DBS1: Host-Microbe Interactions & Microbiology Methodologies

Vocabulary flashcards covering oral microbiology, ecological niches, host-microbe symbiotic relationships, dysbiosis, opportunistic oral infections, antimicrobial control, and molecular identification methods.

Dental Plaque

The community of micro-organisms found on the tooth surface as a biofilm embedded in a matrix of polymers of salivary and bacterial origin.

Fissure Plaque

Biofilm accumulated within the anatomical fissures on the occlusal surfaces of teeth, typically containing $1\text{--}33 \times 10^6$ bacteria per fissure.

Sub-gingival Plaque

Dental biofilm located below the gum margin within the gingival crevice, typically containing $10^3\text{--}10^6$ bacteria per crevice.

Two-Tone Plaque Disclosing

A differential staining technique that identifies mature dental plaque as purple and newly formed dental plaque as pink.

Desquamation (Oral Mucosa)

The continuous shedding of epithelial cells from oral mucosal surfaces, which maintains a low microbial load on non-keratinised and keratinised tissues.

Tongue Dorsum (Microbial Habitat)

A specialized oral niche with a papillary structure (covered in projections or finger-like structures) harbouring approximately $100$ bacteria per epithelial cell.

Saliva (Oral Microbiology)

A fluid composed of $99\%$ water, $0.3\%$ protein, and $0.2\%$ inorganic molecules, lipids, and hormones; it serves as the primary source of nutrients for oral microbes and contains approximately $10^8$ viable microbes per millilitre.

Gingival Crevicular Fluid (GCF)

A serum-like exudate located at the junctional epithelium of the gingivae that is rich in nutrients for microbes and carries host inflammatory elements.

Dysbiosis

An imbalance in a microbial community where the natural composition and symbiotic equilibrium of microorganisms is disrupted.

Pathogen

A microorganism capable of causing damage or disease to the host.

Pathobiont

A member of the resident microbiota that causes disease when a disruption of the normal balance between the host and microbiota (dysbiosis) occurs.

Symbiont

A member of the resident microbiota that confers beneficial functions to the host organism.

Mutualism

A symbiotic host-microbe relationship in which both partners derive benefit, such as bacteria producing nutritional metabolites or protective hydrogen peroxide for the host.

Commensalism

A symbiotic relationship wherein the microbe benefits while remaining harmless to the host, exemplified by early colonising bacteria such as Streptococci.

Parasitism

A symbiotic interaction in which the microbe benefits at the expense of host harm, exemplified by Porphyromonas gingivalis degrading host tissues for nutrients.

Amensalism

An ecological interaction where one organism or host is harmed or inhibited while the other is unaffected.

Opportunistic Pathogen

An organism that typically does not cause disease in healthy individuals but can establish infection when host defences, barrier tissues, or normal microbiota balance are compromised.

Xerostomia

The clinical condition of oral dryness due to decreased salivary flow, which serves as a non-immunological factor predisposing to oral dysbiosis.

16S rRNA Gene

A bacterial gene consisting of conserved regions (used for universal PCR primer annealing) interspersed with nine variable regions ($V_1\text{--}V_9$) that allow group- or species-specific taxonomic differentiation.

Denaturing Gradient Gel Electrophoresis (DGGE)

A molecular fingerprinting method that separates PCR-amplified DNA fragments based on sequence-dependent melting behavior across an increasing gradient of chemical denaturants.

DNA-DNA Checkerboard

A high-throughput molecular technique that simultaneously detects and quantifies multiple bacterial species across numerous clinical samples using a grid-arranged panel of labelled DNA probes (typically $40$ plaque-associated species).

Human Oral Microbe Identification Microarray (HOMIM)

A microarray tool that uses 16S rRNA gene-targeted probes on a chip to detect and evaluate the relative abundance of approximately $300$ known oral bacterial species.

Amplicon Sequence Variants (ASVs)

Exact, single-nucleotide-resolved biological sequences resolved from raw high-throughput sequencing data (e.g., 16S rRNA gene sequencing) that are matched against public reference databases to assign taxonomy.

DNA-FISH (Fluorescence In-Situ Hybridisation)

An imaging technique employing fluorescently labelled DNA probes complementary to target sequences to visualise and locate specific microbial taxa directly within intact spatial structures like biofilms.

Metagenomics

The untargeted sequencing and computational reconstruction of all collective genomic DNA directly recovered from a clinical or environmental sample to assess both community taxonomy and metabolic pathways.

MinION (Oxford Nanopore Sequencing)

A portable, real-time sequencing device that reads native long DNA or RNA strands by pulling them through a membrane-embedded protein nanopore and measuring disruptions in ionic current.

Antimicrobial Resistance (AMR)

The acquired or intrinsic ability of bacteria to resist antimicrobial therapies, projected to cause $10\text{ million}$ deaths globally per year by $2050$.

Sterilisation

A process that completely destroys or eliminates all forms of viable microbial life, including bacterial endospores, often carried out via steam autoclaving.

Pasteurisation

A controlled heat treatment applied to liquids (such as milk) to destroy pathogenic vegetative microorganisms and reduce spoilage flora without complete sterilization.

Chlorhexidine

A broad-spectrum antiseptic chemical agent commonly used in antimicrobial mouthwashes and oral hygiene products to inhibit oral plaque bacteria.