General microbiology
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I now have sufficient content from Jawetz, Melnick & Adelberg's Medical Microbiology to compile a thorough general microbiology overview. Let me write the comprehensive response.
General Microbiology - Comprehensive Overview
Based on Jawetz, Melnick & Adelberg's Medical Microbiology, 28th Edition
1. What is Microbiology?
Microbiology is the study of microorganisms - a large, diverse group of microscopic organisms that exist as single cells or cell clusters, plus viruses (microscopic but not cellular). Their impact is enormous:
- There are 5 × 10³⁰ microbial cells on Earth; excluding cellulose, they make up ~90% of the biomass of the entire biosphere
- 50-60% of the cells in the human body are microbes
- The human gut flora alone contains 150× more genes than the human genome
- Ocean viruses cause ~1 × 10²³ infections per second, removing 20-40% of all bacterial cells daily
- Jawetz Medical Microbiology, 28e, Ch. 1
2. Classification of Microorganisms
| Group | Type | Key Features |
|---|---|---|
| Bacteria | Prokaryote | No true nucleus, peptidoglycan cell wall |
| Archaea | Prokaryote | Extremophiles, no peptidoglycan |
| Fungi | Eukaryote | Chitin cell wall, absorptive nutrition |
| Protozoa | Eukaryote | Unicellular, often motile |
| Algae | Eukaryote | Photosynthetic, aquatic |
| Viruses | Acellular | Obligate intracellular, DNA or RNA genome |
| Prions | Acellular | Infectious misfolded proteins |
| Viroids | Acellular | Naked circular RNA (plant pathogens) |
Prokaryote vs. Eukaryote - Key Differences
| Feature | Prokaryote (Bacteria) | Eukaryote (Fungi, Protozoa) |
|---|---|---|
| Nucleus | Absent (nucleoid only) | True membrane-bound nucleus |
| Chromosome | Usually single circular DNA | Multiple linear chromosomes |
| Mitochondria | Absent | Present |
| Ribosomes | 70S (50S + 30S) | 80S (60S + 40S) |
| Cell division | Binary fission | Mitosis/meiosis |
| Cell wall | Peptidoglycan (most bacteria) | Chitin (fungi) or absent |
- Jawetz Medical Microbiology, 28e, Ch. 2
3. Bacterial Cell Structure
The Nucleoid
Prokaryotes have no true nucleus; instead they package their DNA in a structure called the nucleoid. Most bacteria have a single, continuous circular chromosome (0.58 to ~10 million base pairs). Key exceptions:
- Vibrio cholerae and Brucella melitensis - two dissimilar chromosomes
- Borrelia burgdorferi and Streptomyces coelicolor - linear chromosomes
Rapidly growing bacteria have more nucleoids per cell than slowly growing ones. All copies are identical - prokaryotic cells are haploid.
Cytoplasmic Structures
- No mitochondria or chloroplasts - electron transport enzymes are in the cytoplasm membrane instead
- 70S ribosomes (50S + 30S subunits) - the target of many antibiotics (aminoglycosides, macrolides, tetracyclines, chloramphenicol)
- Plasmids - small, extrachromosomal circular DNA molecules carrying genes for antibiotic resistance, toxins, and other virulence factors
The Cell Envelope (Critical!)
The cell envelope is actually more complex in prokaryotes than in eukaryotes.
Gram-Positive vs. Gram-Negative Cell Walls
| Feature | Gram-Positive (purple) | Gram-Negative (pink/red) |
|---|---|---|
| Peptidoglycan layer | Thick | Thin |
| Teichoic acids | Present | Absent |
| Outer membrane | Absent | Present |
| Lipopolysaccharide (LPS/endotoxin) | Absent | Present |
| Porin proteins | Absent | Present |
| Periplasmic space | Absent | Present |
| Examples | Staphylococcus, Streptococcus, Bacillus | Escherichia, Neisseria, Pseudomonas |
The Gram stain works because Gram-positive bacteria retain the crystal violet-iodine complex after alcohol wash; Gram-negatives lose it (their thin peptidoglycan and lipid-rich outer membrane allow the dye to leach out) and are counterstained red with safranin.
Peptidoglycan
A complex polymer with:
- Backbone: alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
- Tetrapeptide side chains attached to NAM
- Cross-links between side chains (more extensive in Gram-positives)
This layer gives osmotic protection against the 5-20 atm internal pressure of bacterial cells. Beta-lactam antibiotics (penicillins, cephalosporins) and vancomycin target its synthesis.
Acid-Fast Cell Wall (Mycobacteria)
Contains large amounts of long-chain mycolic acids bound to arabinogalactan. The waxy lipid coat makes them resistant to ordinary stains and many disinfectants. The Ziehl-Neelsen (acid-fast) stain uses heated carbol fuchsin.
External Structures
| Structure | Function | Clinical Relevance |
|---|---|---|
| Capsule / Glycocalyx | Anti-phagocytic; protects against desiccation | Virulence factor - encapsulated bacteria (e.g., S. pneumoniae) evade phagocytosis |
| Flagella | Locomotion (chemotaxis) | Monotrichous, peritrichous, etc.; H-antigen in serotyping |
| Pili (Fimbriae) | Adhesion to host surfaces; sex pili for conjugation | Virulence - adhesins; horizontal gene transfer |
| Endospores | Survival under nutrient starvation | Highly resistant to heat, desiccation, chemicals |
Endospores
Formed by Bacillus (aerobic) and Clostridium (anaerobic). Triggered by carbon, nitrogen, or phosphorus depletion. A 7-stage differentiation process produces a metabolically dormant spore surrounded by a cortex of modified peptidoglycan and a spore coat. Spores contain dipicolinic acid (helps heat resistance) and small acid-soluble spore proteins (SASPs) protecting DNA.
Germination is triggered by favorable nutrients + activation stimulus. The spore's extreme resistance means spore-forming bacteria require autoclaving (121°C, 15 psi, 15-20 min) for sterilization.
4. Viruses
Viruses are obligate intracellular parasites. They lack ribosomes and cannot self-replicate - they only acquire the ability to reproduce when infecting a host cell.
Structure
- Nucleic acid core: either DNA or RNA (never both), single- or double-stranded
- Capsid: protein coat protecting the nucleic acid; determines host specificity
- Envelope (some viruses): lipid bilayer derived from host cell, with viral glycoproteins embedded (e.g., HIV gp120, influenza hemagglutinin)
Capsid symmetry:
- Icosahedral (e.g., adenovirus, poliovirus)
- Helical (e.g., rabies, Ebola)
- Complex (e.g., poxviruses, bacteriophages)
Viral Replication Cycle
- Attachment - viral surface protein binds specific host receptor (tropism)
- Penetration / Entry - whole virus or nucleic acid enters cell
- Uncoating - capsid removed, genome exposed
- Replication - viral genome redirects host machinery to make viral components
- Assembly - new virions assembled
- Release - via budding (enveloped) or cell lysis (non-enveloped)
Provirus: viral DNA integrated into host chromosome (retroviruses like HIV, herpesviruses in latency)
Viroids vs. Prions
- Viroids: naked circular ssRNA, no protein coat, no protein-encoding genes, infect plants (e.g., potato spindle tuber viroid). Replicated by host RNA polymerase.
- Prions: infectious misfolded proteins (PrP^Sc). Cause spongiform encephalopathies (Creutzfeldt-Jakob disease, scrapie, BSE). No nucleic acid - protein alone is infectious.
5. Fungi
Eukaryotes with chitin cell walls. Two main morphologies:
- Yeasts: unicellular, reproduce by budding (e.g., Candida, Cryptococcus)
- Molds (Hyphae/Mycelium): multicellular, filamentous (e.g., Aspergillus, Rhizopus)
- Dimorphic fungi: switch between forms depending on temperature - mold at 25°C (environment), yeast at 37°C (host) - e.g., Histoplasma, Blastomyces, Coccidioides
The fungal cell membrane contains ergosterol (vs. cholesterol in humans) - target of antifungals (azoles, amphotericin B, nystatin).
6. Protozoa
Unicellular eukaryotes, often motile. Classified by locomotion:
- Amoebae - pseudopods (Entamoeba histolytica - dysentery)
- Flagellates - flagella (Giardia, Trypanosoma, Leishmania)
- Ciliates - cilia (Balantidium coli)
- Sporozoa (Apicomplexa) - no independent motility (Plasmodium - malaria, Toxoplasma, Cryptosporidium)
7. Bacterial Growth
Growth Curve (Batch Culture)
- Lag phase: metabolic activity, enzyme synthesis - no cell division yet
- Log (exponential) phase: maximal growth rate; most susceptible to antibiotics; doubling time constant
- Stationary phase: nutrient depletion = death rate; growth rate = death rate; total count stable
- Death (decline) phase: death > growth; toxic metabolite accumulation
Growth Requirements
| Requirement | Categories |
|---|---|
| O₂ | Obligate aerobe, obligate anaerobe, facultative anaerobe, microaerophile, aerotolerant anaerobe |
| Temperature | Psychrophile (<20°C), mesophile (20-45°C, most pathogens), thermophile (>45°C) |
| pH | Most bacteria: 6.5-7.5; H. pylori tolerates acidic stomach |
| Carbon source | Autotrophs (CO₂) vs. heterotrophs (organic carbon) |
| Energy source | Phototrophs (light) vs. chemotrophs (chemical oxidation) |
Generation Time
Most pathogenic bacteria divide every 20-60 minutes under ideal conditions (E. coli ~20 min; M. tuberculosis ~20 hours - explains why TB treatment takes months).
8. Bacterial Genetics
DNA Transfer Mechanisms
| Mechanism | Description | Requires Cell Contact? |
|---|---|---|
| Transformation | Uptake of naked DNA from environment | No |
| Transduction | DNA transfer via bacteriophage | No |
| Conjugation | Direct cell-to-cell DNA transfer via sex pilus | Yes |
These mechanisms drive horizontal gene transfer (HGT) - the main mechanism by which antibiotic resistance spreads between bacteria.
Mutations
- Point mutations: substitution, insertion, deletion
- Transposons: mobile genetic elements that "jump" between DNA regions; carry resistance genes
- Plasmids: extrachromosomal DNA; resistance plasmids (R-plasmids) transferable by conjugation
9. Staining Techniques
| Stain | Target | Result |
|---|---|---|
| Gram stain | Cell wall | G+: purple; G-: pink |
| Acid-fast (Ziehl-Neelsen) | Mycolic acid (Mycobacteria, Nocardia) | AFB: red; background: blue |
| Giemsa | Blood parasites, Chlamydia, Rickettsia | Variable colors |
| India ink (negative stain) | Cryptococcus capsule | Clear halo on dark background |
| PAS stain | Fungal cell walls, Whipple's disease | Magenta/red |
| Silver stain (Gomori) | Fungi, Pneumocystis jirovecii | Black |
| Spore stain (Schaeffer-Fulton) | Endospores | Spores: green; vegetative cells: red |
10. Sterilization & Disinfection
| Method | Mechanism | Application |
|---|---|---|
| Autoclave (121°C, 15 min) | Moist heat denaturation | Kills all including spores - TRUE sterilization |
| Dry heat (160°C, 2 hr) | Oxidation | Glassware, powders |
| Pasteurization | Kills non-spore-forming pathogens | Milk, liquids |
| Filtration (0.22 µm) | Mechanical removal | Heat-sensitive solutions, air (HEPA) |
| UV radiation | DNA thymine dimer formation | Surface decontamination |
| Gamma radiation | DNA damage | Single-use medical devices |
| Ethylene oxide gas | Alkylation of proteins/DNA | Heat-sensitive equipment |
| Alcohol (70%) | Protein denaturation + lipid dissolution | Skin antisepsis |
| Bleach (hypochlorite) | Oxidation | Surface disinfection |
11. Antimicrobial Drug Targets (Overview)
| Target | Drug Class | Example |
|---|---|---|
| Cell wall synthesis | Beta-lactams | Penicillin, amoxicillin, cephalosporins |
| Cell wall synthesis | Glycopeptides | Vancomycin |
| Cell membrane | Polymyxins | Colistin |
| 30S ribosome | Aminoglycosides | Gentamicin |
| 30S ribosome | Tetracyclines | Doxycycline |
| 50S ribosome | Macrolides | Azithromycin |
| 50S ribosome | Chloramphenicol | Chloramphenicol |
| DNA gyrase/topoisomerase | Fluoroquinolones | Ciprofloxacin |
| DNA replication | Metronidazole | Metronidazole (anaerobes/protozoa) |
| Folate synthesis | Sulfonamides + trimethoprim | Co-trimoxazole |
| RNA synthesis | Rifamycins | Rifampicin |
| Ergosterol (fungi) | Azoles | Fluconazole |
| Ergosterol (fungi) | Polyenes | Amphotericin B |
Summary Table: The Microorganism Kingdom at a Glance
| Group | Prokaryote/Eukaryote | Cell Wall | Nucleic Acid | Key Diseases |
|---|---|---|---|---|
| Bacteria | Prokaryote | Peptidoglycan | DNA + RNA | TB, pneumonia, UTI, sepsis |
| Archaea | Prokaryote | Variable (no peptidoglycan) | DNA + RNA | Rarely pathogenic |
| Fungi | Eukaryote | Chitin | DNA + RNA | Candidiasis, aspergillosis |
| Protozoa | Eukaryote | Absent | DNA + RNA | Malaria, giardiasis, amoebiasis |
| Viruses | Acellular | None | DNA or RNA | Influenza, HIV, hepatitis |
| Prions | Acellular | None | None (protein only) | CJD, BSE, Kuru |
Sources: Jawetz, Melnick & Adelberg's Medical Microbiology, 28th Edition (Chapters 1, 2, 3); Medical Microbiology 9e; Sherris & Ryan's Medical Microbiology, 8th Edition.
This covers the full sweep of general microbiology. If you'd like a deeper dive into any specific area - such as bacteriology of a particular pathogen, viral replication in detail, antimicrobial resistance mechanisms, mycology, parasitology, or microbial genetics - just ask!
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