Glossary · Microbiota
Microbiota
In one sentence
The microbiota is the community of living microorganisms (bacteria, archaea, fungi, protozoa) that inhabits a specific site of the body, such as the gut, mouth, skin or vagina.
Also known as: gut microbiota · intestinal microbiota · gut flora · microflora
What is the microbiota?
The word refers to the organisms themselves: the bacteria, archaea, fungi, protozoa and viruses that live with us in a given habitat. That is why we speak of the gut, oral, skin or vaginal microbiota. Each site hosts a different community, shaped by its pH, oxygen levels and available nutrients.
The gut microbiota, concentrated mainly in the colon, is the most studied. For decades it was said that bacteria outnumbered human cells ten to one. A 2016 analysis by Sender, Fuchs and Milo in PLoS Biology revised that figure to roughly one to one: around 38 trillion bacteria against about 30 trillion human cells in a reference adult.
It should not be confused with the microbiome, which also covers the genes and functions of that community and its environment.
What it does
The gut microbiota contributes to functions the body cannot carry out on its own:
- It ferments dietary fibre into short-chain fatty acids such as butyrate, a key energy source for colonic cells.
- It takes part in the synthesis of certain vitamins and in bile acid metabolism.
- It occupies niches and competes for nutrients, making it harder for pathogens to settle.
- It interacts with the immune system and with the intestinal barrier.
The NIH-funded Human Microbiome Project (Nature, 2012) found that composition varies widely between healthy people, while metabolic functions are far more consistent. There is no single “normal” microbiota, which is why terms such as eubiosis and dysbiosis need to be used with care.
How it is analysed
Conventional culture recovers only part of the gut community, because many organisms are strict anaerobes that are hard to grow. Current methods read the DNA in a stool sample using next-generation sequencing. 16S rRNA gene sequencing identifies bacteria from a marker gene, while shotgun metagenomics sequences all the genetic material present. Reports usually show the relative abundance of each group and alpha and beta diversity.
Example
A gastroenterologist sees a patient with persistent loose stools after several courses of antibiotics and first rules out organic causes. She then requests a stool microbiota analysis. The report shows low diversity and few butyrate-producing bacteria. On its own this is not a diagnosis: she weighs it alongside the clinical picture and other tests to plan the next steps.
Microbiota at Xenogene
Xenogene’s Gut Microbiota test analyses a stool sample with Nanopore NGS sequencing. It detects bacteria, parasites and intestinal worms, and reports parameters such as bacterial diversity, hydrogen sulphide and methane. The test is always requested by a healthcare professional, who interprets the report in the light of the patient’s clinical context.
Frequently asked questions
Is gut flora the same as gut microbiota?
They refer to the same thing, but "flora" is an older term dating from when bacteria were classified as plants. Scientific literature now prefers "microbiota", which is more accurate.
What damages the gut microbiota?
The best-documented factors are antibiotics, a diet low in fibre and some digestive diseases. Others, such as stress or poor sleep, are associated with changes, but their individual effect is harder to measure. A change in the microbiota does not necessarily mean a clinical problem.
Can symptoms tell me what my microbiota looks like?
No. Digestive symptoms are non-specific and have many possible causes. The composition of the microbiota can only be known by analysing a sample, and the result is interpreted by the healthcare professional who requests the test.
Related terms
- Microbiome
The microbiome is the microbial community of a habitat together with its "theatre of activity": its genes, metabolites and surrounding environmental conditions. It is broader than the microbiota.
- Eubiosis
Eubiosis is the state in which the microbiota is stable, diverse and compatible with the host's health. It is the opposite of dysbiosis, although neither term has an agreed operational definition.
- Dysbiosis
Dysbiosis is a change in the composition or function of the microbiota away from what is considered compatible with health: loss of diversity, loss of beneficial microbes or overgrowth of others.
- Short-chain fatty acids
Short-chain fatty acids (SCFAs) are fatty acids with one to six carbon atoms produced by colonic bacteria when they ferment fibre and other non-digestible carbohydrates. The main ones are acetate, propionate and butyrate.
- NGS (next-generation sequencing)
NGS (next-generation sequencing) is a family of technologies that read millions of DNA or RNA fragments in parallel in a single run, making it possible to study whole genomes, targeted genes or entire microbial communities at scale.
Educational content for healthcare professionals and the general public. It does not replace assessment by a healthcare professional: ordering and interpreting any test is the responsibility of the requesting clinician.
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