What is the Difference Between Microbiome and Microbiota?

Medicine is continually advancing. New bodily mechanisms are uncovered and understood as analytical platforms improve. It happens almost by a zeitgeist, with several locations around the world happening upon similar discoveries and subsequent researchers leveraging those findings to prompt an evolution of those understandings. The transformation manifests by a sudden influx of publications describing the phenomenon, but this change is evident in the volume of work surrounding the discovery. It also becomes apparent in the vocabulary used to describe elements of the mechanism.

Lately, microbial communities have received increased attention and a relative explosion in study volume, but there are still misunderstandings about what each term means exactly. This article will review the vocabulary related to the body’s microbial communities and explain how the terms differ from one another.

What is Microbiome?

Microbiome refers to the entire habitat. The term includes microorganisms such as bacteria and eukaryotes as well the genes that comprise them and the environmental factors that influence them. While some people limit the definition of microbiome to include only the collection of genes or genomes in a microbiota, that combination is more accurately called a metagenome.

In 2008, the National Institutes of Health (NIH) developed the Human Microbiome Project. It sequences the microbes contained in the human body and catalogs them. Read more about that HERE.

What is Microbiota?

Microbiota is the unique combination of microorganisms that exist in a specific environment. This may include bacteria, archaea, or eukaryotes. The term itself comes from a 2001 paper by Lederberg and McCray on buzzwords in genomics and proteomics, although the word biome predates 1920. Microbiota is the result of genetics and environment.

Microbiome v Microbiota

Microbiota is very different from microbiome. While microbiome may contain microbiota, microbiome is MORE than microbiota alone. To put it simply, if microbiome is a house, the microbiota is the people who live there. There are other things in the house, such as furniture. In the next section, we will review some of those components as well as words that sound and look similar and could be confused.


The metagenome is the genes and genomes that exist within the microbiota. The metagenome is identified through DNA extraction (metagenomics). Identifying the metagenome may help explain the way specific microbiota function.


Microflora is a very old term, but it has only more recently been applied toward humans. Traditionally, it primarily referred to microscopic plants. Today, that definition has been expanded to encompass all manner of bacteria and microorganisms, including human intestinal flora. However, microflora, in the latter sense, is more appropriate for popular literature. It lacks the specificity necessary for inclusion in medical literature or science as a whole.

Understanding Immunotherapy Drugs and Microbiome

This article reviewed common terms related to microbial communities. It is the first in a series of articles that explain the connection between microbiome and immunotherapy drugs (IOD). In our next post, we will discuss the impact of microbiota on cancer and cancer therapies. Stay tuned!


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