Biology of the Human Microbiota – Key Vocabulary

Vocabulary flashcards covering key terms and definitions from the lecture on the human microbiota, its roles in health, disease associations, and methods of study.

Human microbiota

The community of bacteria, archaea, yeasts, protists and viruses that live on and inside the healthy human body.

Microbiome

The collective genomes (genetic content) of all microorganisms that make up the human microbiota.

Volatile Fatty Acids (VFAs)

Short-chain fatty acids produced by gut bacteria from complex carbohydrates; serve as energy sources and signalling molecules for the host.

Essential amino acids

Ten amino acids that humans cannot synthesise and must obtain from diet or microbial metabolism in the gut.

Folate

Vitamin B9; synthesised by certain gut microbes, especially enriched in the infant microbiome to compensate for possible dietary lack.

Vitamin K

Vitamin produced by gut bacteria and required for prothrombin formation and normal blood clotting.

Germ-free mice

Laboratory animals raised without microorganisms, used to show links between gut microbiota composition and host traits such as body-fat proportion.

Firmicutes

A bacterial phylum; relative increase (with methanogenic Archaea) in obese phenotypes and during late pregnancy.

Bacteroidetes

A dominant gut bacterial phylum; decreased in certain obesity models but genus Prevotella can be enriched in humans.

Methanogenic Archaea

Archaea that produce methane; increased abundance correlates with higher energy harvest from the gut.

Colonisation resistance

Protection conferred by commensal microbiota that prevents pathogens from establishing through competition for space, nutrients and production of antimicrobials.

Bacteriocins

Proteinaceous toxins produced by bacteria (e.g., B. thuringiensis) that inhibit growth of closely related or pathogenic species such as Clostridioides difficile.

Competitive exclusion

Mechanism by which resident microbes occupy niches and resources, preventing pathogen colonisation.

Bifidobacterium

Genus of gut commensals that secrete organic acids and peptides reducing adhesion of pathogenic E. coli to enterocytes.

Bacteroides thetaiotaomicron

Gut commensal able to out-compete Citrobacter rodentium for carbohydrates and to stimulate antimicrobial peptide REGIIIγ production.

Segmented Filamentous Bacteria (SFB)

Gram-positive, spore-forming, non-culturable Clostridia-related bacteria that potently stimulate mucosal immune responses.

Dysbiosis

An imbalance in the composition or function of the microbiota associated with disease states.

Antibiotic-associated diarrhoeal disease

Condition where broad-spectrum antibiotics disrupt gut microbiota, allowing pathogenic overgrowth and diarrhoea.

Clostridioides difficile

Endospore-forming Gram-positive bacterium producing up to three toxins; major cause of antibiotic-associated diarrhoea and pseudomembranous colitis.

Faecal microbiota transplant (FMT)

Therapy that transfers stool from a healthy donor to restore normal gut microbiota, used in recurrent C. difficile infection.

Inflammatory Bowel Disease (IBD)

Chronic inflammation of the gastrointestinal tract linked to periods of gut dysbiosis and altered microbial-host interactions.

Periodontal disease (Periodontitis)

Chronic inflammatory condition of the gums involving Gram-negative bacteria and systemic risk factors; affects ~35–50 % of people.

Dental caries (Tooth decay)

Microbially driven demineralisation of tooth enamel and dentine influenced by diet, oral hygiene and biofilm succession.

Biofilm (oral)

Structured microbial community on oral surfaces (e.g., plaque) containing species such as Streptococcus, Haemophilus and Actinomyces.

Gut-Lung Axis

Bidirectional interaction where gut microbiota metabolites modulate lung immunity, impacting asthma, COPD and infection outcomes.

Gut-Skin Axis

Relationship whereby gut dysbiosis affects skin immunity and barrier function, contributing to acne, psoriasis and atopic dermatitis.

Gut-Brain Axis

Network linking gut microbiota to nervous system and mental health, with associations to depression, ASD, MS and neurodegeneration.

Virome

The total collection of eukaryotic, bacterial and archaeal viruses present in and on the human body.

Virus-Like Particles (VLPs)

Non-infectious viral particles counted to estimate viral abundance at body sites (e.g., 10⁹ VLPs g⁻¹ in faeces).

crAssphage

Highly abundant podovirus infecting Bacteroidetes; makes up ~90 % of the gut virome in half the global population.

Bacteriophage (phage)

Virus that infects bacteria; dominates the gut virome and is often acquired early from bacterial genomes.

Cutibacterium

Skin commensal genus whose abundance declines with ageing, often replaced by potentially pathogenic taxa.

Actinobacteria

Phylum containing many skin and oral commensals (e.g., Corynebacterium, Cutibacterium); part of four dominant skin phyla.

Proteobacteria

Phylum including Betaproteobacteria on dry skin and increased gut members in late pregnancy dysbiosis.

Staphylococci

Genus prevalent on moist and oily skin sites; some species are harmless commensals, others opportunistic pathogens.

Archaea

Domain of single-celled microorganisms; methanogenic archaea contribute to gut metabolism and may influence obesity.

Koch’s postulates (revised)

Modern criteria, accommodating unculturable and polymicrobial pathogens, used to link microorganisms to disease causation.

Microbial metagenomics

Sequencing-based approach that analyses all microbial DNA in a sample, enabling identification of uncultured microbes and virome members.