2.1 Taxonomic Classification

Taxonomy is the science of classifying living organisms. The hierarchical classification system organizes organisms from general to specific categories:

Microorganisms are named using a binomial nomenclature system, where the first part indicates the genus and the second part indicates the species. For example, Escherichia coli (commonly abbreviated as E. coli).

2.2 The Three Domains of Life

Modern biological classification divides all living organisms into three domains:

3.1 Bacterial Morphology

Bacteria exhibit three main morphological forms:

Some bacteria have specialized structures:

• Pleomorphic bacteria: Can change their shape (e.g., Mycoplasma)
• Filamentous bacteria: Form long filaments (e.g., Actinomyces)
• Stalked bacteria: Have extensions called stalks (e.g., Caulobacter)
• Appendaged bacteria: Have appendages (e.g., Ancalomicrobium)

3.2 Viral Morphology

Viruses are much smaller than bacteria and consist of genetic material (DNA or RNA) surrounded by a protein coat called a capsid. Some viruses also have a lipid envelope.

Based on their shape, viruses can be classified as:

• Icosahedral: 20-sided symmetrical structures (e.g., Adenovirus, Poliovirus)
• Helical: Coiled nucleic acid with protein coating (e.g., Influenza virus, Tobacco mosaic virus)
• Complex: Combination of different symmetries or unique shapes (e.g., Bacteriophages with head and tail)
• Envelope: Presence of lipid bilayer derived from host cell membranes (e.g., HIV, Herpes viruses)

3.3 Fungal Morphology

Fungi are eukaryotic organisms that can exist in two basic morphological forms:

• Yeasts: Unicellular fungi that reproduce by budding (e.g., Candida albicans, Saccharomyces cerevisiae)
• Molds/Filamentous fungi: Multicellular fungi that grow as branching, thread-like structures called hyphae, which collectively form a mycelium (e.g., Aspergillus, Penicillium)
• Dimorphic fungi: Can exist as either yeast or mold depending on environmental conditions (e.g., Histoplasma capsulatum, Blastomyces dermatitidis)

Fungal cell walls contain chitin, a polysaccharide not found in plant or bacterial cell walls. This unique composition makes fungi susceptible to different antimicrobial agents than bacteria.

3.4 Protozoal Morphology

Protozoa are single-celled eukaryotic microorganisms that can be classified based on their locomotion method:

• Amoebae: Move using pseudopodia (temporary extensions of cytoplasm) (e.g., Entamoeba histolytica)
• Flagellates: Move using whip-like structures called flagella (e.g., Giardia lamblia, Trichomonas vaginalis)
• Ciliates: Move using hair-like structures called cilia (e.g., Paramecium)
• Sporozoans: Non-motile as adults, form spores during reproduction (e.g., Plasmodium species, which cause malaria)

4.1 Basic Shapes and Arrangements

Bacterial size typically ranges from 0.2 to 2.0 micrometers (μm) in diameter for cocci, and 0.5 to 5.0 μm in length for bacilli. For comparison, human red blood cells are approximately 7-8 μm in diameter.

                        COCCI (Spherical)                BACILLI (Rod-shaped)               SPIRILLA (Spiral)
                        ├── Single (Micrococcus)         ├── Single (E. coli)               ├── Vibrio (comma)
                        ├── Pairs (Diplococci)           ├── Pairs (Diplobacilli)           ├── Spirilla (rigid spiral)
                        │   └── Streptococcus pneumoniae │   └── Klebsiella pneumoniae      │   └── Campylobacter
                        ├── Chains (Streptococci)        ├── Chains (Streptobacilli)        └── Spirochetes (flexible)
                        │   └── Streptococcus pyogenes   │   └── Bacillus anthracis             └── Treponema pallidum
                        ├── Clusters (Staphylococci)     ├── Palisades (Corynebacterium)
                        │   └── Staphylococcus aureus    └── Coccobacilli (Haemophilus)
                        ├── Tetrads (Micrococcus)
                        └── Cubes/Sarcinae (Sarcina)
                    

The size and shape of bacteria are determined by their cell wall and cytoskeleton components. The bacterial cell wall provides structural support, maintains cell shape, and prevents osmotic lysis in hypotonic environments.

4.2 Cell Wall Structure and Gram Staining

The Gram stain is a differential staining technique used to classify bacteria into two groups based on their cell wall composition:

Some bacteria lack a cell wall entirely (e.g., Mycoplasma) or have modified cell walls that do not respond typically to Gram staining (e.g., Mycobacteria, which require acid-fast staining).

5.1 Flagellar Movement

Flagella are thin, whip-like appendages that provide locomotion for many bacteria. They are composed primarily of the protein flagellin and extend from the bacterial cell surface.

Based on the number and arrangement of flagella, bacteria can be classified as:

• Monotrichous: Single flagellum at one end (e.g., Vibrio cholerae)
• Lophotrichous: Multiple flagella at one end (e.g., Pseudomonas fluorescens)
• Amphitrichous: Flagella at both ends (e.g., Spirillum volutans)
• Peritrichous: Flagella all over the surface (e.g., Escherichia coli, Salmonella typhi)

Flagellar motility allows bacteria to:

• Move toward nutrients (chemotaxis)
• Escape harmful substances
• Disperse to new environments
• Increase pathogenicity by enabling invasion of host tissues

5.2 Other Forms of Microbial Movement

Axial Filaments (Endoflagella): Spirochetes like Treponema pallidum (causative agent of syphilis) have flagella wrapped around their cell body between the cell membrane and outer sheath, giving them a corkscrew-like motion.

Gliding Motility: Some bacteria (e.g., Myxococcus, Cytophaga) can move across solid surfaces without visible appendages through secretion of slime or by using focal adhesion complexes.

Twitching Motility: Mediated by type IV pili that extend, attach to a surface, and then retract, pulling the bacterium forward (e.g., Pseudomonas aeruginosa, Neisseria gonorrhoeae).

Swimming Motility: Bacteria with flagella can swim through liquid environments. The flagella rotate like propellers, driven by a molecular motor at the base.

6.1 Biofilm Formation

Biofilms are complex communities of microorganisms attached to surfaces and embedded in a self-produced extracellular polymeric substance (EPS) matrix. This lifestyle offers several advantages to the microbes:

                        1. Initial Attachment      2. Irreversible      3. Maturation I      4. Maturation II      5. Dispersion
                           (reversible)               Attachment          (early)              (late)
                               ↓                          ↓                   ↓                    ↓                   ↓
                        Planktonic cells → Surface adhesion → Microcolony → EPS production → Mature biofilm → Cell release
                                                                           formation        3D structure
                    

Biofilms are clinically significant because they:

• Increase resistance to antimicrobial agents (up to 1,000 times more resistant)
• Protect against host immune defenses
• Allow bacterial communication through quorum sensing
• Enable nutrient capture and metabolic cooperation
• Contribute to persistent and chronic infections

Common examples of biofilm-associated infections include:

• Dental plaque (leading to caries and periodontal disease)
• Catheter-associated urinary tract infections
• Chronic wounds
• Cystic fibrosis lung infections (particularly with Pseudomonas aeruginosa)
• Prosthetic joint infections
• Endocarditis

6.2 The Human Microbiome

The human microbiome refers to all microorganisms living on and inside the human body. Different body sites harbor distinct microbial communities adapted to local conditions:

7.1 Nutritional Types of Microorganisms

Microorganisms can be classified based on their carbon and energy sources:

Based on oxygen requirements, microorganisms can be classified as:

• Obligate aerobes: Require oxygen for growth (e.g., Mycobacterium tuberculosis, Pseudomonas aeruginosa)
• Microaerophiles: Require oxygen but at concentrations lower than atmospheric levels (e.g., Campylobacter jejuni, Helicobacter pylori)
• Facultative anaerobes: Can grow with or without oxygen (e.g., Escherichia coli, Staphylococcus aureus)
• Obligate anaerobes: Cannot tolerate oxygen and are killed by it (e.g., Clostridium species, Bacteroides fragilis)
• Aerotolerant anaerobes: Do not use oxygen but can tolerate its presence (e.g., Lactobacillus)

7.2 Microbial Growth Phases

In a closed system (batch culture), bacterial growth follows a predictable pattern with four distinct phases:

                    Number of
    Bacteria (log)
         ^
         |                              Stationary Phase
         |                        ______________________
         |                       /
         |                      /
         |                     /  Exponential/Log Phase
         |                    /
         |                   /
         |                  /
         |                 /
         |                /
         |   Lag Phase   /                 Death Phase
         |   __________/                    \
         |  /                                \
         | /                                  \
         |/                                    \
         +------------------------------------------>
                                Time
                    

1. Lag Phase: Cells adapt to the new environment, synthesize enzymes, and prepare for reproduction. Little or no cell division occurs.
2. Exponential/Log Phase: Cells divide at a constant rate, with population doubling at regular intervals. This is the period of most rapid growth.
3. Stationary Phase: Growth rate equals death rate, resulting in a stable population. This occurs when nutrients become limiting or waste products accumulate to inhibitory levels.
4. Death/Decline Phase: Death rate exceeds growth rate, leading to a decrease in viable cells.

The generation time (doubling time) varies among bacterial species:

• E. coli: ~20 minutes under optimal conditions
• Staphylococcus aureus: ~30 minutes
• Mycobacterium tuberculosis: ~24 hours

7.3 Measuring Microbial Growth

Several methods are used to measure microbial growth in laboratory and clinical settings:

8.1 Temperature Effects

Temperature profoundly affects microbial growth rates and survival. Microorganisms can be classified based on their temperature preferences:

Temperature affects:

• Enzyme activity and protein stability
• Membrane fluidity and permeability
• Nucleic acid stability (DNA and RNA)
• Metabolic rates and overall growth kinetics

8.2 Moisture Requirements

Water availability is critical for microbial growth. Water activity (aw) is a measure of the available water in a substance, with pure water having an aw of 1.0.

Based on water requirements, microorganisms can be classified as:

• Hydrophiles: Require high water activity (aw > 0.95) for growth (most bacteria, including all human pathogens)
• Xerotolerant: Can grow at reduced water activity (aw = 0.80-0.90) (some yeasts and molds)
• Xerophiles: Prefer or require low water activity (aw < 0.80) (some fungi and halophilic archaea)

Methods for controlling microbial growth by reducing water activity include:

• Drying/Dehydration: Removing water (e.g., dried foods, lyophilization)
• Adding Solutes: Increasing osmotic pressure (e.g., salting, sugaring)
• Freeze-drying: Combining freezing with dehydration under vacuum

8.3 Blood and Body Fluids as Microbial Environments

Blood and body fluids provide rich nutrients for microbial growth but also contain antimicrobial factors that help prevent infections:

Blood as a Microbial Environment:

• Normally sterile in healthy individuals (bacteremia is abnormal)
• Rich in nutrients (glucose, proteins, minerals)
• Contains antimicrobial components:
  • Complement system
  • Antibodies
  • Phagocytic cells (neutrophils, monocytes)
  • Antimicrobial peptides (e.g., defensins)
  • Transferrin (binds and sequesters iron)
• Supports growth of many pathogens if they can overcome host defenses

Other Body Fluids: