Microbiome & Gut Health

Akkermansia muciniphila is a Gram-negative gut bacterium that eats mucin and lives in your intestinal mucus layer. It is usually a small share of a healthy microbiome (under 1%…

The Bacteroidetes/Firmicutes ratio was prominently proposed in the mid-2000s as a marker of your gut microbiome's health. It came from observations in obese mice and small human…

Bifidobacterium is a genus of Gram-positive, anaerobic, branched-rod bacteria, in the phylum Actinobacteria. It is one of the first colonizers of a baby's gut, especially in…

Bile acids begin as digestion helpers. But they double as powerful signals, and your gut bacteria reshape them. Your liver makes the 'primary' ones from cholesterol. There are…

Butyrate is a four-carbon short-chain fatty acid (SCFA), made in your colon when anaerobic bacteria ferment dietary fiber. The main producers are Faecalibacterium prausnitzii and…

When scientists study people who reach extreme old age, they keep finding a different gut microbiome. Two studies stand out. An Italian group (Biagi and Franceschi) looked at…

Christensenella minuta is a strictly anaerobic gut bacterium, in the Christensenellaceae family. In the TwinsUK study, Goodrich and colleagues (2014) made a key find. It is the…

Dysbiosis is when your gut microbial community drifts away from a healthy state. The drift can be in its makeup, its diversity, or its chemical output. It is a working term, not…

Enterotypes are proposed 'types' of gut microbial community. Think blood types, but for your gut bugs. Arumugam et al. (2011, Nature) first defined them. They used 39 metagenomes…

Faecal microbiota transplant (FMT) moves processed stool from a healthy donor into a recipient's gut. The goal is to rebuild a disrupted microbial community. It has exactly one…

Faecalibacterium prausnitzii is a strict-anaerobe Firmicute, and one of the most abundant butyrate-making bacteria in a healthy adult colon. It often makes up several percent of…

Your gut microbiota is the community of roughly 38 trillion bacteria (plus archaea, fungi, and viruses) living in your gut, densest in the colon. Together they carry a gene…

The gut-brain axis is the two-way communication line between your gut and your brain. It runs over several channels: the gut's own nervous system, the vagus nerve, the…

Indole-3-propionic acid (IPA) is a compound your gut microbes make from dietary tryptophan. Almost only one strict anaerobe, Clostridium sporogenes, produces it, by converting…

Intestinal permeability is the regulated passage of molecules between the cells lining your gut. It is controlled by 'tight junction' complexes (claudins, occludin, ZO-1, and…

Lactobacillus is a group of Gram-positive bacteria. They make lactic acid. You meet them in fermented foods and probiotics. In 2020, Zheng and colleagues reorganized the genus.…

Lipopolysaccharide (LPS) is a building block of the outer wall of Gram-negative bacteria. When bacteria die or divide and shed it, LPS is the single most potent trigger for an…

Microbial beta-glucuronidases (GUS) are enzymes made by many of your gut bacteria. (They live in the Firmicutes, Bacteroidota, and Enterobacteriaceae.) They snip off glucuronide…

Microbiome diversity measures how rich and even your gut community is. 'Alpha diversity' is within one sample. 'Beta diversity' is across samples. The Shannon index is a popular…

The oral microbiome is the community of roughly 700 bacterial types in your mouth. They live on your teeth, gums, tongue, and lining. One species stands out: Porphyromonas…

A postbiotic is a preparation of dead microbes or their parts that still benefits your health. That is the ISAPP 2021 consensus definition. Here is the key difference from…

A prebiotic is food for your good gut microbes. The official definition comes from ISAPP (the International Scientific Association for Probiotics and Prebiotics). It is a…

Probiotics are live microbes that, given in large enough amounts, bring a health benefit to the host. WHO/FAO set that definition in 2001. ISAPP reaffirmed it in 2014 (Hill et…

Roseburia is a genus of bacteria that make butyrate. (Butyrate is a beneficial gut fat.) It belongs to the Lachnospiraceae family, part of the Firmicutes. Its best-studied…

Short-chain fatty acids (SCFAs) are the helpful byproducts your gut bacteria make. The main three are acetate, propionate, and butyrate. They form when anaerobic gut microbes…

TMAO (trimethylamine-N-oxide) is a small compound your gut bacteria help make. They convert dietary choline, phosphatidylcholine, and L-carnitine (abundant in red meat, eggs, and…