Characterizing and Classifying Prokaryotes: Structure, Diversity, and Pathogenicity

Classification of Microorganisms

Three Domains of Life

The classification of microorganisms is based on evolutionary relationships, primarily determined by ribosomal RNA (rRNA) sequencing. The three domains are:

• Domain Bacteria: Includes true bacteria.

• Domain Archaea: Includes archaea, often extremophiles.

• Domain Eukarya: Includes protists (multiple kingdoms), kingdom Plantae, Fungi (yeasts and molds), and Animalia.

Carl Woese pioneered the use of rRNA sequencing for classification, which is now the standard method.

Modern classification also considers cultural, morphological, and physiological characteristics.

Prokaryotic Cell Arrangements and Morphology

Cell Shapes and Arrangements

Prokaryotes are the most diverse and ubiquitous organisms. Their cell arrangements result from the planes in which cells divide and whether daughter cells separate after division.

• Coccus: Spherical cells.

• Bacillus: Rod-shaped cells.

• Spirochete: Highly undulate, spiral-shaped cells.

• Coccobacillus: Short rods, e.g., Escherichia coli.

• Spirillum: Spiral, e.g., Helicobacter pylori.

• Vibrio: Comma-shaped.

• Star-shaped and pleomorphic: Variable shapes; pleomorphic means variability in form.

There are no staphylobacilli arrangements (bacilli do not form clusters like cocci).

Prokaryotic Cell Structure

Gram-Positive vs. Gram-Negative Bacteria

Bacteria are classified based on their cell wall structure:

• Gram-Positive: Thick peptidoglycan layer, teichoic acids, no outer membrane.

• Gram-Negative: Thin peptidoglycan layer, outer membrane with lipopolysaccharide (LPS). LPS contains Lipid A (endotoxin) and O antigen (used for identification).

Gram-positive and Gram-negative bacteria differ structurally and chemically.

Survey of Bacteria: Low G+C Gram-Positives

Clostridium Species

• Clostridium tetani: Causes tetanus (spastic paralysis). Exotoxin blocks GABA release, preventing muscle relaxation. Death from respiratory paralysis.

• Clostridium botulinum: Causes botulism (flaccid paralysis). Exotoxin prevents acetylcholine release, preventing muscle contraction. Used in cosmetic "BoTox" injections. Deadliest natural toxin.

• Clostridium perfringens: Causes gas gangrene (death of body tissue due to infection or lack of blood flow).

• Clostridium difficile: Causes infectious diarrhea, common in hospitals and long-term care. Spread via fecal-oral route.

Bacillus Species

• Bacillus thuringiensis: Produces toxin used as insecticide ("mosquito dunks").

• Bacillus polymyxa: Produces antibiotic polymyxa B.

• Bacillus anthracis: Causes anthrax. Has three exotoxins and a capsule (both encoded on plasmids). Forms: cutaneous, gastrointestinal, inhalational.

Staphylococcus Species

• Staphylococcus aureus: Normal skin/nasal flora; can cause pneumonia, wound infections, toxic shock syndrome (TSS), joint infections, and infections of implanted medical devices. Produces toxins, forms biofilms, and is often multi-drug resistant (MRSA).

• Staphylococcus epidermidis, S. agalactiae, S. saprophyticus: Other species with varying pathogenicity.

• Staphylococcal food poisoning: Rapid generation time (~30 min).

• MRSA: Methicillin-resistant S. aureus; difficult to eradicate, persists in hospitals, can survive on surfaces for extended periods.

Streptococcus Species

• Hemolysis Types:

  • Alpha: Partial hemolysis (greenish color).

  • Beta: Complete hemolysis (clear zone).

  • Gamma: No hemolysis.

• Lancefield Classification: Based on carbohydrate antigens on cell wall.

  • Group A: S. pyogenes (strep throat, scarlet fever, impetigo).

  • Group B: S. agalactiae (mastitis).

  • Group C: S. equi (strangles).

  • Group D: Enterococcus faecalis, S. bovis (gastroenteritis).

  • Group K: S. salivarius.

  • Viridans group: S. mutans (dental caries), S. mitis.

  • Pneumococci: S. pneumoniae (pneumonia, meningitis).

Listeria

• Listeria monocytogenes: Gram-positive, small rod, facultative anaerobe, psychrophile. Can contaminate milk and meat, reproduce under refrigeration, survive inside phagocytic WBCs, cross placental barrier. Causes meningitis and bacteremia in immunocompromised individuals.

Corynebacterium

• Corynebacterium diphtheriae: Causes diphtheria via exotoxin. Blocks trachea and bronchi, dangerous in children (up to 40% mortality). DTaP vaccine for children, TDaP for adults.

Mycobacterium

• Mycobacterium tuberculosis: Causes tuberculosis.

• Mycobacterium leprae: Causes leprosy. Slow-growing, requires acid-fast staining due to mycolic acids in cell wall.

Survey of Bacteria: Gram-Negative Proteobacteria

Proteobacteria Classes

Proteobacteria are the largest and most diverse group of Gram-negative bacteria, divided into five classes:

• Alphaproteobacteria

• Betaproteobacteria

• Gammaproteobacteria (emphasis in lab)

• Deltaproteobacteria

• Epsilonproteobacteria

Other important groups: Spirochetes and Bacteroids.

Environmental and Agricultural Importance

• Nitrogen fixation: Conversion of N2 to NH3 by bacteria such as Azospirillum and Rhizobium, which associate with plant roots.

• Aerobes: Live in low-nutrient environments.

Pathogenic Proteobacteria

• Rickettsia: Causes Rocky Mountain Spotted Fever, transmitted by ticks (vector-borne). Intracellular pathogens, obtain energy from host cell.

• Brucella: Causes brucellosis (zoonosis), leading to animal abortions/sterility and bacteremia in humans. Risk for slaughterhouse workers, veterinarians, lab techs.

• Neisseria: Gram-negative diplococci inhabiting mammalian mucous membranes. Causes meningitis, breaks down blood-brain barrier, can cause petechiae (skin hemorrhages).

• Escherichia coli: Normal gut flora, but pathogenic strains (EHEC, UPEC) cause diarrhea and UTIs. E. coli O157:H7 is a notable serotype.

• Salmonella: Not normal flora; S. typhi causes typhoid fever. Motile, H2S-producing, does not ferment lactose; associated with poultry.

• Shigella: Not normal flora; S. dysenteriae causes dysentery. Nonmotile, does not ferment lactose.

• Pseudomonads: Bacilli with flagella, psychrophilic, spoilage of meat and dairy products.

• Helicobacter pylori: Spiral, flagellated, acidophile. Causes gastric and duodenal ulcers. Proven by Barry Marshall's self-experimentation.

Bacteroides

• Bacteroides: Obligate anaerobes in human and animal intestines. Most numerous organisms in the human colon, secrete enzymes to digest complex polysaccharides and cellulose. Can cause abdominal and pelvic infections if intestine is ruptured.

• About 30% of daily intestinal output is bacteria; >1010 bacteroids per gram of feces.

Serological and Epidemiological Concepts

Antigens and Antibodies

• Antigen: Foreign substance (e.g., bacteria, viruses, blood type antigens) that elicits an immune response.

• Antibody: Protein produced by the immune system that binds to antigens to neutralize or eliminate them.

• Serological testing: Uses antigen-antibody reactions to identify pathogens.

Epidemiology

• Epidemiology: Study of disease distribution and determinants in populations.

Table: Comparison of Gram-Positive and Gram-Negative Bacteria

Feature	Gram-Positive	Gram-Negative
Cell Wall	Thick peptidoglycan, teichoic acids	Thin peptidoglycan, outer membrane with LPS
Outer Membrane	Absent	Present
LPS (Lipopolysaccharide)	Absent	Present (contains Lipid A and O antigen)
Staining	Retains crystal violet (purple)	Does not retain crystal violet (pink/red)
Examples	Staphylococcus, Streptococcus, Bacillus, Clostridium	Escherichia, Salmonella, Neisseria, Pseudomonas

Table: Lancefield Classification of Streptococci

Group	Species	Associated Diseases
A	S. pyogenes	Strep throat, scarlet fever, impetigo
B	S. agalactiae	Mastitis
C	S. equi	Strangles
D	Enterococcus faecalis, S. bovis	Gastroenteritis
K	S. salivarius	Normal oral flora
Viridans	S. mutans, S. mitis	Dental caries
Pneumococci	S. pneumoniae	Pneumonia, meningitis

Additional info:

• Synergism: The combined effect of multiple antibiotics can be greater than the sum of their individual effects.

• DNA Structure: Double helix, sugar-phosphate backbone, base pairing (A-T, C-G), hydrogen bonds.

• Neutrophils: Elevated in bacterial infections; Lymphocytes: Elevated in viral infections.

• Cellulase: Enzyme that breaks down cellulose, produced by some gut bacteria.

• Vector: An organism (often arthropod) that transmits pathogens.