🕰️ History & scope of microbiology
Founding figures
| Scientist | Contribution |
|---|---|
| Antonie van Leeuwenhoek | first to observe & describe microorganisms ("animalcules") with a single-lens microscope |
| Louis Pasteur | disproved spontaneous generation (swan-neck flask); pasteurization; rabies & anthrax vaccines; father of microbiology |
| Robert Koch | germ theory of disease; Koch's postulates; isolated M. tuberculosis & V. cholerae; solid culture media |
| Joseph Lister | introduced antiseptic surgical technique (carbolic acid) |
| Edward Jenner | first vaccination (cowpox → smallpox immunity) |
| Alexander Fleming | discovered penicillin from Penicillium notatum (1928) |
| Paul Ehrlich | "magic bullet" concept; salvarsan for syphilis; father of chemotherapy |
| Hans Christian Gram | developed the Gram stain (1884) |
| Dmitri Ivanovsky / Martinus Beijerinck | discovery of viruses (tobacco mosaic virus) as filterable agents |
| Elie Metchnikoff | discovered phagocytosis; cellular immunity |
Branches of microbiology
- Bacteriology – study of bacteria
- Virology – study of viruses
- Mycology – study of fungi
- Parasitology – study of protozoa & helminths
- Immunology – host defense mechanisms
- Epidemiology – patterns & spread of disease
- Microbial genetics – heredity & variation in microbes
- Applied/industrial microbiology – food, fermentation, biotechnology
📌 Key concept: germ theory of disease (Koch, building on Pasteur) established that specific microorganisms cause specific diseases — the conceptual foundation of all modern microbiology.
🗂️ Classification & taxonomy
Taxonomic hierarchy
Domain→
Kingdom→
Phylum→
Class→
Order→
Family→
Genus→
Species
Three domains of life
- Bacteria – prokaryotic, peptidoglycan cell wall (most)
- Archaea – prokaryotic, no peptidoglycan; extremophiles; not known to cause human disease
- Eukarya – includes fungi, protozoa, helminths, and humans
Nomenclature rules
- Binomial system: Genus species (e.g., Staphylococcus aureus) — genus capitalized, species lowercase, both italicized
- Abbreviated after first use: S. aureus
- Strain/subspecies may follow: E. coli O157:H7
Where do viruses, prions & viroids fit?
| Agent | Nature | Notes |
|---|---|---|
| Viruses | DNA or RNA genome + protein coat; obligate intracellular | Not classified within the three domains — acellular |
| Viroids | naked circular RNA, no protein coat | Plant pathogens |
| Prions | misfolded infectious protein, no nucleic acid | Cause spongiform encephalopathies (CJD, kuru, mad cow disease) |
Approaches to classification
- Phenotypic – morphology, staining, biochemical reactions, growth requirements
- Genotypic – 16S rRNA sequencing, GC content, DNA-DNA hybridization
- Serologic – antigenic structure (O, H, K/Vi antigens)
🔬 Prokaryotic vs eukaryotic organization
| Feature | Prokaryotes (bacteria) | Eukaryotes (fungi, protozoa, human cells) |
|---|---|---|
| Nucleus | absent (nucleoid, no membrane) | true membrane-bound nucleus |
| Chromosome | single circular, haploid | multiple linear, diploid, histone-associated |
| Ribosomes | 70S (30S + 50S) | 80S (40S + 60S); mitochondrial/chloroplast ribosomes are 70S |
| Cell wall | peptidoglycan (most bacteria) | chitin (fungi), cellulose (plants), absent in protozoa/animal cells |
| Membrane sterols | absent (except Mycoplasma – has sterols) | present (ergosterol in fungi, cholesterol in animal cells) |
| Organelles | none membrane-bound | mitochondria, ER, Golgi, lysosomes present |
| Cell division | binary fission | mitosis/meiosis |
| Size | ~1–10 µm | ~10–100 µm |
📌 Clinical relevance: differences between prokaryotic and eukaryotic ribosomes (70S vs 80S) and cell walls (peptidoglycan vs none/chitin) are the basis of selective toxicity for antibiotics and antifungals — human cells are spared.
Bacterial shapes
- Cocci – spherical (single, diplococci, chains, clusters)
- Bacilli – rod-shaped
- Coccobacilli – short, oval rods
- Spirochetes/spirilla – helical/spiral
- Vibrios – curved rods (comma-shaped)
- Pleomorphic – variable shape (e.g., Mycoplasma)
📈 Microbial growth & culture requirements
Bacterial growth curve
Lag phase→
Log (exponential)→
Stationary→
Death/decline
- Lag phase – metabolic adaptation, no division; enzyme synthesis
- Log phase – rapid, exponential division; most susceptible to antibiotics (cell-wall agents target actively dividing cells)
- Stationary phase – nutrient depletion/waste accumulation, growth rate = death rate; spore formation begins here
- Death phase – nutrient exhaustion, toxic waste buildup, exponential decline in viable cells
Requirements for growth
| Classification | Basis | Examples |
|---|---|---|
| Obligate aerobe | requires O₂ | Mycobacterium tuberculosis, Pseudomonas aeruginosa, Nocardia |
| Obligate anaerobe | killed by O₂ (lacks catalase/SOD) | Clostridium, Bacteroides |
| Facultative anaerobe | grows with or without O₂ | E. coli, Staphylococcus, most Enterobacteriaceae |
| Aerotolerant anaerobe | ignores O₂ (no catalase but has SOD or peroxidase) | Lactobacillus |
| Microaerophile | needs small amounts of O₂ | Campylobacter, Helicobacter |
| Capnophile | needs increased CO₂ | Neisseria, Haemophilus |
Other growth variables
- Temperature – most human pathogens are mesophiles (optimal ~37°C)
- pH – most bacteria prefer neutral pH (6.5–7.5); Lactobacillus tolerates acidic pH (vaginal flora)
- Osmotic pressure – halophiles require high salt (Staphylococcus aureus tolerates high salt; Vibrio requires NaCl)
Culture media types
- Enriched – blood agar, chocolate agar
- Selective – suppresses unwanted flora (e.g., MacConkey, Thayer-Martin)
- Differential – distinguishes organisms by visible reaction (e.g., lactose fermentation on MacConkey)
- Enrichment (broth) – favors growth of specific organism over others in mixed sample
🧴 Sterilization, disinfection & microbial control
Key definitions
- Sterilization – complete destruction/removal of all forms of microbial life, including spores
- Disinfection – elimination of most pathogenic organisms from inanimate surfaces (not necessarily spores)
- Antisepsis – application of a disinfectant to living tissue/skin
- Sanitization – reducing microbial load to a safe public-health level
- -cidal vs -static – "-cidal" kills organisms (bactericidal); "-static" inhibits growth without killing (bacteriostatic)
Physical methods
| Method | Mechanism / use |
|---|---|
| Autoclave (moist heat, 121°C, 15 psi) | denatures proteins; gold standard — kills spores; used for surgical instruments |
| Dry heat (160–180°C) | oxidation; for materials damaged by moisture (glassware, oils) |
| Pasteurization | brief heat (~72°C/15 sec) kills pathogens without sterilizing (kills most vegetative cells, not spores) |
| Filtration | removes microbes from heat-labile solutions/air (HEPA filters, 0.22 µm membrane filters) |
| Ionizing radiation (gamma) | damages DNA; sterilizes disposable plastics/medical supplies |
| UV radiation | forms pyrimidine (thymine) dimers in DNA; surface/air disinfection, does not penetrate |
Chemical methods
- Alcohols (ethanol/isopropanol 70%) – denature proteins; skin antisepsis; not sporicidal
- Halogens (iodine, chlorine) – oxidize/halogenate proteins; wound antisepsis, water treatment
- Aldehydes (glutaraldehyde, formaldehyde) – cross-link/alkylate proteins & nucleic acids; high-level disinfection of instruments
- Ethylene oxide gas – alkylates nucleic acids; sterilizes heat-sensitive equipment
- Quaternary ammonium compounds – disrupt membranes; surface disinfectants (limited spectrum)
- Heavy metals (silver, mercury) – denature proteins; silver sulfadiazine for burns
⚠️ High-yield distinction: bacterial endospores (Bacillus, Clostridium) are the most resistant biological structures known — resistant to boiling, alcohols, and most disinfectants. Only autoclaving, ethylene oxide gas, and prolonged exposure to high-level chemical sterilants reliably kill spores.
🤝 Normal microbiota & host relationships
Types of symbiotic relationships
| Relationship | Effect on host | Effect on microbe | Example |
|---|---|---|---|
| Mutualism | benefit | benefit | gut flora synthesizing vitamin K |
| Commensalism | no effect | benefit | skin flora (S. epidermidis) |
| Parasitism | harm | benefit | pathogenic infection |
Major normal flora sites
- Skin – S. epidermidis, diphtheroids, Propionibacterium acnes
- Nasopharynx – Viridans strep, S. aureus (carriage), Neisseria spp.
- Oral cavity – Viridans strep (dental caries, subacute endocarditis)
- Colon – highest density; Bacteroides > E. coli by count; anaerobes predominate 1000:1 over aerobes
- Vagina – Lactobacillus (maintains acidic pH, inhibits pathogen overgrowth)
- Stomach & lower respiratory tract – essentially sterile in health
Why normal flora matters
- Competitive exclusion of pathogens (colonization resistance)
- Antibiotic disruption → overgrowth of opportunists (e.g., C. difficile colitis after clindamycin, Candida after broad-spectrum antibiotics)
- Endogenous infection – normal flora causing disease outside its usual site (e.g., E. coli UTI, Bacteroides abscess after bowel perforation)
📋 Koch's postulates & establishing causation
The four classic postulates
- The organism must be found in all cases of the disease and absent from healthy individuals
- The organism must be isolated from the diseased host and grown in pure culture
- The cultured organism must cause disease when introduced into a healthy, susceptible host
- The organism must be re-isolated from the experimentally infected host and match the original
⚠️ Limitations: cannot be fulfilled for organisms that can't be cultured in vitro (e.g., Treponema pallidum, Mycobacterium leprae), viruses requiring cell culture, or asymptomatic carriers/healthy individuals who harbor the organism without disease.
Molecular Koch's postulates (updated for genes/virulence factors)
- The gene/phenotype should be associated with pathogenic strains, not avirulent ones
- Inactivating the gene should reduce virulence
- Restoring the gene should restore virulence
Chain of infection (general epidemiology model)
Reservoir→
Portal of exit→
Mode of transmission→
Portal of entry→
Susceptible host
📌 Clinical pearls: pathogenicity = ability to cause disease; virulence = degree/severity of pathogenicity; commensals become pathogenic when host defenses are breached or flora reaches an abnormal site — the recurring theme that links normal microbiota, virulence factors, and Koch's postulates together.
✔️ All concepts synthesized independently — educational use only
high‑yield