Biology of Infectious Microorganisms – Core Vocabulary

Learning Outcomes

• LO1 – Define key terminology for microorganisms causing disease.
• LO2 – Describe biological features of microorganisms.
• LO3 – Explain how microorganisms can be classified and why this matters.

Key Terminology (Disease-Causing Microorganisms)

• Pathogen – agent capable of causing damage to a host.
• Non-pathogenic – microorganism that does NOT cause host damage.
• Obligate pathogen – ALWAYS causes disease (e.g. Salmonella Typhi).
• Opportunistic pathogen – causes disease only when conditions permit (e.g. Clostridioides difficile).
• Commensal – normally harmless; benefits without harming host (e.g. Bifidobacterium spp.).

Historical Foundations of Microbiology

• 1665 – Robert Hooke builds a compound microscope; publishes “Micrographia” → first use of word “cell.”
• 1684 – Antoni van Leeuwenhoek observes “animalcules” (bacteria & protozoa) in dental plaque; produces detailed drawings.
• Early microscopy laid groundwork for recognizing microbial diversity but detection/classification remained challenging due to microscopic size.

Domains of Life & Cellular Classification

• Three-domain system (Woese 1990): Bacteria, Archaea, Eukarya; all traced back to LUCA (Last Universal Common Ancestor).
• Viruses sit outside cellular life; are obligate intracellular parasites – require host machinery for replication.

Shared vs Unique Cellular Features

• Shared (core of life): genetic code, ribosomes, central dogma, membrane boundary, energy metabolism.
• Unique/diagnostic for microbes: peptidoglycan (Bacteria), ether lipids (Archaea), organelles (Eukarya), viral capsid forms, etc.

Virus Classification – Baltimore System

• Class I & VII – dsDNA viruses (e.g. T4 phage, Hepatitis B); VII involves reverse transcription.
• Class II – ssDNA (+) (e.g. ΦΧ174).
• Class III – dsRNA (e.g. Rotavirus).
• Class IV – ssRNA (+), genome serves directly as mRNA (e.g. Poliovirus).
• Class V – ssRNA (-) (e.g. Influenza, Rabies); requires synthesis of complementary + strand.
• Class VI – ssRNA (+) retroviruses (e.g. HIV); reverse transcription to dsDNA intermediate.
• Central determinant = route from genome → mRNA.

Prokaryote vs Eukaryote Cell Biology

• Nucleus: Absent in Bacteria/Archaea, present in Eukarya.
• Ribosome size: 70S = 50S+30S in Prokaryotes; 80S = 60S+40S in Eukaryotes.
• RNA polymerase(s): One in Bacteria, several in Archaea, three in Eukarya.
• Cell-wall muramic acid: present in Bacteria only.
• Membrane lipid linkage: ester (Bacteria & Eukarya) vs ether (Archaea).
• Antibiotic sensitivity: Prokaryotic 23S/16S rRNA targeted by chloramphenicol, streptomycin, kanamycin; eukaryotic 28S/18S rRNA less affected.

How Does the Immune System Recognise Microbes?

• Pattern-recognition receptors (PRRs) detect PAMPs (e.g. LPS, peptidoglycan, flagellin, viral dsRNA).
• Differences across groups:
– Bacteria → LPS, lipoteichoic acid, CpG DNA.
– Viruses → dsRNA, unmethylated CpG, envelope glycoproteins.
– Parasites → glycosylphosphatidylinositols, variant surface glycoproteins.

Morphological & Phenotypic Diversity of Bacteria

• Colony morphologies on LB agar distinguish pathogens (e.g. Enterobacter aerogenes, Staphylococcus epidermidis, Pseudomonas aeruginosa pigmented, etc.).
• Microscopy reveals:
– Gram − rods: E. coli, P. aeruginosa, Klebsiella pneumoniae.
– Gram + cocci: S. aureus, S. epidermidis.
– Acid-fast bacilli: Mycobacterium tuberculosis (Ziehl-Neelsen stain).
• Unique pigments (e.g. red prodigiosin by Serratia marcescens).

Cell Shapes (Brock 2019)

• Coccus – spheres (Staphylococcus aureus).
• Rod – bacilli (E. coli, Bacillus anthracis).
• Spirillum – rigid spiral (Campylobacter jejuni).
• Spirochete – flexible spiral (Borrelia burgdorferi).
• Budding/appendaged – stalked (Caulobacter crescentus).
• Filamentous – long chains (cyanobacteria).

Cell Wall & Gram Type

• Gram-positive: thick peptidoglycan with teichoic acids, possible S-layer; N-acetylmuramic acid present; stain purple.
• Gram-negative: thin peptidoglycan + outer membrane containing lipopolysaccharide (LPS) – endotoxin; O-antigens, capsule; stain pink.

Motility Variations

• Flagellation patterns:
– Polar/monotrichous.
– Lophotrichous (tuft at one pole).
– Peritrichous (distributed) – classic run-and-tumble.
• Campylobacter jejuni integrates cell shape + opposed polar flagella (Cohen 2020); fluorescence/biophysics visualisation (Turner 2016).

Endospore Formation

• Genera: Bacillus, Clostridium.
• Resistant to heat, desiccation, radiation, chemicals.
• Spore position helps ID: central, subterminal, terminal.
• Microscopy: TEM shows dense core; fluorescence tags coat proteins.

Metabolic Diversity & Strategies

• Carbon source:
– Autotrophs – CO2 fixation. – Heterotrophs – organic C (glucose, chitin, CH₄). – Mixotrophs – flexible. • Energy source: – Phototrophs – photons. – Chemotrophs – chemical bond oxidation. • Combine prefixes (energy)(donor)(carbon): – Example: Photoorganoautotroph uses light + organic e⁻ donor + CO2.
– Chemo­litho­autotroph uses chemical energy + inorganic e⁻ donor + CO_2 (e.g. nitrifiers, manganese oxidisers (Yu 2020)).

Microbial Metabolism Pathways

• Fermentation: organic terminal e⁻ acceptor → 2\,ATP + acids/alcohols.
• Aerobic respiration: O2 terminal acceptor → 38\,ATP (via TCA & ETS). • Anaerobic respiration: inorganic acceptors (e.g. NO3^-, SO4^{2-}) → \approx34\,ATP + reduced products (NH3, H_2S).
• KEGG shows ability to degrade xenobiotics (toluene, atrazine, bisphenol) & cycles (nitrogen, sulfur, methane).

Cultivation Bias & “Microbial Dark Matter”

• “Great Plate Anomaly” (Staley & Konopka 1985): microscopic counts ≫ colony counts; most microbes uncultured.
• Single-cell genomics & metagenomics (Rinke 2013) uncover novel phyla; expand phylogenetic tree.

Taxonomy & Phylogeny Concepts

• Taxonomy = Systematics + Classification + Nomenclature (“taxonomic trilogy”).
• Systematics assesses diversity & relationships; phylogeny traces evolutionary lines.
• Classic taxonomy relied on phenotype (morphology, metabolism, habitat). Molecular era integrates sequence data.
• Enterobacteriaceae example hierarchy: Domain → Phylum Proteobacteria → Class \gamma-proteobacteria → Order Enterobacterales → Family Enterobacteriaceae → Genus Escherichia → Species coli.

Ribosomal RNA Phylogeny

• rRNA (non-coding) essential, universal, slowly evolving; variable regions (V1–V9) encode phylogenetic signal.
• 16S rRNA (Bacteria/Archaea) & 18S (Eukarya); ~1550\,nt length.
• Limitations: high similarity among close genera (E. coli, Shigella); multiple divergent copies per genome; PCR/Sanger errors; requires reference database.

Expanded Tree of Life

• Hug et al. 2016: 3083 genomes (many uncultured) + 16 concatenated ribosomal proteins → revised tree; Eukarya placed via SSU rRNA.
• Highlights >1300 bacterial phyla; environmental clades dominate.

Representative Pathogenic Lineages

• Protists (Eukarya):
– Euglenozoa: Trypanosoma brucei (African sleeping sickness), T. cruzi (Chagas).
– Apicomplexa: Plasmodium falciparum (malaria).
– Amoebozoa: Acanthamoeba spp. (keratitis).
– Fornicata: Giardia lamblia (diarrhea).
– Opisthokonta: Candida dubliniensis (yeast infections).
• Bacterial phyla of clinical interest: Spirochaetota (Borrelia), Pseudomonadota/Proteobacteria (Vibrio cholerae, Shigella), Bacillota/Firmicutes (Streptococcus pyogenes), Actinomycetota (Mycobacterium tuberculosis), Mycoplasmatota (Mycoplasma pneumoniae).

Whole-Genome Phylogeny

• Genome-scale trees (Zhu 2019) use 381 conserved markers across 10{,}575 prokaryote genomes → higher resolution than single-gene trees; informs taxonomy & function.

Biomedical Importance of Accurate Identification

• Clinical diagnostics → select correct antimicrobials, guide infection control.
• Public-health surveillance & epidemiology → outbreak tracing.
• Research → understand pathogenic mechanisms, vaccine/therapy development.
• Laboratory safety → match containment level to organism.

Reading & References

• Brock Biology of Microorganisms, 15th ed.:
– Chapter 1 “The Microbial World.”
– Chapter 14 “Phylogenetic Diversity of Bacteria.”
• Key papers:
– Cohen EJ et al. 2020 PLoS Pathog (flagellar coordination in C. jejuni).
– Turner L et al. 2016 Biophys J (visualising flagella).
– Yu H & Leadbetter JR 2020 Nature (manganese-oxidising chemolithoautotrophy).