Why is the term microbiome used to describe the microbes that live in or on the human body?

So, you’re feeling inquisitive and you perform a quick internet search. You type definition of microbiome or define microbiota – the words are different but the results are pretty similar. Well, let us explain.

Table of contents

Animals, plants, and even oceans and soils have their own individual biomes made up of specific inhabitants.

Our bodies are not just ours, they are home to a vast collection of microorganisms. Ask most people to define microbiome, and a handful might say that it refers to a bacterial ecosystem that lives in a specific place. They may even mention the gut.

For scientists, a biome is an ecosystem made up of flora and fauna. They use the word micro to indicate that this ecosystem is invisible to the human eye. It is made up of mostly bacteria, but also viruses, archaea, and fungi, which all play a role in maintaining the environment's stability.

The human microbiome encompasses trillions of microbes that can be separated into subsections dependent on their location. When we say gut microbiome, we mean the microorganisms (and their genes) that reside in your colon.

But the microbiome isn’t just a feature of human beings - animals, plants, soils, and oceans have their own ones too. And no matter how you look at it, the gut microbiome plays a major role in human health.

Home to trillions of microbial cells, it is an essential part of our biology that supports many physiological functions, helps maintain the integrity of our gut lining, and protects us from disease and illness.

Although the terms are used interchangeably, there is a slight difference between microbiome and microbiota.

In many contexts, like on this blog, microbiota and microbiome are often synonymous, but you could be forgiven for thinking they are separate entities. It's better to think of them as overlapping definitions instead.

Basically, there are some small but relevant differences for researchers, as Miguel Toribio-Mateas, a nutritionist and clinical neuroscientist, explains: “Although they’re often used interchangeably, microbiota is the actual bugs and microbiome is the bugs AND their genes.”

There are many types of bacteria present in the gut microbiota. However, although it was previously estimated that the body was home to 10 times more bacterial cells than human cells, it’s now believed that we have approximately the same number of both.

Some bacteria are beneficial because they provide an essential function for health, like the production of vitamins or butyrate. Others are deemed probiotic when they contribute several important functions, like Bifidobacterium and Lactobacillus.

We also have small amounts of opportunistic microbes, which have the ability to make us sick if they aren't controlled by the rest of our microbiota. And finally, there are many commensal microbes, which are harmless and live in harmony in the ecosystem.

In other words, when we define microbiome, we’re referring to the microbes and their genetic material, and how they contribute to the health (or not) of the human body. Remember, pathogens will also make up some of your microbiome, not just the beneficial or commensal ones.

The gut microbiota definition refers to the microorganisms found in a specific environment by type. This includes bacteria, fungi, viruses, protozoa, and archaea, and the diversity of the microbiota will vary from person to person.

Different bacteria have specific names determined by a branch of science called taxonomy, where biology experts are tasked with allocating a name and a rank in the tree of life.

For example, the probiotic L. rhamnosus is actually a species of Lactobacillus, a genus that belongs to the Firmicutes phylum, which is a member of the Kingdom of Bacteria (as opposed to that of plants or animals).

Different bacteria live on different parts of the body, prefer different foods, and perform different functions. There is an oral microbiota of the mouth, a microbiota of the skin that has many subcategories (the armpits, nose, feet, etc.), and a gut microbiota - among many others of course.

☝️FACT☝️ Microbiota plural is often microbiota, but if referencing different types or a collection, the term microbiotas may be used.

The trillions of bacteria in your gut have a profound influence on our health, metabolism, and even disease protection.

When we hear the words microbe, bacteria, or virus, we tend to think of something bad, but not all of these microorganisms cause disease. In fact, we rely on them to perform the functions we may not be able to.

A balanced microbiota with beneficial and probiotic bacteria performs many other functions, like maintaining the correct pH to deter pathogens and keeping the gut lining healthy. Research even shows that gut microbes are involved in maintaining a healthy body weight.

Explore your gut bacteria and their functions with microbiome test. It can give you real insight into the unique ecosystem of your gut.

The Atlas Microbiome Test uses advanced DNA sequencing technology to screen the genes of your gut microbes and determine what bacteria are inside you and what they're doing. Just order the test online, collect a tiny stool sample, and send it back. Here's what you can learn from it:

• See how well your gut microbes protect you from disease
• Find out how your diet is affecting your gut microbes
• Discover your gut microbes ability to make vitamins
• Get personalised food recommendations based on your results

Just remember this

Microbiota describes the actual bacteria, and microbiome is the bacteria AND their genes.

The terms microbiota and microbiome are used so interchangeably that it’s easy to think they mean exactly the same thing. While they are not exactly identical, you'll be fine if you use one or the other. We do on the blog too, and all of our articles are reviewed by microbiome experts.

So unless you’re conducting some very specific scientific research, you don’t need to beat yourself up about the tiny differences. Be it gut microbiome or gut microbiota, we are still referring to the trillions of microbial cells in your colon.

As for the definition of microbiomes, each microbiome refers to all the microorganisms and their genetic material that are found in an environment. Remember, microbiome and microbiota are not just in humans, there are microbiomes even on buildings, in the underground, and the ocean.

☝️FACT☝️The definition of microbiotic can be either the adjective of microbiota (a noun) or a confusion with the term “macrobiotic” used to describe a type of diet.

• Amon, P and Sanderson, I, What is the microbiome?, 2017
• Marchesi, J, R and Ravel, J., The Vocabulary of Microbiome Research: A Proposal, 2015
• Thursby, E and Juge, N., Introduction to the Human Gut Microbiota, 2017
• Ursell, L, K et al., Defining the Human Microbiome. 2013

The assemblage of microorganisms present in a defined environment. The term microbiota was first defined by Lederberg and McCray [1] who emphasized the importance of microorganisms inhabiting the human body in health and disease. This microbial census is established using molecular methods relying predominantly on the analysis of 16S rRNA genes, 18S rRNA genes, or other marker genes and genomic regions, amplified and sequenced from given biological samples. Taxonomic assignments are performed using a variety of tools that assign each sequence to a microbial taxon (bacteria, archaea, or lower eukaryotes) at different taxonomic levels from phylum to species.

Metataxonomics

Metataxonomics is a term we propose and define as the high-throughput process used to characterize the entire microbiota and create a metataxonomic tree, which shows the relationships between all sequences obtained. While viruses are an integral part of the microbiota, no universal viral marker genes are available to perform such taxonomic assignments.

Metagenome

The collection of genomes and genes from the members of a microbiota. This collection is obtained through shotgun sequencing of DNA extracted from a sample (metagenomics) followed by assembly or mapping to a reference database followed by annotation. Metataxonomic analysis, because it relies on the amplification and sequencing of taxonomic marker genes, is not metagenomics. Metagenomics is the process used to characterize the metagenome, from which information on the potential function of the microbiota can be gained.

Metagenomics was first used by Handelsman et al. [2]; however, it was in the context of what the authors called functional metagenomics, an approach where random fragments of environmental DNA are cloned into a suitable vector for maintenance in a surrogate host for functional screening, looking for gain of function in the surrogate host.

Microbiome

This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of “biome,” the biotic and abiotic factors of given environments. Others in the field limit the definition of microbiome to the collection of genes and genomes of members of a microbiota. It is argued that this is the definition of metagenome, which combined with the environment constitutes the microbiome. The microbiome is characterized by the application of one or combinations of metagenomics, metabonomics, metatranscriptomics, and metaproteomics combined with clinical or environmental metadata.

Metabolomics

This term describes the analytical approaches used to determine the metabolite profile(s) in any given strain or single tissue. The resulting census of all metabolites present in any given strain or single tissue is called the metabolome. Most commonly used platforms to characterize the metabolome include nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) linked to a liquid chromatography separation system.

Metabonomics

The term is a variant of the metabolomic approach; however, it describes the approach used to generate a metabolite profile(s) from complex systems, e.g., mammals in which more than one strain or tissue has contributed to the total metabolite pool, for example, fecal water, urine, or plasma. This term avoids the clumsy use of meta-metabolomics and was first defined by Jeremy Nicholson [3].

Metatranscriptomics

This term refers to the analysis of the suite of expressed RNAs (meta-RNAs) by high-throughput sequencing of the corresponding meta-cDNAs. This approach provides information on the regulation and expression profiles of complex microbiomes.

Metaproteomics

First coined by Rodriguez-Valera [4] and refined by Wilmes and Bond [5], this term refers to the large-scale characterization of the entire protein complement of environmental or clinical samples at a given point in time. The method indiscriminately identifies proteins from the microbiota and the host/environments (metagenome). Computational analyses afford assignments of these proteins to their biological origins. It is often performed using liquid-chromatography-based separation coupled to mass spectrometry for peptide identification.

Misnomers and correct usage of the terms

Misnomers are often found in studies discussing metataxonomic analyses relying on sequencing and analysis of 16S rRNA genes. In the literature, one can find the use of “16S survey,” “16S sequencing,” or “16S analysis,” for example. There is no such thing as “16S.” The “S” in 16S is a non-SI unit for sedimentation rate and stands for the Svedberg unit. The Svedberg unit offers a measure of particle size based on its rate of travel in a tube subjected to high g force. The small subunits of the bacterial and archaeal ribosomes are 30S and comprise one structural 16S ribosomal RNA (rRNA, ~1540 nucleotides) bound to 21 proteins. Thus, we would like to argue that the proper terms should be “16S rRNA genes” or “16S rRNA gene sequencing/analysis.”

Additionally, the word microflora has been used for a long time in the scientific and medical literature. However, its definition does not justify its use to describe microbial communities associated with human (i.e., microbiota). Its definition has evolved over time, but remains “microscopic plants, or the plants or flora of a microhabitat.” The origin of the definition dates back to the early 1900s. Furthermore, the definition of the word “flora” further highlights the inappropriateness of the word microflora in the microbiome scientific literature: “the plants of a particular region or period, listed by species and considered as a whole” or “a work systematically describing plants” or “plants, as distinguished from fauna.” The definition of flora dates back to mid 1600s and has its origin in the Latin name “Flora,” the Roman goddess of flowers and the Latin word “flor,” meaning flower. These definitions and their origins make it obvious that “microflora” refers to plants and not microbes. While some dictionaries are now including a third definition for microflora, “the aggregate of bacteria, fungi, and other microorganisms normally occurring on or in the bodies of humans and other animals: intestinal flora,” these newly added definitions are the results of over one century of misuse of the word, driven by a limited understanding of the microbes associated with humans. Our knowledge of microbial communities is such that the scientific community should not continue to use the word in the scientific literature. It is time to change, and we suggest that to describe the assemblage of microbes living in a microhabitat we use “microbiota.” Interestingly, microflora is almost exclusively used in the literature referring to microbial community associated with human or animal, but rarely in those associated with the environment. We believe that microflora has still its place in the popular literature or in a yogurt/probiotic advertisement destined to the general public, but it does not in the scientific and medical literature.

The public, the scientific popular press, medical doctors, and other scientists need to be educated, but this will come if the scientific community adopts a common language. The word microbiota is adequate and appropriate to describe the composition and abundance of microbial communities whether they inhabit the human body or the environment.

This editorial was informed from papers and other communications we have had with colleagues. We hope that a consensus use of these terms could be adopted in the near future. This editorial aims at stimulating a discussion and standardizing the vocabulary of microbiome research. Microbiome will continue to strive toward a standardization of the vocabulary used in this ever-expanding field of research.