Biology of Infectious Microorganisms – Core Vocabulary

Vocabulary flashcards covering terminology on microbial biology, diversity, classification and pathogenicity presented in the lecture notes.

Microorganism

An organism too small to be seen with the naked eye, including bacteria, archaea, micro-eukaryotes and viruses.

Virus

An obligate intracellular parasite that relies on host cells for replication.

Obligate Parasite

A microbe, such as a virus, that can replicate only inside a living host cell.

Microbial Diversity

The vast range of different microorganisms, reflected in their morphology, genetics, metabolism and ecology.

Robert Hooke

Seventeenth-century scientist who published “Micrographia” (1665) and used a compound microscope to describe cells.

Antoni van Leeuwenhoek

Dutch lens-grinder who first observed and sketched single-celled “animalcules” (1684).

Domains of Life

The three major cellular lineages: Bacteria, Archaea and Eukarya.

LUCA

Last Universal Common Ancestor from which all cellular life diverged.

Baltimore Classification

System that groups viruses into seven classes based on genome type and replication strategy.

dsDNA Virus (Class I)

Virus with a double-stranded DNA genome; replicates by semi-conservative DNA synthesis.

ssRNA (+) Virus (Class IV)

Virus whose single-stranded RNA genome can act directly as mRNA (e.g., poliovirus).

Retrovirus (Class VI)

ssRNA (+) virus that uses reverse transcriptase to make a DNA intermediate (e.g., HIV).

Prokaryote

Single-celled organism lacking a membrane-bound nucleus; includes Bacteria and Archaea.

Eukaryote

Cell type with a membrane-bound nucleus and organelles; includes protists, fungi, plants and animals.

Pathogen

Any agent capable of causing damage or disease in a host.

Non-pathogenic Microbe

Microorganism that does not normally cause host damage.

Obligate Pathogen

Microbe that always causes disease when present (e.g., Salmonella Typhi).

Opportunistic Pathogen

Microbe that causes disease only under certain conditions, such as host immune compromise (e.g., Clostridioides difficile).

Commensal

Microorganism living on or in a host without causing disease (e.g., Bifidobacterium spp.).

Gram-Positive Bacterium

Bacterium with thick peptidoglycan and teichoic acids; stains purple in Gram stain.

Gram-Negative Bacterium

Bacterium with thin peptidoglycan and an outer membrane rich in lipopolysaccharide; stains pink.

Lipopolysaccharide (LPS)

Endotoxin found in the outer membrane of Gram-negative bacteria; contains O antigens.

Teichoic Acid

Cell-wall polymer characteristic of Gram-positive bacteria that contributes to cell rigidity and antigenicity.

Peptidoglycan

Polymer of N-acetylglucosamine and N-acetylmuramic acid forming bacterial cell-wall mesh.

Muramic Acid

Sugar derivative (N-acetylmuramic acid) unique to bacterial peptidoglycan.

Coccus

Spherical bacterial cell shape (e.g., Staphylococcus aureus).

Bacillus (Rod)

Rod-shaped bacterial morphology (e.g., Escherichia coli).

Spirillum

Rigid spiral-shaped bacterium (e.g., Campylobacter jejuni).

Spirochete

Flexible, tightly coiled bacterium with axial filaments (e.g., Borrelia burgdorferi).

Endospore

Highly resistant dormant structure produced by certain Gram-positives (e.g., Bacillus).

Polar Flagella

Flagella located at one or both cell poles enabling motility.

Peritrichous Flagella

Multiple flagella distributed over the entire cell surface.

Lophotrichous Flagella

Tuft of flagella at one cell pole.

Autotroph

Organism deriving carbon from CO₂ fixation.

Heterotroph

Organism obtaining carbon from organic molecules.

Mixotroph

Microbe capable of both autotrophic and heterotrophic carbon acquisition.

Phototroph

Organism using light energy for metabolism.

Chemotroph

Organism obtaining energy from chemical bond oxidation.

Lithotroph

Organism using inorganic molecules as electron donors.

Organotroph

Organism using organic molecules as electron donors.

Fermentation

Energy-yielding metabolism with organic compound as final electron acceptor; produces 2 ATP plus acids/alcohols.

Aerobic Respiration

Catabolism where oxygen is the terminal electron acceptor; yields up to 38 ATP per glucose.

Anaerobic Respiration

Respiration using inorganic electron acceptors other than oxygen (e.g., NO₃⁻, SO₄²⁻).

Great Plate Anomaly

Observation that most microbes seen microscopically cannot be cultured on standard media.

Microbial Dark Matter

Genetically detected but yet-uncultured microbial lineages revealed by single-cell and metagenomic sequencing.

Taxonomy

Science of classifying organisms into hierarchical groups.

Phylogeny

Evolutionary history and relationships among organisms.

Systematics

Field integrating taxonomy and phylogeny to understand organismal diversity.

Nomenclature

Rules and conventions for naming organisms.

16S rRNA

Small-subunit ribosomal RNA gene used as a universal bacterial phylogenetic marker (~1550 nt).

18S rRNA

Eukaryotic small-subunit ribosomal RNA gene used for phylogenetic studies of eukaryotes.

Variable Regions (V1–V9)

Hyper-variable segments within 16S rRNA that provide species-level discrimination.

Enterobacteriaceae

Family of Gram-negative rods in the order Enterobacterales (e.g., Escherichia, Salmonella).

Proteobacteria

Large bacterial phylum including classes Alpha-, Beta-, Gamma-, Delta- and Epsilonproteobacteria.

Firmicutes (Bacillota)

Phylum of mostly Gram-positive bacteria including Bacillus and Clostridium.

Actinobacteria (Actinomycetota)

Phylum of high-G+C Gram-positive bacteria (e.g., Mycobacterium).

Whole-Genome Phylogeny

Evolutionary analysis based on conserved genes across complete genomes.

Diagnostics

Laboratory methods used to identify causative microorganisms in clinical samples.

Infection Control

Policies and procedures implemented to prevent pathogen transmission in healthcare settings.

Epidemiology

Study of disease distribution and determinants in populations.

Metagenomics

Sequencing and analysis of genetic material recovered directly from environmental or clinical samples.