolic reactions; require a host cell to replicate and are inert outside a living cell.

Classification of microbes (three-domain system)

• Carl Woese and George Fox (1978) proposed a three-domain system:
  • Bacteria
  • Archaea (no peptidoglycan in their cell walls)
  • Eukarya, which includes Protists, Fungi, Plants, and Animals

History and great experiments in Microbiology

• Topics covered: the presence of microbes, blocking disease transmission, treating disease, and current problems/priorities in microbiology.

Early naturalists and disease

• 13th century: disease transmission understood to some extent; quarantines implemented.
• During the Dark Ages: illness attributed to miasma (bad air) rather than microbial causes.

Microbiology: A Brief History

• 1665: Discovery of the cell by Robert Hooke; observed dried cork cells; marks the start of cell theory (cells as fundamental units of life).
• 1673: Antoni van Leeuwenhoek observes the first microbes with the first true microscope; described what he called "animalcules"; evidence for bacteria and protozoa.

Biogenesis vs. spontaneous generation

• Early debate: do microbes arise from pre-existing life (biogenesis) or spontaneously from non-living matter?
• Biogenesis: life arises from life.
• Spontaneous generation: life arises spontaneously without life antecedents.

Spontaneous generation experiments (historical view)

• Francesco Redi (1668): sealed meat experiments showed no maggots when flies could not land on meat; challenged spontaneous generation for macro-organisms.
• John Needham (1745): boiled broths appeared teeming with microbes after sealing; claimed spontaneous generation occurred.
• Leo Spallanzani: boiled broths in sealed containers did not show growth; argued that Needham’s results were due to air exposure or imperfect sealing.

Pasteur and biogenesis

• 1861: Louis Pasteur refutes spontaneous generation and supports biogenesis.
• Key design insight: create a closure system that allows air in but prevents microbial entry, demonstrating that sterile media fail to support microbial growth without external contamination.

Pasteur’s great experiment (Swan-neck flask)

• Setup shows air enters but dust and microorganisms are trapped in the neck; over time, sterile broth remains free of life if entry is blocked.
• Experiments demonstrated: life in the broth comes from microbes in the air; heat kills microorganisms; nutrient access can be blocked to prevent growth.

Beyond spontaneous generation

• Pasteur’s work extended to show microbes in air and on living/non-living matter; established heat sterilization and aseptic techniques that prevent contamination of surfaces and materials by microbes.
• Aseptic technique: a set of procedures to prevent unwanted microbial contamination; foundational to modern lab work and clinical practice.

Blocking disease transmission (early public health and vaccines)

• 1798: Edward Jenner develops the smallpox vaccine by using cowpox to primed immunity against smallpox.
• 1854: John Snow maps cholera cases in London; links outbreak to a contaminated water source and ends the outbreak by removing the source.
• Pasteur’s fermentation work influences disease control and food safety (see pasteurization).
• Lister’s aseptic surgery: applying antiseptic techniques (carbolic acid/phenol) to surgical equipment and wounds reduced postoperative infections.
• Koch’s postulates (1876): a framework to link specific microbes to specific diseases; still foundational today.

Koch’s postulates (steps)

• Postulate 1: The same microorganisms are present in every case of the disease.
• Postulate 2: The microorganisms are isolated from diseased tissue and grown in pure culture.
• Postulate 3: The microorganisms from the pure culture are inoculated into a healthy, susceptible animal; disease is reproduced.
• Postulate 4: The identical microorganisms are isolated and recultivated from the experimental animal.

Blocking disease (summary of key researchers)

• Jenner: smallpox vaccine from cowpox primed the body for future pathogen exposure.
• Snow: epidemiology showing transmission via contaminated water.
• Pasteur: spoilage in products linked to microbes; developed pasteurization.
• Lister: aseptic surgical techniques improved patient outcomes.
• Koch: established postulates to identify disease-causing microbes; method still used to trace illness sources.
• Together, these contributions underpin the germ theory of disease: microorganisms cause disease.

Treating disease

• Prevention is ideal but not always possible; emphasis on treating infections when they occur.
• Antibiotics have dramatically extended life expectancy; antibiotics have been in use for less than a century, yet life expectancy has risen by about 30 years, illustrating the impact of antimicrobial therapy.

Oldest known treatments for disease

• 2000 BCE: Egyptians reportedly produced/ingested tetracycline as a contaminant in beer.
• ~1700: Quinine used to treat malaria by European powers; roots in traditional/native usage.
• 1910: Ehrlich pioneers chemotherapy with salvarsan (an arsenic-containing compound) to treat syphilis.

Fleming and the birth of antibiotics

• 1928: Alexander Fleming discovers penicillin when mold inhibits bacterial growth; later purified and mass-produced by Florey and Chain by 1940.
• World War II relevance: penicillin mass production timely for WWII.

Treating disease (current antimicrobial landscape)

• A broad range of antimicrobial agents exists against bacteria, fungi, protists, and viruses.
• Problems: there is a slowdown in new antibiotic discovery; resistance is rising as existing drugs are reused and misused.
• Many novel antibiotics are not reaching late-stage development; risk of resistance outpacing new drugs.

DNA structure and the modern era

• 1953: James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin determine the structure of DNA; Franklin contributed critical experimental work.
• Note: Franklin did experimental work; Nobel Prize awarded to the others in 1962; historical discussions around recognition.

Modern Microbiology disciplines

• Bacteriology: study of bacteria
• Mycology: study of fungi
• Parasitology: study of parasites and protozoa
• Immunology: study of immunity
• Virology: study of viruses
• Recombinant DNA Technology: genetic engineering
• Epidemiology: study of disease spread and control

Microbes and disease

• Normal microbiota (flora): bacteria that are a natural, harmless, and sometimes beneficial part of the human body.
• Pathogens: microbes that cause infectious disease.
• Infectious disease is a major global health issue with a spectrum of illnesses and death tolls.

Infectious diseases: global impact

• Examples of major infectious diseases include respiratory infections, diarrheal diseases, HIV/AIDS, tuberculosis, malaria, meningitis, pertussis, measles, hepatitis B, among others.
• Mortality scales with disease burden across populations; data illustrate global impact (illustrative counts shown in public health data).

Problems facing modern microbiologists

• Mobility and globalization: high rates of travel facilitate rapid disease spread; example: in 2011, approximately 4 imes10^9 people flew on domestic airlines, enabling rapid cross-border transmission.
• Emerging and re-emerging diseases: more new human diseases identified in the last few decades; diseases spreading to new regions (e.g., West Nile Virus, Zika).
• Antimicrobial resistance: overuse/misuse of antibiotics in humans and animals drives resistance; resistance is increasing faster than new drugs are developed; some pathogens become untreatable with existing drugs.
• Climate change: shifting habitats alter the distribution of vectors (ticks, mosquitoes) and pathogens; leads to new disease risks.
• Human factors: risk of harmful misuse or weaponization of biological agents (e.g., smallpox, plague, anthrax) with potentially catastrophic consequences if diverted to intentional misuse.

Closing thoughts

• Significant progress has occurred in microbiology over a relatively short time, particularly in the last century.
• Current challenges span mobility, disease emergence, antimicrobial resistance, climate change, and potential misuse of biological agents.
• Solutions require collaboration across disciplines and proactive investment in science and public health—this could include you as a future contributor, contingent on sustained funding and support.

Lab and preparation notes

• Reading tip: Review the first lab materials before the lab class to connect theoretical concepts with practical techniques.