Introduction to Microbiology: Microbes, Classification, and Bacterial Structure

Chapter 1: Microbes and Microbiology

Introduction to Microbiology

Microbiology is the study of microscopic living organisms and certain nonliving entities. It encompasses a wide range of organisms, from bacteria and archaea to viruses and prions.

• Biology: The study of living organisms.

• Microbes: Extremely small (microscopic) living organisms and certain nonliving entities.

• Cellular microbes: Living microbes, including bacteria, archaea, some algae, protozoa, and some fungi.

• Acellular microbes: Non-living microbes, such as viruses, prions, and viroids.

• Microbes are ubiquitous (found virtually everywhere).

• Disease-causing microbes are called pathogens.

• Microbes that live in and on our bodies are called indigenous microbiota.

  • Some indigenous microbiota are opportunistic pathogens: non-pathogenic until the host is weakened.

  • True pathogens cause disease regardless of host condition.

• Pathogens cause two categories of diseases: infectious diseases and microbial intoxications.

Acellular and Cellular Microbes

Microbes can be classified as acellular (not composed of cells) or cellular (composed of cells).

• Acellular Infectious Agents: Viruses, prions, viroids.

• Cellular Microorganisms:

  • Prokaryotes: Bacteria, Archaea

  • Eukaryotes: Fungi, Algae, Protozoa

Categories of Microorganisms

According to Leeuwenhoek, microorganisms can be grouped into six categories:

• Bacteria

• Archaea

• Fungi

• Protozoa

• Algae

• Small multicellular animals

Microbe Classification

• Bacteria and Archaea:

  • Unicellular, lack nuclei, smaller than eukaryotes.

  • Found everywhere with sufficient moisture, including extreme environments.

  • Bacterial cell walls contain peptidoglycan (some lack cell walls).

  • Archaeal cell walls are composed of polymers other than peptidoglycan.

• Fungi:

  • Eukaryotic (have membrane-bound nucleus).

  • Obtain food from other organisms.

  • Possess cell walls.

  • Include yeast (unicellular, reproduce asexually by budding, some produce sexual spores).

• Protozoa:

  • Single-celled eukaryotes.

  • Similar to animals in nutrient needs and cellular structure.

  • Live freely in water, some live in animal hosts.

  • Mostly asexual but also sexual reproduction.

  • Motility via:

    • Pseudopods: Cell extensions that flow in direction of travel.

    • Cilia: Numerous short protrusions that propel organisms.

    • Flagella: Fewer, longer, whip-like extensions.

• Algae:

  • Unicellular or multicellular.

  • Photosynthetic.

  • Simple reproductive structures.

  • Categorized by pigmentation and cell wall composition.

Note: Parasites cannot live on their own and must harness resources from a host.

Categories of Infectious Diseases

Pathogens cause two main categories of diseases:

Infectious Disease	Microbial Intoxication
Caused by the presence and growth of pathogenic microbes in the host	Caused by ingestion of toxins produced by microbes
Examples: Tuberculosis, Influenza	Examples: Botulism, Staphylococcal food poisoning

Koch's Postulates

Koch's postulates are a set of criteria used to establish a causative relationship between a microbe and a disease.

1. The microbe must be found in all cases of the disease and not in healthy individuals.

2. The microbe must be isolated from the diseased host and grown in pure culture.

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

4. The same microbe must be re-isolated from the experimentally infected host.

• If an organism fulfills Koch's postulates, it is proven to be the cause of a particular infectious disease.

• Koch's postulates support the Germ Theory of Disease.

• Some circumstances exist where Koch's postulates cannot be fulfilled (e.g., viruses that cannot be cultured).

What is an Organism?

• Organism: A living system made of one or more cells. Microorganisms can be prokaryotic or eukaryotic.

Bacteria and Archaea

• Bacteria:

  • Mostly unicellular, some form filaments.

  • Commonly associate in biofilms.

  • Most have a rigid cell wall (shapes: spheres, spirals, rods).

  • Obtain food from the environment.

• Archaea:

  • Superficially resemble bacteria but are evolutionarily unique.

  • Many are extremophiles (e.g., hot springs, acid mines).

  • Also found in temperate soil, water, and animal digestive tracts.

  • None are known to be pathogenic.

Microbial Eukaryotes: Protists and Fungi

• Protists:

  • Include protozoa and single-celled algae.

  • 10 to 50 times larger than prokaryotes.

  • May be free-living or associated with plants/animals.

  • Algae can perform photosynthesis and have cell walls.

• Fungi:

  • Non-photosynthetic, many are decomposers.

  • Form: single-celled yeast, filamentous molds.

  • Generally not pathogenic, some opportunists.

  • Responsible for some food flavor (e.g., cheeses).

Other Infectious Agents: The Viruses

• Acellular, not considered organisms.

• Genetic material is either DNA or RNA, not both.

• Protein coat surrounds genetic material.

• Most infect an organism to replicate (lack metabolic machinery).

Drug Resistant Pathogens

• Declining effectiveness of many antibiotics.

• Bacteria can acquire resistance genes from other bacteria.

• Antibiotic misuse leads to 'super bugs'.

Emerging and Re-emerging Diseases

• Emerging diseases: First time in human population (often zoonotic).

• Re-emerging diseases: Previously under control, now resurging (e.g., tuberculosis).

• Control: Outbreak surveillance, hygiene, vaccination, antimicrobial drugs.

Table 3.1: Characteristics of Life and Their Distribution in Microbes

Characteristic	Bacteria, Archaea, Eukaryotes	Viruses
Growth	Occurs in all	Growth does not occur
Reproduction	Occurs in all	Host cell replicates the virus
Responsiveness	Occurs in all	Reaction to host cells seen in some viruses
Metabolism	Occurs in all	Viruses use host cell's metabolism
Cellular structure	Present in all	Viruses lack cytoplasmic membrane or cellular structure

Chapter 2: Bacterial Structure and Function

External Structure of Bacterial Cells

• Glycocalyx:

  • Gelatinous, sticky substance surrounding the cell.

  • Composed of polysaccharides, polypeptides, or both.

  • Types:

    • Capsule: Organized repeating units, firmly attached, may prevent recognition by host.

    • Slime layer: Loosely attached, water soluble, allows attachment to surfaces.

• Flagella:

  • Long structures for movement, extend beyond cell surface.

  • Composed of filament, hook, and basal body.

  • Function: Propel bacterium, rotation can be clockwise or counterclockwise, response to stimuli (taxis).

• Fimbriae and Pili:

  • Fimbriae: Sticky, bristle-like projections, shorter than flagella, important in biofilms.

  • Pili: Special type of fimbriae, longer than fimbriae but shorter than flagella, used for DNA transfer (conjugation).

Bacterial Cell Walls

• Provide structure and shape, protect from osmotic forces.

• Composed of peptidoglycan.

• Two types:

  • Gram-positive: Thick peptidoglycan, teichoic acids, purple in Gram stain.

  • Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), pink in Gram stain, LPS can cause fever and shock.

• Some bacteria lack cell walls (e.g., Mycoplasma).

Bacterial Cytoplasmic Membrane

• Structure: Phospholipid bilayer with integral and peripheral proteins (fluid mosaic model).

• Function:

  • Controls passage of substances in/out of cell.

  • Harvests light energy in photosynthetic bacteria.

  • Selective permeability.

  • Proteins allow substances to cross membrane.

  • Maintains concentration and electrical gradient.

Table 3.2: Transport Processes Across Bacterial Cytoplasmic Membranes

Process	Description	Examples	Type of Substances
Passive Transport: Diffusion	Movement down concentration gradient, no energy required	Oxygen, carbon dioxide	Small, lipid-soluble chemicals
Facilitated Diffusion	Diffusion through a protein channel	Glucose, fructose, urea	Large or electrically charged molecules
Osmosis	Diffusion of water through a selectively permeable membrane	Water	Water
Active Transport	Movement against concentration gradient, requires ATP	Na+, K+, Ca2+, H+, Cl-	Ions, some sugars, amino acids

Osmosis Breakdown

• Isotonic: Equal solute concentration inside and outside the cell.

• Hypertonic: Higher solute concentration outside the cell; water leaves cell, cell shrinks.

• Hypotonic: Lower solute concentration outside the cell; water enters cell, cell swells.

Cytoplasm of Bacteria

• Cytosol: Liquid portion, mostly water, contains DNA in nucleoid region.

• Inclusions: Reserve deposits of chemicals.

• Endospores: Unique structures for survival under harsh conditions, resistant to heat, radiation, chemicals.

Bacterial Nonmembranous Organelles

• Ribosomes: Synthesize proteins, made of rRNA and proteins.

• Cytoskeleton: Internal scaffolding, made of protein fibers.