What is the microbiome? It is the word probiotic labels reach for more than any other, and it shows up on packaging, in podcasts and in headlines as if everyone already agreed on what it means. Most people could not define it in a sentence. Many assume it is just a fancier way to say "gut bacteria." It is not quite that.

The search data says plenty of people are asking. According to Google Trends, for US searches over the past seven days related to the seed term "microbiome," the top related queries included "gut microbiome" at 100, "what is microbiome" at 36, "what is the microbiome" at 23, "human microbiome" at 21, "what is a microbiome" at 19, "the human microbiome" at 15, "what is gut microbiome" at 14, "what is the gut microbiome" at 10 and "skin microbiome" at 8. The rising query "microorganism definition" was up 70%.

A quick note on those numbers. Google Trends scores are relative within each seed term: 100 marks the most searched query in that set, and the others are scaled against it. They are not search counts. A rising percentage measures growth in interest, not volume.

So people want the definition, and they want it starting from the smallest unit. This piece builds the vocabulary in order: what a microorganism is, what "microbiome" names, how it differs from "microbiota," and why the word gets attached to the gut, the skin and other places. Every definition comes with its source.

Microorganism definition: the smallest word first

Start with the unit everything else is built from. Dictionary.com defines a microorganism as "any organism too small to be viewed by the unaided eye, as bacteria, protozoa, and some fungi and algae." Its science entry puts it another way: "An organism that can be seen only with the aid of a microscope and that typically consists of only a single cell."

The word itself is not new. Dictionary.com dates it as first recorded in 1875 to 1880, formed from "micro-" plus "organism." Notice what the definition is based on: size. A microorganism is not a type of creature. It is any living thing small enough that you need a microscope to see it, which is why the category spans bacteria, some fungi, protozoa and some algae.

Keep the word "living" in mind. It matters in a minute, when we get to viruses.

What is the microbiome, and what is a microbiome?

The National Human Genome Research Institute (NHGRI) defines it in its genetics glossary: "The microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment." The same entry adds that in humans, the term is often used for "the microorganisms that live in or on a particular part of the body," naming the skin and the gastrointestinal tract as examples.

The National Institute of Environmental Health Sciences (NIEHS) gives a closely related definition: "The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us." Note the phrase "and their genes." That small addition is the key to the next section.

That also settles the grammar question behind "what is a microbiome" versus "what is the microbiome." Both are right. "A microbiome" is any community of microorganisms in a particular environment, and the NHGRI definition is written that broadly. "The microbiome" usually means the human one, or a specific one named by context, such as "the gut microbiome."

The word started outside medicine. A 2020 paper in the journal Microbiome by Berg and colleagues, "Microbiome definition re-visited: old concepts and new challenges," credits Whipps and colleagues, who were studying microorganisms around plant roots, with the first definition of the term in 1988. According to Berg and colleagues, Whipps described the microbiome as a combination of the words "micro" and "biome," naming a "characteristic microbial community" in a "reasonably well-defined habitat" along with its "theatre of activity."

Microbiome vs microbiota: the organisms, or the whole setting

Here is the distinction most labels skip. The two words are often used as if they were interchangeable. In the research literature they are not.

A 2015 editorial in Microbiome by Marchesi and Ravel, "The vocabulary of microbiome research: a proposal," set out working definitions:

• Microbiota: "The assemblage of microorganisms present in a defined environment."
• Microbiome: "This term refers to the entire habitat, including the microorganisms," their genomes (meaning their genes), and the surrounding environmental conditions.
• Metagenome: "The collection of genomes and genes from the members of a microbiota."

So microbiota is the list of residents. Microbiome is the residents plus their genes plus the place they live. Marchesi and Ravel also note that the term microbiota was first defined by Lederberg and McCray, in a 2001 piece in The Scientist.

Now back to viruses. Berg and colleagues note that because phages, viruses, plasmids and free DNA "are usually not considered as living microorganisms," they do not belong to the microbiota. Whether they count as part of the microbiome is, in their words, "one of the most controversial points" in the definition, and their survey of researchers produced no clear answer. If you have read our explainer on what a bacteriophage is, this is where that word sits in the vocabulary: outside the microbiota, and debated at the edge of the microbiome.

Gut microbiome, skin microbiome and the human microbiome

Because a microbiome is defined by its environment, the word takes a place name in front of it. The NIEHS says that "each body site, for example, the gut, skin, and oral and nasal cavities, has a different community of microbes." That is why you see "gut microbiome," "skin microbiome," and so on. Each is a separate community in a separate setting.

What is the gut microbiome, specifically? Cleveland Clinic describes the gut as "a miniature biome, populated by trillions of microscopic organisms," and says most of them are in the large intestine (colon). It lists the members as including "over a thousand species of bacteria, as well as viruses, fungi and parasites."

The skin microbiome follows the same naming logic. The NHGRI glossary names the skin directly as one of the body parts the term is used for, and the NIEHS lists skin as its own body site with its own community.

"The human microbiome" is the umbrella term for all of these together. It also names a federal research program. According to the NIH Common Fund, the Human Microbiome Project was funded through the Common Fund from 2007 to 2016, and it was set up to build research resources for the "comprehensive characterization of the human microbiota." Notice that even the program description switches between the two words exactly as Marchesi and Ravel define them: the project is named for the microbiome, and its stated aim is to characterize the microbiota.

Our take

Read the word precisely. "Microbiome" is not a synonym for "good bacteria," and it is not a synonym for "probiotic." It names a whole setting: the microorganisms, their genes and the conditions they live in.

That gives you a simple test for any label or headline. If the sentence is about the organisms themselves, the precise word is microbiota. If it is about the organisms plus their genes and their environment, microbiome fits. Plenty of writers use them loosely. Now you can tell which one they mean.

The word also tells you where, not what. "Gut microbiome" and "skin microbiome" name places, and the word on its own says nothing about which species are present or in what amounts. When you want to know what a product actually contains, read the ingredient panel, not the umbrella term.

Two companion pieces finish the vocabulary. Our guide to what prebiotic, probiotic and postbiotic mean covers the three -biotic words, and our explainer on how to read Lactobacillus and Bifidobacterium names decodes the Latin. Questions about your own body belong with a clinician.

Why we carry it at PRSPR

This piece started with a label on our own shelf. Our FLORÉ Probiotic is a once-daily capsule whose listing carries a four-word tagline: Prebiotic, Probiotic, Postbiotic and Saffron. The listing names targeted probiotic strains, Saccharomyces boulardii, PreforPro® bacteriophages, prebiotic acacia fiber, a heat-treated postbiotic culture and Affron® saffron. With the vocabulary above, you can sort those names yourself: which are microorganisms, which is a virus, and which are neither.

Like everything we carry, it is made in a GMP-certified facility and third-party batch tested, so what's on the label is what's in the bottle. It sits in our Gut Digestion collection, listed at $61.36.

If you want to read the full ingredient list for yourself, read the FLORÉ Probiotic listing at PRSPR.

FAQ

What is the microbiome?

The NHGRI defines the microbiome as "the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment." The NIEHS adds "their genes" to the definition.

What is a microbiome, as opposed to microbiota?

Marchesi and Ravel (2015) define microbiota as "the assemblage of microorganisms present in a defined environment," and the microbiome as the entire habitat: the microorganisms, their genes and the surrounding environmental conditions.

What is the gut microbiome?

Cleveland Clinic describes the gut as "a miniature biome, populated by trillions of microscopic organisms," mostly in the large intestine, including bacteria, viruses, fungi and parasites.

What is the human microbiome?

It is the umbrella term for the microbial communities that live in and on the body. The NIEHS notes that each body site, such as the gut, skin, and oral and nasal cavities, has a different community of microbes.

What is the microorganism definition?

Dictionary.com defines a microorganism as "any organism too small to be viewed by the unaided eye, as bacteria, protozoa, and some fungi and algae," and dates the word to 1875 to 1880.