Exam 3: Classification, Microbial Diversity, Viruses, and Pathogenesis

Chapter 10: Classification of Microorganisms

Three Domains of Life

The three domains—Bacteria, Archaea, and Eukarya—represent the highest taxonomic ranks in the classification of life. Each domain is defined by unique cellular and genetic characteristics.

• Bacteria: Prokaryotic, cell walls contain peptidoglycan, diverse metabolic pathways, reproduce by binary fission.

• Archaea: Prokaryotic, cell walls lack peptidoglycan, often inhabit extreme environments, unique membrane lipids.

• Eukarya: Eukaryotic cells with membrane-bound organelles, includes kingdoms Plantae, Animalia, Fungi, and Protista.

Kingdom Classification for Eukaryotes

• Plantae: Multicellular, photosynthetic, cell walls of cellulose.

• Animalia: Multicellular, heterotrophic, lack cell walls.

• Fungi: Unicellular or multicellular, chitin cell walls, absorb nutrients.

• Protista: Mostly unicellular, diverse modes of nutrition and reproduction.

Species Definitions

• Prokaryotic species: A population of cells with similar characteristics.

• Eukaryotic species: A group of closely related organisms that can breed among themselves.

• Viral species: A population of viruses with similar characteristics that occupies a particular ecological niche.

Binomial Nomenclature

The binomial system assigns each organism a two-part Latin name: Genus species (e.g., Escherichia coli). This system standardizes naming and facilitates scientific communication.

Methods for Identifying Bacteria

• Morphological characteristics: Cell shape, arrangement, and staining properties (e.g., Gram stain).

• Biochemical tests: Enzyme activities, metabolic capabilities (e.g., fermentation of sugars).

• Other methods:

  • Serology: Identification using antibodies.

  • Phage typing: Susceptibility to bacteriophages.

  • Fatty acid profiles: Analysis of membrane lipids.

  • Flow cytometry: Cell sorting and counting.

  • DNA-based methods: DNA base composition, DNA fingerprinting, NAATs/PCR, nucleic acid hybridization, DNA chips.

Example: The Gram stain differentiates bacteria into Gram-positive and Gram-negative based on cell wall structure.

Chapter 11: The Prokaryotes: Domains Bacteria and Archaea

Bergey’s Manual and Phylogenetic System

Bergey’s Manual of Systematic Bacteriology provides a comprehensive classification of bacteria based on phylogenetic relationships, primarily using genetic sequencing data (e.g., 16S rRNA gene sequences).

• Unique aspect: Emphasizes evolutionary relationships rather than solely phenotypic traits.

Relationships Among the Three Domains

• Bacteria and Archaea are both prokaryotic but differ significantly in cell wall composition, membrane lipids, and genetic machinery.

• Eukarya shares some genetic similarities with Archaea, suggesting a closer evolutionary relationship.

Bacterial Subgroups

• Bacteria are divided into subgroups based on genetic, morphological, and metabolic characteristics to reflect evolutionary relationships and facilitate identification.

Chapter 12: The Eukaryotes: Fungi, Algae, Protozoa, and Helminths

Defining Characteristics

• Fungi: Eukaryotic, chitin cell walls, absorb nutrients, reproduce by spores (e.g., yeasts, molds).

• Algae: Eukaryotic, mostly aquatic, photosynthetic, cell walls of cellulose, produce oxygen.

• Protozoa: Unicellular, lack cell walls, motile (cilia, flagella, pseudopods), heterotrophic.

• Helminths: Multicellular parasitic worms (e.g., flatworms, roundworms), complex life cycles, often involve multiple hosts.

Chapter 13: Viruses, Viroids, and Prions

Basic Characteristics of Viruses

• Noncellular, obligate intracellular parasites.

• Consist of nucleic acid (DNA or RNA) enclosed in a protein coat (capsid); some have envelopes.

• Reproduce only inside host cells.

Viral Species Definition

• A viral species is a group of viruses sharing the same genetic information and ecological niche.

• This differs from cellular species, which are defined by reproductive compatibility.

Lytic vs. Lysogenic Cycles of Bacteriophages

• Lytic cycle: Virus replicates inside host, causing cell lysis and release of new virions.

• Lysogenic cycle: Viral DNA integrates into host genome (prophage), replicates with host, can later enter lytic cycle.

Prions and Viroids

• Prions: Infectious proteins causing neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease).

• Viroids: Infectious RNA molecules, lack protein coat, cause plant diseases.

• Both lack the cellular structure of typical pathogens.

Chapter 14: Principles of Disease and Epidemiology

Key Terminology

• Pathology: Study of disease.

• Etiology: Study of the cause of disease.

• Infection: Invasion and growth of pathogens in the body.

• Disease: Abnormal state in which the body is not functioning normally.

Normal, Transient, and Opportunistic Microbes

• Normal microbiota: Permanently colonize the host without causing disease under normal conditions.

• Transient microbiota: Present for a short time without causing disease.

• Opportunistic microbes: Normally harmless but can cause disease under certain conditions (e.g., immunosuppression).

Koch’s Postulates

• Set of criteria to establish a causative relationship between a microbe and a disease:

  1. The microorganism must be found in all cases of the disease.

  2. It must be isolated and grown in pure culture.

  3. The cultured microbe must cause disease when introduced into a healthy host.

  4. It must be re-isolated from the experimentally infected host.

• Significance: Foundation for identifying disease-causing agents.

Classification of Diseases

• By frequency: Sporadic, endemic, epidemic, pandemic.

• By severity/duration: Acute, chronic, subacute, latent.

• By extent of host involvement: Local, systemic, focal.

Herd Immunity

• Occurs when a high percentage of the population is immune, reducing disease spread.

• Important for protecting vulnerable individuals.

Development of Disease

• Sequence: Incubation period → prodromal period → period of illness → period of decline → period of convalescence.

Reservoirs of Infection

• Human reservoirs: Carriers of disease (symptomatic or asymptomatic).

• Animal reservoirs: Zoonoses—diseases transmitted from animals to humans.

• Nonliving reservoirs: Soil, water, and inanimate objects.

Methods of Disease Transmission

• Contact transmission: Direct, indirect, droplet.

• Vehicle transmission: Via water, food, or air.

• Vector transmission: Via arthropods (mechanical or biological).

Hospital-Acquired Infections (HAIs)

• Common causes: Contaminated equipment, staff-to-patient transmission, patient immune status.

• Prevention: Hand hygiene, sterilization, isolation procedures.

Re-emerging Infectious Diseases

• Reasons: Microbial evolution, antibiotic resistance, changes in human behavior, environmental changes, breakdown in public health measures.

Chapter 15: Microbial Mechanisms of Pathogenicity

Portals of Entry and Exit

• Common portals: Mucous membranes (respiratory, gastrointestinal, genitourinary tracts), skin, parenteral route (breaks in skin).

• Portals of exit: Usually same as entry; important for disease transmission.

Microbial Adherence

• Microbes use adhesins (surface molecules) to attach to host cells (e.g., Streptococcus pyogenes uses M protein).

Role of Capsules and Cell Wall Components

• Capsules prevent phagocytosis (e.g., Streptococcus pneumoniae).

• Cell wall components (e.g., M protein, mycolic acid) enhance virulence.

Enzymes Contributing to Pathogenicity

• Coagulases: Clot fibrinogen, protecting bacteria from immune cells.

• Kinases: Digest fibrin clots, aiding spread.

• Hyaluronidase: Hydrolyzes hyaluronic acid, spreading infection.

• Collagenase: Breaks down collagen, facilitating tissue invasion.

• IgA protease: Destroys IgA antibodies, evading immune response.

Siderophores

• Proteins secreted by bacteria to scavenge iron from the host, essential for bacterial growth.

Direct Damage vs. Toxin Production

• Direct damage: Pathogens disrupt host cells by entering and multiplying.

• Toxin production: Bacteria release toxins that damage host tissues.

Exotoxins vs. Endotoxins

Feature	Exotoxins	Endotoxins
Chemical nature	Proteins	Lipopolysaccharide (LPS)
Source	Mostly Gram-positive bacteria	Gram-negative bacteria
Heat stability	Unstable (destroyed by heat)	Stable
Toxicity	High	Low
Effect	Specific (e.g., neurotoxins)	General (fever, shock)

Mechanisms of Toxin Action

• A-B toxins: Two-part toxins; A (active) component disrupts cell function, B (binding) component attaches to host cell.

• Membrane-disrupting toxins: Cause cell lysis by disrupting plasma membranes.

• Superantigens: Cause excessive immune response, leading to shock.