Microbiome & Gut Health

Akkermansia muciniphila is a Gram-negative mucin-degrading bacterium that colonises the intestinal mucus layer and is typically present at <1 % to a few percent of the healthy…

The Bacteroidetes/Firmicutes ratio was prominently proposed in the mid-2000s as a functional biomarker of gut microbiome health, based on observations in obese mice and small…

Bifidobacterium is a genus of Gram-positive, anaerobic, non-motile, branched-rod bacteria belonging to the phylum Actinobacteria (Actinomycetota); it is among the first…

Primary bile acids — cholic acid and chenodeoxycholic acid — are synthesised in the liver from cholesterol and conjugated to glycine or taurine before secretion into the small…

Butyrate is a four-carbon short-chain fatty acid (SCFA) produced in the colon when anaerobic bacteria — principally Faecalibacterium prausnitzii and Roseburia intestinalis…

Several studies of extreme longevity — notably the Italian group led by Biagi and Franceschi analysing semi-supercentenarians (105–109 years) and Sato and colleagues in Japanese…

Christensenella minuta is a strictly anaerobic bacterium of the family Christensenellaceae, identified in the TwinsUK cohort by Goodrich and colleagues in 2014 as the most…

Dysbiosis describes a shift in the composition, diversity or metabolic output of the microbiota away from a configuration associated with host health, though it is an operational…

Enterotypes are proposed discrete clusters of human gut microbial community composition, originally defined by Arumugam et al. (2011, Nature; n = 39 metagenomes, six…

Faecal microbiota transplant (FMT) is the transfer of processed stool from a healthy donor into the gastrointestinal tract of a recipient, with the aim of reconstituting a…

Faecalibacterium prausnitzii is an obligate-anaerobic Firmicute and one of the most abundant butyrate-producing bacteria in the healthy adult colon, often making up several…

The gut microbiota comprises approximately 38 trillion bacteria — plus archaea, fungi, viruses and other microorganisms — that colonise the human gastrointestinal tract, with the…

The gut-brain axis is the bidirectional communication network linking the enteric nervous system, vagus nerve, hypothalamic-pituitary-adrenal (HPA) axis, immune signalling and…

Indole-3-propionic acid (IPA) is a gut-microbiota-derived catabolite of dietary tryptophan produced almost exclusively by the obligate anaerobe Clostridium sporogenes via…

Intestinal permeability refers to the regulated paracellular passage of molecules across the intestinal epithelium, governed by tight junction complexes — claudins, occludin,…

Lactobacillus is a Gram-positive, lactic-acid-producing bacterial group historically used in fermented foods and probiotics. In 2020 Zheng and colleagues used whole-genome…

Lipopolysaccharide (LPS) is a structural component of the outer membrane of Gram-negative bacteria; when shed by bacteria at cell death or division, it is the most potent ligand…

Microbial beta-glucuronidases (GUS) are bacterial enzymes encoded by gus genes in many gut Firmicutes, Bacteroidota and Enterobacteriaceae. They cleave glucuronide groups added…

Microbiome diversity describes the richness and evenness of microbial community composition within a single sample (alpha diversity) or across samples (beta diversity). The…

The oral microbiome comprises roughly 700 bacterial taxa colonising teeth, gingival sulcus, tongue and mucosa. Porphyromonas gingivalis is a Gram-negative anaerobe widely…

The ISAPP 2021 consensus definition characterises a postbiotic as a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host. The…

According to the International Scientific Association for Probiotics and Prebiotics (ISAPP), a prebiotic is defined as a substrate that is selectively utilised by host…

Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host — the definition formalised by WHO/FAO in 2001 and reaffirmed…

Roseburia is a genus of motile, butyrate-producing bacteria in the family Lachnospiraceae (phylum Bacillota, formerly Firmicutes), with R. intestinalis and R. hominis among the…

Short-chain fatty acids — principally acetate, propionate and butyrate — are produced when anaerobic gut bacteria ferment dietary fibre and resistant starch that reaches the…

Trimethylamine-N-oxide (TMAO) is a small organic compound produced when gut bacteria convert dietary choline, phosphatidylcholine and L-carnitine — abundant in red meat, eggs and…