Glossary · Microbiota
Microbiome
In one sentence
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.
Also known as: human microbiome · gut microbiome · intestinal microbiome
What is the microbiome?
“Microbiome” is often used interchangeably with microbiota, but the two are not quite the same. In 2020 a group of experts brought together by the EU-funded MicrobiomeSupport project published a proposed definition in the journal Microbiome (Berg et al.). Building on an earlier definition by Whipps and colleagues, they describe the microbiome as a characteristic microbial community in a defined habitat plus its “theatre of activity”: structural elements, genes, metabolites and the environmental conditions around it.
Put simply, the microbiota answers “who is there”, whereas the microbiome adds “what they can do, and in what setting”. Some authors use “metagenome” for the collective genes alone.
How it is studied
A major step forward came with the Human Microbiome Project, funded by the US National Institutes of Health. Its consortium published a characterisation of several body sites in healthy adults in Nature in 2012. Two of its findings remain useful in practice:
- Composition varies considerably from person to person, even in the absence of disease.
- The metabolic pathways present are more consistent than the individual species.
The microbiome is studied with next-generation sequencing. Shotgun metagenomics sequences all the DNA in a sample, allowing genes and functions to be inferred as well as species. Metabolomics measures some products of microbial activity directly, such as short-chain fatty acids.
Example
A gastroenterology consultant reviews gut microbiota reports from two patients whose dominant species are quite different. Both, however, show a similar potential for butyrate production. The contrast illustrates the difference between composition (microbiota) and function (microbiome): different species can cover similar roles, so results are assessed as a whole rather than species by species.
What the evidence says
Many studies link changes in the microbiome with digestive, metabolic and inflammatory conditions. Most of these are associations: it is often unclear whether the change is a cause, a consequence of the disease or its treatment, or a parallel phenomenon. Caution is therefore needed when describing a microbiome as “healthy” or “disrupted”, and any finding should be read together with the clinical history.
Microbiome at Xenogene
Xenogene studies the gut microbiome from a stool sample with its Gut Microbiota test, based on Nanopore NGS sequencing. The analysis identifies the microorganisms present and reports on microbiota functions, bacterial diversity and parameters such as hydrogen sulphide and methane. It is only performed on a prescription, and interpretation rests with the healthcare professional who requests it.
Frequently asked questions
What is the difference between microbiota and microbiome?
The microbiota is the microorganisms themselves. The microbiome also includes their genes, their products and the environment they live in. In everyday use the two words are often treated as synonyms, although strictly they are not.
Does everyone have a different microbiome?
Yes. The Human Microbiome Project found large differences in composition between healthy people, influenced by diet, environment, medication and age. Results are therefore interpreted against broad ranges rather than a single template.
Can a microbiome test diagnose disease?
Generally not on its own. It describes the composition and functional potential of the community, which the healthcare professional combines with the clinical picture and other tests. Associations reported in research do not amount to an individual diagnosis.
Related terms
- Microbiota
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.
- Shotgun metagenomics
Shotgun metagenomics sequences all the DNA in a sample in an untargeted way, without amplifying a single marker gene. It can identify bacteria, DNA viruses, fungi and parasites, often to species level, and reveal their functional and resistance genes.
- 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.
- 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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