---

Introduction to Microbiology: Science, Divisions, and Classification

---

Part A: Introduction to the Science of Microbiology

Definition

• Jawetz Melnick & Adelberg's Medical Microbiology, 28e, p. 6

Scale and Significance

• There are 5 × 10^30 microbial cells on Earth; excluding cellulose, they constitute ~90% of the biomass of the entire biosphere.
• There are 13 × 10^28 bacteria in the oceans - 100 million times more than stars in the known universe.
• Viral infections in the oceans occur at ~1 × 10^23 per second, removing 20-40% of all bacterial cells daily.
• 50-60% of the cells in the human body are microbes. The bacteria in the average human gut weigh ~1 kg.
• Gut flora genes outnumber human genome genes by 150-fold.

Historical Perspective

• Medical Microbiology 9e, p. 16

Biological Principles Illustrated by Microbiology

• Mutualism (Symbiosis): e.g., lichens - a fungus + a phototropic alga or cyanobacterium living together, benefiting each other.
• Parasitism: a host provides benefit to the parasite - e.g., pathogenic bacteria and viruses.
• Diversity: Microorganisms encompass the widest range of biochemical and genetic mechanisms in all of biology.

---

Part B: Major Divisions of the Microbial World

1. Viruses

• Smallest infectious particles: 18-600 nm diameter (most <200 nm; not visible by light microscopy).
• Genome: either DNA or RNA (never both), enclosed in a protein shell (capsid), with or without a lipid membrane envelope.
• True obligate intracellular parasites - require host cells for replication.

• 2,000 species described; ~650 infect humans and animals.

• Can cause acute lytic infection, chronic latent infection, or tumor-promoting disease (e.g., HPV, HBV).
• Not cellular; acellular entities.

2. Prions

• Non-living members of the microbial world.
• Proteinaceous infectious particles; contain no nucleic acid.
• Cause neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease, BSE/"mad cow disease").
• Mechanism: conversion of normal host sialoglycoprotein to a protease-resistant abnormal form.
• Variant CJD (vCJD) linked to ingestion of prion-infected beef.

3. Prokaryotes (Bacteria and Archaebacteria)

• Distinguished by small size (~1 µm) and absence of nuclear membrane.
• DNA is a single circular chromosome (haploid), organized in a nucleoid.
• No mitochondria, Golgi bodies, or endoplasmic reticulum.
• Reproduce by asexual binary fission.
• Number of genes varies: ~468 (Mycoplasma genitalium) to 7,825 (Streptomyces coelicolor).
• Bacteria: most common pathogens; gram-positive (thick peptidoglycan) or gram-negative (thin peptidoglycan + outer membrane).
• Archaebacteria: structurally similar to bacteria but biochemically distinct; generally do NOT cause disease in humans.

Prokaryotic Communities and Diversity

• Energy strategies range from photosynthesis (purple bacteria, cyanobacteria) to chemolithotrophy.
• Exist in extreme environments: thermophiles, halophiles, acidophiles.
• Form biofilms and microbial communities.

4. Protists (Eukaryotic Microbes)

5. Fungi

• Eukaryotic, non-photosynthetic organisms with cell walls made of chitin (not peptidoglycan).
• May be unicellular (yeasts) or multicellular with hyphae (molds).
• Reproduce sexually and asexually.
• Cause superficial, subcutaneous, or systemic (deep) mycoses.
• Examples: Candida (yeast), Aspergillus (mold), Cryptococcus.

6. Parasites

• Eukaryotic organisms that depend on a host.
• Include protozoa (e.g., Plasmodium, Toxoplasma) and helminths (worms).

---

Part C: Relationship Among the Microbial Divisions

---

Part D: Methods of Classification of Microbes

1. Morphological (Phenotypic) Classification

• Size and shape: cocci (spheres), bacilli (rods), spirilla/spirochetes (spirals)
• Arrangement: single, pairs (diplococci), chains (streptococci), clusters (staphylococci)
• Gram stain reaction: Gram-positive (purple) vs. Gram-negative (pink)
• Acid-fast stain: used for Mycobacteria
• Motility: flagella type (monotrichous, amphitrichous, lophotrichous, peritrichous)
• Spore formation: endospore (e.g., Bacillus, Clostridium)

2. Cultural Classification

• Growth characteristics on culture media (colony morphology, pigment, hemolysis).
• Nutritional requirements: autotrophs vs. heterotrophs.
• Oxygen requirement: aerobe, anaerobe, facultative anaerobe, microaerophile.
• Temperature preference: mesophile, thermophile, psychrophile.

3. Biochemical Classification

• Metabolic activities: fermentation patterns, enzyme production (catalase, oxidase, urease, coagulase).
• Sugar utilization profiles.
• Used in standard ID systems (API strips, VITEK system).

4. Antigenic (Serological) Classification

• Based on surface antigens: somatic O antigen, flagellar H antigen, capsular K antigen.
• Examples: Salmonella Kauffmann-White scheme; Streptococcal Lancefield groups (A, B, C...).

5. Genetic/Molecular Classification (Modern - Gold Standard)

• G+C content: percentage of guanine + cytosine in DNA.
• DNA hybridization: measures genetic relatedness.
• 16S rRNA gene sequencing: universal phylogenetic marker; basis of the modern classification tree of life (Woese & Fox, 1977).
• Whole genome sequencing (WGS): now used for definitive species identification and epidemiological tracking.
• Organisms are classified by: Kingdom → Phylum → Class → Order → Family → Genus → Species.

6. Ecological/Epidemiological Classification

• Based on habitat, transmission route, reservoir.
• Zoonotic vs. anthroponotic; vector-borne vs. direct contact.

---

Part E: Study of Key Microbial Groups

Bacteria

• Cell wall: Gram-positive = thick peptidoglycan (murein); Gram-negative = thin peptidoglycan + outer membrane (lipopolysaccharide/LPS).
• Some bacteria (e.g., Mycobacterium) have waxy mycolic acid cell walls - detected by Ziehl-Neelsen stain.
• Others lack cell walls entirely: Mycoplasma (survives inside host or in hypertonic media).

---

Fungi

• Yeasts: Unicellular; reproduce by budding (e.g., Candida, Cryptococcus). Candida forms pseudohyphae.
• Molds: Multicellular with hyphae; form mycelium. E.g., Aspergillus, Rhizopus, Dermatophytes.
• Dimorphic fungi: Exist as mold in environment (25°C) and yeast in host (37°C). E.g., Histoplasma, Blastomyces, Coccidioides, Sporothrix (mnemonic: "HBCS").
• Cell wall: Chitin + glucan (target of antifungals like echinocandins).
• Cell membrane: Ergosterol (not cholesterol) - target of azoles and amphotericin B.

---

Viruses

• Capsid: Protein shell around nucleic acid; either icosahedral, helical, or complex symmetry.
• Genome: Either DNA or RNA (single or double stranded; linear or circular).
• Envelope: Some viruses have a lipid bilayer envelope (derived from host membrane) studded with viral glycoproteins; others are non-enveloped (naked).
• Enveloped viruses are more sensitive to disinfectants (e.g., HIV, influenza, herpes).
• Non-enveloped viruses are more resistant (e.g., poliovirus, rotavirus, adenovirus).

---

Rickettsiae

• Small, obligate intracellular Gram-negative bacteria (cannot be cultured on artificial media).
• Size: 0.3-1.0 µm.
• Transmitted by arthropod vectors (ticks, mites, lice, fleas).
• Have both DNA and RNA; divide by binary fission (unlike viruses).
• Cell wall structure similar to Gram-negative bacteria; have LPS.
• Weil-Felix reaction: used for serological diagnosis (cross-reactivity with Proteus OX strains).
• Staining: Giemsa or Gimenez stain (not standard Gram stain - too small).

---

Spirochetes

• Slender, tightly coiled, helical (corkscrew-shaped) Gram-negative bacteria.
• 5-20 µm long; 0.1-0.5 µm wide.
• Unique structure: Endoflagella (axial filaments / periplasmic flagella) run in the periplasmic space between the outer sheath and cytoplasmic membrane - responsible for their characteristic corkscrew motility.
• Too thin to be seen on Gram stain; visualized by:
  • Darkfield microscopy
  • Silver impregnation stains
  • Immunofluorescence

• Spirochetes CAN be cultured (some, e.g., Leptospira, on special media like EMJH).
• Spirochetes are NOT obligate intracellular.
• Spirochetes are visible by darkfield microscopy; Rickettsiae are not.
• Rickettsiae are vector-borne; Spirochetes may be vector-borne (Borrelia) or not (Treponema = sexual; Leptospira = water exposure).

---

Summary Table: Comparison of All Major Groups

---