The human body is host to trillions of microbes, or bacteria. Some of these are useful, and some are harmful.

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Some scientists have estimated that there are 10 times more microbial cells in the body than there are human cells, while others say that the ratio may be closer to 1:1.

Recent scientific advances in genetics mean that humans know a lot more about the microbes in the body.

Many countries have invested a lot in researching the interactions within the human body’s ecosystem and their relevance to health and disease.

The two terms microbiota and microbiome are often used to mean the same thing and are used interchangeably. This article will explain the differences between them and how both are being used and research in modern medicine.

Fast facts on the gut microbiota

  • The human microbiota is made up of trillions of cells, including bacteria, viruses, and fungi.
  • The biggest populations of microbes reside in the gut. Other popular habitats include the skin and genitals.
  • The microbial cells and their genetic material, the microbiome, live with humans from birth. This relationship is vital to normal health.
  • The microorganisms living inside the gastrointestinal tract amount to around 4 pounds of biomass. Every individual has a unique mix of species.
  • The microbiota is important for nutrition, immunity, and effects on the brain and behavior. It is implicated in a number of diseases that cause a disturbance in the normal balance of microbes.

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The gut microbiota is with humans from birth and affects function throughout the body.

The human microbiota consists of a wide variety of bacteria, viruses, fungi, and other single-celled animals that live in the body.

The microbiome is the name given to all of the genes inside these microbial cells.

Every human being harbors anywhere between 10 trillion and 100 trillion microbial cells in a symbiotic relationship. This benefits both the 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 microorganism making up the human microbiota.

There are plenty of projects trying to decode the human genome by sequencing all human genes. In a similar way, the microbiome has been subject to intensive efforts to unravel all its genetic information.

The following video about the human ecosystem, produced by the Genetic Science Learning Center of the University of Utah, Salt Lake City, will help create a picture of this delicate but vital relationship.

It is a good introduction to the range of habitats for different types of microbe in the body, including the differences between the dry environment of the forearm and the wet and oily environment of the armpit.

The microbes in the body are so small that they make up only about 2 to 3 percent of the total weight of the human body, despite outnumbering the cells.[S2]

A 2012 study published in Nature by the Human Microbiome Project Consortium found the following:

  • Samples of mouth and stool microbial communities are particularly diverse
  • In contrast, samples from vaginal sites show particularly simple microbial communities.

The study demonstrated the great diversity of the human microbiome across a large group of healthy Western people but poses questions for further research. How do microbial populations within each of us vary across a lifetime, and are patterns of colonization by beneficial microbes the same as those shown by disease-causing microbes?

The gut microbiota used to be called the microflora of the gut.

Around this time, in 1996, Dr. Rodney Berg, of Louisiana State University’s Microbiology and Immunology department, wrote about the gut microbiota, summing up its “profound” importance.

The indigenous gastrointestinal tract microflora has profound effects on the anatomical, physiological, and immunological development of the host,” Dr. Berg wrote, in a paper published in Trends in Microbiology.

The paper adds:

“The indigenous microflora stimulates the host immune system to respond more quickly to pathogen challenge and, through bacterial antagonism, inhibits colonization of the GI tract by overt exogenous pathogens.”

This symbiotic relationship benefits humans, and the presence of this normal flora includes microorganisms that are so present in the environment that they can be found in practically all animals from the same habitat.

However, these native microbes also include harmful bacteria that can overcome the body’s defenses that separate them from vital systems and organs. Examples include

In summary, there are beneficial bacteria in the gut, and there are harmful bacteria that can cross into wider systems and can cause local infections of the GI tract. These infections include food poisoning and other GI diseases that result in diarrhea and vomiting.

The gut microbiota contains over 3 million genes, making it 150 times more genetically varied than the human body.

The gut microbiota of each individual is unique. It can heavily contribute to how a person fights disease, digests food, and even their mood and psychological processes.

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Links have been found between gut microbes and heart disease

Microorganisms have evolved alongside humans and form an integral part of life, carrying out a range of vital functions.

They are implicated in both health and disease, and research has found links between bacterial populations, whether normal or disturbed, and the following diseases:

The human microbiome has an influence on the following four broad areas of importance to health:

  • nutrition
  • immunity
  • behaviour
  • disease


As well as absorbing energy from food, gut microbes are essential to helping humans take in nutrients. Gut bacteria help us break down complex molecules in meats and vegetables, for example. Without the aid of gut bacteria, plant cellulose is indigestible.

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

The diversity of the microbiota is related to the diversity of the diet. Younger adults trying out a wide variety of foods display a more varied gut microbiota than adults who follow a distinct dietary pattern.


From the moment an animal is born, they start building their microbiome. Humans acquire their first microbes from the entrance of their mother’s cervix on arrival into the world.

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

Rodents that are completely clean of microorganisms show a range of pathological effects, and an underdeveloped immune system is among them.

The microbiota also relates to autoimmune conditions and allergies, which can be more likely to develop when exposure to microbes is disturbed early on.


The microbiota can affect the brain, which is also involved in digestion. Some have even called the gut microbiota a “second brain.”

Small molecules released by the activity of gut bacteria trigger the response of nerves in the gastrointestinal tract.

Researchers have also observed links between the gut microbiome and psychological disorders, such as depression and autistic spectrum disorder (ASD).


Bacterial populations in the gastrointestinal system have provided insights into gut conditions, including inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis. Low microbial diversity in the gut has been linked to IBD as well as obesity and type 2 diabetes.

The status of the gut microbiota has been linked to metabolic syndrome. Changing the diet by including prebiotics, probiotics, and other supplements has reduced these risk factors.

Gut microbes and their genetics affect energy balance, brain development, and cognitive function. Research is ongoing on exactly how this occurs and ways this relationship can be used for human benefit.

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

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

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Research is ongoing into the impact of the gut microbiota on overall health.

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 (NIH) launched the Human Microbiome Project in 2007, a research project that aims to define the microbial species that affect humans and their relationships to health by producing large, publicly available datasets from genetic studies.

Most of the microorganisms living in humans are found in the gastrointestinal system, and this is also where most new discoveries are being made.

Recent developments include further confirmation of ways to insert 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.

Seaweed was used to control the gut microbiota of several mice in this study.

There has also been recent research into how potential pathogens from outside the body go about invading and how they relate to the gut microbiota. This will help identify ways to limit the invasion of potentially harmful microbes and their disease-causing effects.

The gut microbiota is becoming a cornerstone of preventive medicine.