The human gut microbiota refers to the trillions of microbes, such as bacteria, that live in the human gut. The microbiome is the environment they live in. Most microbes in the body are useful, but they may become harmful when out of balance.

People often use the two terms microbiota and microbiome interchangeably. However, this is incorrect.

The microbiota consists of a wide variety of bacteria, viruses, fungi, and other microorganisms present in a singular environment, such as the human digestive tract.

The microbiome refers to the entire habitat of the body, including its microorganisms, genomes, and the surrounding environmental conditions.

This article explores the differences between the microbiota and microbiome.

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Every human being harbors between 10 trillion and 100 trillion microbial cells in a symbiotic relationship. Some research estimates that there are around 10 times more microbial cells in the body than human cells, while other scientists claim the ratio is closer to 1:1.

This symbiotic relationship benefits microbes and their hosts as long as the body is in a healthy state. Estimates vary, but there could be over 1,000 different species of microorganisms making up the human microbiota.

The composition of the human biome can greatly vary between people. Different parts of the body will also host different microbial communities.

For example, the oral cavity, genital organs, skin, gastrointestinal system, and respiratory tract all contain many microbial cells. Still, the types and levels and functions will vary between locations.

The gut microbiota is a vast and complex collection of microorganisms that profoundly affects human health. Previously, people referred to the gut microbiota as microflora of the gut.

The gut microbiota assists in a range of bodily functions, including:

  • harvesting energy from digested food
  • protecting against pathogens
  • regulating immune function
  • strengthening biochemical barriers of the gut and intestine

Changes in microbiota composition can affect these functions.

While there are beneficial bacteria in the gut, there are also harmful bacteria that can enter the GI tract and cause infection.. These infections include food poisoning and other GI diseases that result in diarrhea and vomiting.

Microorganisms are integral to human life and carry out various vital functions. In fact, there are roughly 10 times more bacterial cells than human cells in the gastrointestinal system.

Research suggests that bacterial population makeup and potential disturbances have links to:


As well as absorbing energy from food, gut microbes are essential to helping humans absorb nutrients. Gut bacteria help the body to break down complex molecules in meats and vegetables, for example. Without the aid of gut bacteria, the body cannot digest plant cellulose.

Gut microbes may also use their metabolic activities to influence food cravings and feelings of being full.

The diversity of a person’s diet affects the diversity of their gut.


Some research suggests that the body’s first exposure to microbes may occur before birth.

Without these early microbial guests, adaptive immunity would not exist. This vital defensive mechanism learns how to respond to microbes after encountering them. This allows for a quicker and more effective response to disease-causing organisms.

A person’s gut microbiota develops from the first microbial exposure and typically reaches a full composition at 3-5 years. Disturbances to these early exposures can hamper the development of the microbiota.


A person’s gut microbiota and brain constantly communicate with each other. The gut-brain axis primarily affects intestinal function.

However, researchers have also observed links between the gut microbiota and psychological disorders, such as depression and ASD.


Research suggests that bacterial populations in the gastrointestinal system play a role in developing gut conditions, including inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis. Low microbial diversity in the gut also has links to obesity and type 2 diabetes.

The status of the gut microbiota also has links to metabolic syndrome. Changing the diet by including prebiotics, probiotics, and other supplements may reduce these risk factors.

Disturbing the microbiota with antibiotics can also lead to disease, including infections that become resistant to antibiotics.

The microbiota also plays an important role in resisting intestinal overgrowth of externally introduced populations that otherwise cause disease – the “good” bacteria compete with the “bad,” with some even releasing anti-inflammatory compounds.

Huge investment has gone into research about microbial populations in the body and their genetics, exploring links with health and disease.

The National Institutes of Health’s Human Microbiome Project was a large-scale initiative to assess various microbiome compositions on health and whether there are identifiably “healthy” makeups.

The project helped establish links between specific microbial compositions and diseases across demographics. Due to the project, researchers can better understand the genetic composition of the gut microbiota and establish methods of classifying and analyzing their varying microbial compositions.

Recent developments include further confirmation of inserting a new strain into an existing microbiota using nutrient availability without affecting the overall balance and function of the microbiome. This opens up the potential for probiotic treatments and new methods of analyzing the makeup of the gut microbiota.

The gut microbiota is the system of microorganisms in a person’s gastrointestinal system. This includes many bacteria, fungi, viruses, and other organisms. The gut microbiota exists symbiotically within the human digestive system and helps support energy harvesting, digestion, and immune defense.

There are many different microbiotas in the body, including complex systems in the oral and vaginal cavities, colon and skin. The human microbiome is the overall composition of all microbiota in the body.