9. Gut Microbiome Summary

Vocabulary practice flashcards covering the components, profiling methodologies, dietary effects, and causality models of the human and animal gut microbiota from Dr Matthew Snelson's lecture.

Microbiota

The entire collection of living microorganisms—including bacteria, archaea, fungi, viruses, and bacteriophages—residing in a specific ecological niche.

Microbiome

The collective genetic material and genomes of all microorganisms within a defined microbial community.

Bacteriophage

A virus that infects and replicates within bacteria, existing at an estimated ratio of $10:1$ relative to bacterial cells in the gut.

Phageome

The component of the gut microbiota consisting specifically of bacteriophages.

Virome

The viral community of the gut, which encompasses approximately $10^9 - 10^{10}$ virus-like particles ($\text{VLP}$) per gram of feces and constitutes roughly $5.8\%$ of total fecal DNA.

Mycobiome

The fungal members of the gut microbial ecosystem, representing approximately $10^2 - 10^6\,\text{cfu}\cdot\text{g}^{-1}$ of feces and about $0.1\%$ of total fecal DNA.

16S rRNA Gene

A bacterial and archaeal gene possessing nine variable regions ($\text{V1}$ to $\text{V9}$) flanked by conserved regions, targeted in amplicon sequencing to determine microbial taxonomy.

Internal Transcribed Spacer (ITS)

A non-coding genetic region comprising $\text{ITS1}$ and $\text{ITS2}$ surrounding the $5.8\text{S}$ rRNA gene, targeted in marker gene amplicon sequencing to identify fungal communities.

Shotgun Metagenomics

Untargeted sequencing of all sheared genomic DNA from a community, offering species- or strain-level taxonomic resolution and profiling of functional metabolic potential.

Short-Chain Fatty Acids (SCFAs)

Microbial metabolites—mainly acetate, propionate, and butyrate—produced by commensal bacterial fermentation of non-digestible carbohydrates that fuel colonocytes and regulate systemic inflammation.

Prebiotics

Substrates that are selectively utilized by host microorganisms to confer a health benefit, historically focused on stimulating Bifidobacteria and Lactobacilli.

Inulin

A plant-derived fructan polymer commonly obtained from chicory root that acts as a prebiotic substrate for beneficial gut microbes.

Carboxymethylcellulose (CMC)

A synthetic emulsifier and thickening biopolymer ($\text{E466}$) shown in animal models to alter gut microbial composition, decrease bacterial distance to the epithelium, erode the mucus layer, and drive gut inflammation.

Polysorbate 80 (P80)

A synthetic non-ionic surfactant emulsifier ($\text{E433}$) demonstrated in preclinical models to alter the mucosal microbiome, thin colonic mucus, and increase gut permeability.

Lipocalin-2 (Lcn-2)

A non-invasive fecal protein biomarker used to detect and quantify low-grade intestinal mucosal inflammation in preclinical gut models.

Metabolic Endotoxemia

Elevated concentrations of circulating bacterial lipopolysaccharide ($\text{LPS}$) originating from gut microbiota, typically provoked by high-fat feeding and compromised intestinal barrier integrity.

Akkermansia muciniphila

A mucin-degrading bacterium from the phylum Verrucomicrobia whose abundance is inversely related to obesity and type 2 diabetes, providing improved glucose tolerance and reduced endotoxemia even when pasteurized.

Faecalibacterium prausnitzii

A predominant human commensal butyrate producer and strict obligate anaerobe that loses viability within $2\,\text{minutes}$ of exposure to ambient air.

Faecal Microbiota Transplantation (FMT)

The clinical or experimental procedure of administering donor fecal microbial communities into a recipient's gastrointestinal tract to establish phenotype causality or reconstruct a balanced microbiome.

GRAFT Framework

Guidelines for Reporting on Animal Faecal Transplantation; a consensus reporting checklist designed to standardize reporting across collection, processing, storage, recipient preparation, administration, and confirmation.

Germ-Free (GF) Mice

Gnotobiotic mice reared in sterile isolators with no detectable microorganisms, allowing researchers to study host physiology in the total absence of a microbiome or after defined colonizations.

Specific Pathogen Free (SPF) Mice

Standard lab mice housed under restricted sanitary conditions to exclude specified pathogens, resulting in an immature immune phenotype and limited microbial exposure relative to natural environments.

Wildling Mice

Laboratory mice generated by transferring laboratory mouse embryos into wild surrogate mothers, combining uniform host genetics with complex natural microbiotas to better phenocopy human immune responses.

Harvey Bradshaw Index (HBI)

A clinical assessment index used to score disease activity, symptoms, and therapeutic response in patients with Crohn's disease.