Glossary - Core Microbiology Terms

One-line definitions. Where a full note exists, the term links to it.

Index: Glossary Index · Hub: MOC - Fundamentals of Microbiology

Cell structure

Peptidoglycan — mesh polymer of sugar chains cross-linked by peptides that gives the bacterial wall its strength; the β-lactam target. See Bacterial Cell Wall.
Capsule — outer polysaccharide layer resisting phagocytosis and drying; a major virulence and vaccine target.
Teichoic acid — anionic polymer in Gram-positive walls; surface charge and immune interaction.
LPS (endotoxin) — lipopolysaccharide of the Gram-negative outer membrane; lipid A triggers septic shock.
Porin — outer-membrane channel allowing small hydrophilic molecules in; losing porins reduces antibiotic entry.
Periplasm — compartment between inner and outer membranes of Gram-negatives; where β-lactamases work.
Pilus / fimbria — surface appendage for adhesion; the sex pilus mediates Conjugation.
Endospore — dormant, highly resistant survival structure (Bacillus, Clostridium, Clostridioides difficile).
Biofilm — surface-attached community in a self-produced matrix; tolerant to antibiotics and immunity.

Generation time — time to double; minutes for E. coli, ~18 h for Mycobacterium tuberculosis.
Lag / log / stationary / death phases — the four phases of batch culture.
Obligate aerobe / anaerobe / facultative / microaerophilic — oxygen requirement classes.
Fastidious — needs enriched media or special atmosphere to grow.
Fermentation — ATP generation without an external electron acceptor; the basis of many identification tests.
Auxotroph — cannot synthesize a required nutrient; must be supplied.

Genome — total genetic content; bacterial chromosomes are typically single and circular.
Plasmid — extrachromosomal replicon, often carrying resistance or virulence genes.
Operon — genes transcribed from one promoter as a single mRNA. See Gene Expression.
Horizontal Gene Transfer — acquisition of DNA from a non-parent, by Transformation, Transduction, or Conjugation.
Transposon / insertion sequence — mobile DNA that relocates within or between replicons.
Integron — gene-capture system that collects cassettes, frequently resistance cassettes.
Prophage — bacteriophage genome integrated into the host chromosome.
Mutation — heritable sequence change; the raw material for adaptation.
Hypermutator — strain with defective DNA repair and elevated mutation rate; common in chronic infection.
Competence — physiological state permitting uptake of external DNA.

Taxonomy — the naming and ranking system for organisms.
Species (bacterial) — pragmatic definition; ~95% ANI is the common genomic threshold. See Comparative Genomics.
Strain — an isolate descended from a single colony; the unit of epidemiology.
Serotype — variant defined by surface antigen reactivity (e.g., pneumococcal capsule types).
Clone / clonal complex — group of closely related isolates; see MLST and cgMLST.
16S rRNA gene — conserved gene with variable regions used for phylogeny and identification (Carl Woese, 16S Amplicon Analysis).

Pathogen — organism capable of causing disease.
Opportunist — causes disease mainly when host defences or barriers are compromised.
Commensal / Normal Microbiota — resident organism not normally causing disease.
Colonization vs infection — presence without host response vs presence with tissue damage and response.
Virulence factor — trait contributing to pathogenicity (adhesin, toxin, capsule, secretion system).
Exotoxin / endotoxin — secreted protein toxin vs LPS released from the Gram-negative envelope.
Zoonosis — infection transmissible from animals to humans. See One Health.