Bacterial Nomenclature and Morphology

Bacterial Naming Hierarchy
- Scientific names have a two-part structure consisting of:
- Genus: Broader group designation
- Specific Epithet: Indicates specific species
Formatting Rules:
- Italics: Both genus and species must be italicized (or underlined in handwritten form).
- Capitalization:
- The genus name is always capitalized.
- The species name is always in lowercase.
- Abbreviation: After the first full mention, the genus can be abbreviated to its initial letter (e.g., Escherichia coli can be abbreviated to E. coli).
Meaning Behind the Names:
- Genus: Represents a group of closely related species. For example, the genus Bacillus includes various types of rod-shaped bacteria.
- Species: The smallest unit of biological classification, where members generally share a higher than $>95\%$ DNA similarity.

Definition:
- A strain is a sub-classification below the species level; it refers to the descendants of a single pure microbial culture.
- It can be thought of as similar to a "breed" of dog within the same species (e.g., Canis lupus familiaris includes Beagles and Huskies as different strains).
Use in Nomenclature:
- Strain designation follows the species name.
- Formatting: Strain names are written in plain text, not italicized.
- Examples:
- Escherichia coli K-12
- Staphylococcus aureus NCTC 8325
Importance: Strains of a species can display very different behaviors; for example, the strain E. coli O157:H7 can produce toxins leading to severe food poisoning, unlike the generally harmless strains found in the gut.

Example of E. coli
- Taxonomic Level: Domain: Bacteria
- Phylum: Pseudomonadota (Previously Proteobacteria)
- Class: Gammaproteobacteria
- Order: Enterobacterales
- Family: Enterobacteriaceae
- Genus: Escherichia
- Species: coli
- Strain: K-12
Example of B. subtilis
- Taxonomic Level: Domain: Bacteria
- Phylum: Bacillota (Previously Firmicutes)
- Class: Bacilli
- Order: Bacillales
- Family: Bacillaceae
- Genus: Bacillus
- Species: subtilis
- Strain: 168
Formatting Note:
- The phylum names were officially reclassified in 2021, though older references may still use previous classifications.

sp. (singular):
- Refers to one unknown species within a genus (e.g., Bacillus sp.).
- Common in instances where bacteria are isolated but not fully characterized (often through 16s rRNA sequencing).
spp. (plural):
- Refers to multiple species within a genus (e.g., Salmonella spp.).
Note: These abbreviations are not italicized, despite the genus name being italicized.

Cocci: Spherical bacteria
- Types of Cocci:
- Diplococci: Pairs of cocci
- Staphylococci: Irregular clusters of cocci
- Streptococci: Chains of cocci
- Tetrads: Groups of four cocci
- Sarcina: Cubical packets of cocci
- Coccobacillus: Intermediate form between cocci and bacilli
Bacilli: Rod-shaped bacteria
- Types of Bacilli:
- Diplobacilli: Pairs of bacilli
- Streptobacilli: Chains of bacilli
Others:
- Vibrio: Comma-shaped bacteria
- Spirillum: Helical shape
- Spirochete: Flexible spiral shape
- Filamentous: Long, thread-like structures
- Appendaged bacteria: Have protrusions like stalks (e.g., Caulobacter)

Prokaryotic Cells: Lack membrane-bound organelles but have specialized internal structures:
- Nucleoid:
- Contains the circular, double-stranded DNA chromosome in a compact state.
- It is non-membrane bound, unlike a true nucleus.
- Cytoplasm:
- Internal fluid rich in enzymes responsible for metabolic processes.
- Ribosomes (70S):
- Complexes of RNA and proteins translating genetic code into proteins.
- High-density ribosomes correlate with faster growth rates.
- Inclusion Bodies:
- Denser storage regions used for nutrients (e.g., carbon, phosphate, sulfur) or as repositories for misfolded proteins during stress.
- Vesicles (or Vacuoles):
- Specialized compartments, e.g.
  - Gas Vesicles: Provide buoyancy for aquatic bacteria like cyanobacteria.

Structure: Phospholipid bilayer composed of hydrophilic heads and hydrophobic tails.
Function:
- Regulates passage of molecules through transporters (active or passive transport).
- Locates enzymatic protein complexes essential for metabolic processes.
Structural Elements:
- Unlike eukaryotes, which utilize sterols (cholesterol) for membrane stability, bacteria depend on proteins and other molecules, especially in the absence of a cell wall.

Most bacteria possess a cell wall composed of peptidoglycan, a structure akin to chain mail:
Components:
- Glycan (Sugar) Backbone: Repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
- Peptide Chains: Short amino acid chains linked to NAM units and cross-linked via peptide bonds.
Primary Functions:
- Provides rigidity and determines cell shape (e.g., Cocci, Bacillus).
- Protects against osmotic pressure, preventing lysis in hypotonic environments.

Bacteria are classified based on their response to Gram Staining, indicating morphological differences:

Feature	Gram-Positive	Gram-Negative
Peptidoglycan Layer	Thick (multiple cross-linked layers)	Thin (single or few layers)
Outer Membrane	Absent (Monodermic)	Present (Didermic)
Unique Components	Teichoic Acids	Lipid A (Endotoxin) & O Antigen
Gram Stain Color	Purple (Retains Crystal Violet)	Pink (Retains Safranin)
Examples	Bacillus subtilis	E. coli

Clinical/Immunological Note:
- In Gram-negative bacteria, Lipid A (part of the Lipopolysaccharide layer) serves as an endotoxin that can trigger severe immune responses if introduced into the bloodstream.

Flagella: Specialized structures aiding in motility.
Visibility:
- Typically not visible under standard light microscopy without special staining techniques to increase appendage diameter.