Intro to Microbiology & Bacterial Basics

Definition & Scope of Microbiology

  • Microbiology = study of organisms only visible under a microscope • bacteria • viruses • fungi • protozoa.

  • Predominantly beneficial roles:

    • Humans: resident microbiota aid digestion, vitamin synthesis, immune training.

    • Plants: soil bacteria perform nitrogen fixation → convert atmospheric N<em>2N<em>2 into bio‐available NH</em>3NH</em>3.

    • Ruminant/termite guts: microbes digest cellulose.

    • Industrial applications: fermentation, antibiotic production, bioremediation, enzyme manufacture.

Ways We Classify the Major Microbial Groups

  • Bacteria: primarily by Gram stain reaction (positive vs. negative) & morphology.

  • Viruses: by nucleic-acid type (DNA / RNA) + strandedness (single / double).

  • Fungi: by body plan • molds = multicellular • yeasts = unicellular.

Taxonomic Hierarchy (High → Low)

  • Domain→Kingdom→Phylum→Class→Order→Family→Genus→Species\text{Domain} \rightarrow \text{Kingdom} \rightarrow \text{Phylum} \rightarrow \text{Class} \rightarrow \text{Order} \rightarrow \text{Family} \rightarrow \text{Genus} \rightarrow \text{Species}

  • Mnemonic offered: “Dina’s
    D Ina’s k\text{k}ids pprefer ccandy oover ffried ggreen sspinach.”

The Three Domains

  • Bacteria

  • Archaea

  • Eukarya

Prokaryotes vs. Eukaryotes

  • Prokaryotes (Bacteria + Archaea)

    • Lack true membrane-bound organelles: NO mitochondria, Golgi, ER.

    • Small 70 S ribosomes.

    • Usually have rigid cell wall (peptidoglycan in bacteria).

  • Eukaryotes (Eukarya)

    • Possess organelles.

    • 80 S ribosomes in cytosol.

    • Cell wall ABSENT except in fungi (chitin) & plants (cellulose).

Kingdoms Inside Each Domain

  • Bacteria → single kingdom “Bacteria.”

  • Archaea → single kingdom “Archaea.”

  • Eukarya → four kingdoms: Protists, Fungi, Plants, Animals.

Binomial Nomenclature (How We Name Bacteria)

  • Two words: Genus (capitalised) + species (lower-case); italicised or underlined.

  • Example: Staphylococcus aureus

    • “Staphylo–” = grape-like clusters; “coccus” = round cell; “aureus” = golden pigment on agar.

Common Bacterial Shapes & Arrangements

  • Cocci: spherical.

  • Bacilli (rods): cylindrical.

  • Spirochetes: flexible spirals.

  • Vibrio: curved rod (comma-shaped).

  • Diplococci: pairs of cocci.

  • Coccobacilli: short rods that resemble cocci.

  • Streptococci: chains of cocci.

  • Staphylococci: irregular grape-like clusters of cocci.

  • Tetrads: packets of four cocci.

Bacterial Cell Architecture (Baseline Model)

  • Genome: circular dsDNA (nucleoid region).

  • Cytoplasmic membrane (phospholipid bilayer).

  • Cytoplasm with 70 S ribosomes.

  • Peptidoglycan cell wall (confers shape & osmotic protection).

  • Flagella: helical filaments for motility (chemotaxis).

  • Pili (fimbriae): short hair-like structures for adhesion; specialized sex pilus for conjugation.

  • Plasmids: small extrachromosomal DNA circles → antibiotic resistance, toxins.

  • Glycocalyx (outermost sugar coat)

    • Capsule: organized, firmly attached → antiphagocytic (evades immune cells).

    • Slime layer/biofilm: loose, sticky matrix; important for surface attachment & community living.

  • Porins: β-barrel proteins in Gram-negative outer membrane. Selective entry; mutations can block antibiotics.

  • Mesosomes: invaginations of plasma membrane that partition respiratory enzymes; functional analogue to mitochondria in prokaryotes.

Gram Stain Technique & Outcomes

  1. Crystal violet → all cells purple.

  2. Iodine (mordant) → fixes dye.

  3. Alcohol/acetone decolorizer → differentiates.

  4. Safranin counterstain → colors decolorized cells red.

  • Gram-positive

    • Thick peptidoglycan retains crystal violet–iodine complex → appear blue/purple.

    • Wall contains teichoic & lipoteichoic acids (antigenic, aid adhesion & cation transport).

  • Gram-negative

    • Thin peptidoglycan ⇒ dye lost during alcohol wash; take up safranin → pink/red.

    • Outer membrane: phospholipid bilayer + porins + lipoproteins.

    • Surface lipopolysaccharide (LPS) composed of:

    1. O-antigen (serotyping)

    2. Core polysaccharide

    3. Lipid A = endotoxin.

  • Endotoxin properties:

    • Released on cell lysis.

    • Triggers host innate immunity (TLR-4) → cytokines (IL-1, TNF-α) → fever, weakness, aches, possible septic shock.

    • Exclusively in Gram-negative bacteria.

Practical Connections & Significance

  • Gram reaction influences:

    • Choice of empirical antibiotics (e.g., β-lactams ↑ effective against Gram +; outer membrane of Gram – limits permeability).

    • Vaccine development (protein vs. polysaccharide antigens).

  • Morphology & arrangements aid rapid identification in clinical smears.

  • Capsule presence correlates with virulence (e.g., S. pneumoniae; vaccine targets polysaccharide).

  • Biofilms complicate chronic infections & device contaminations; demand higher drug concentration.

  • Porin loss/mutation = emerging resistance mechanism (e.g., carbapenem resistance in Pseudomonas).

  • Mesosome concept historically debated; regardless, prokaryotic respiration is membrane-based.

Recap Mnemonics & Key Takeaways

  • Taxonomic hierarchy: “D & S kids prefer candy over fried green spinach.”

  • Gram-positive = Purple, Positive, Peptidoglycan-thick.

  • Gram-negative = Negative, New outer membrane with LPS.

  • Capsule = “Killer Coat” (anti-phagocytic).

End of introductory overview. Use these structured notes as a foundation before diving into specific bacterial genera, pathogenic mechanisms, and antimicrobial strategies.