What Is the Human Microbiome and What Does It Do?
Trillions of microorganisms live in and on the human body, and together they form what scientists call the human microbiome. This guide explains what the microbiome actually is, where it is found, how it develops, and what it does for human health, all in plain, everyday language.
By Chris Morais, MSc, MPhil, PhD
The human microbiome is the full community of bacteria, viruses, fungi and other microorganisms living in and on the body, together with their genes and surroundings. Distinct communities live in the gut, on the skin, in the mouth and elsewhere, where they help digest fiber, interact with the immune system and crowd out harmful microbes.
- What Is the Human Microbiome?
- What Is the Difference Between the Microbiome and the Microbiota?
- Which Microorganisms Are Part of the Human Microbiome?
- Where Are the Main Microbiomes Found in the Human Body?
- Why Is the Microbiome Different in Different Parts of the Body?
- Does Everyone Have the Same Microbiome?
- How Does the Human Microbiome Develop From Birth?
- What Does the Microbiome Do in the Human Body?
- What Can Change the Human Microbiome?
- What Does Dysbiosis Mean?
- Is There One Ideal or Healthy Human Microbiome?
- Frequently Asked Questions
.webp "Human Microbiome: Microbial Communities Across the Body")
What Is the Human Microbiome?
The human microbiome is the complete collection of microorganisms living in and on the human body, together with their genetic material and the surrounding environment they exist in[2].
This includes bacteria, viruses, fungi, and other microorganisms found across the skin, gut, mouth, and other body sites. The human microbiome is now considered such an active part of human biology that some researchers describe it as an additional organ, given how directly it interacts with digestion, immunity, and other body functions[2].
What Is the Difference Between the Microbiome and the Microbiota?
The microbiota refers to the actual living microorganisms present in a particular location, while the microbiome refers to those microorganisms together with their combined genes and the environment they live in[2].
This distinction is precise but often blurred in everyday use. If every bacterium, virus, and fungus in the gut could be individually identified, that collection of organisms would be the gut microbiota. The microbiome is the broader concept, including that same community along with its genetic material and surrounding conditions. In general, plain-language writing, the two terms are frequently used interchangeably, and this is widely accepted outside strict scientific contexts.
Which Microorganisms Are Part of the Human Microbiome?
Bacteria make up the largest and most studied portion of the human microbiome, though viruses, fungi, and other microorganisms are also present and considered part of it[1].
Are Viruses and Fungi Part of the Microbiome as Well as Bacteria?
Yes, viruses and fungi are both considered part of the human microbiome, alongside bacteria and other microorganisms[1].
The viral component of the microbiome, sometimes called the virome, includes viruses that infect human cells as well as viruses that infect the bacteria living in the body. The fungal component, sometimes called the mycobiome, is generally much smaller than the bacterial community but still plays a role in the overall balance of the microbiome, particularly in the gut and on the skin.
Where Are the Main Microbiomes Found in the Human Body?
The main microbiomes in the human body are found in the gut, on the skin, in the mouth, and at several other body sites, each hosting a distinct microbial community[1].
What Is the Gut Microbiome?
The gut microbiome is the largest and most diverse microbial community in the human body, located mainly in the large intestine[1].
This community plays a central role in digestion, nutrient production, and communication with the immune system, and it is the most extensively studied microbiome due to its size and its clear connections to health and disease.
What Is the Skin Microbiome?
The skin microbiome is the community of microorganisms living on the surface of the skin, and it varies considerably depending on factors such as moisture, oil production, and exposure to the outside environment at different body locations.
Dry areas of skin, oily areas, and moist folds of skin each support noticeably different microbial populations, since each of these conditions favors different types of organisms.
What Microbial Communities Live in the Mouth and Other Body Sites?
The mouth hosts its own distinct microbial community, and additional communities exist at other body sites, including the respiratory tract and other body openings.
The mouth's community is shaped by constant exposure to food, saliva, and varying surfaces such as teeth and soft tissue, making it one of the more actively studied microbial sites beyond the gut and skin.
| Body Site | Typical Environment | Key Role |
|---|---|---|
| Gut | Warm, low oxygen, nutrient-rich | Digestion, nutrient production, immune interaction |
| Skin | Variable moisture and oil, exposed to air | Surface protection, barrier support |
| Mouth | Moist, frequent food exposure | Early digestion, oral balance |
Why Is the Microbiome Different in Different Parts of the Body?
The microbiome is different in different parts of the body because each location offers a distinct combination of oxygen level, moisture, nutrients, and temperature, which favors different types of microorganisms.
A microorganism that survives well in the low-oxygen, nutrient-rich environment of the gut may not survive at all on the drier, more exposed surface of the skin. Because of this, the human body does not host a single, uniform microbial community, but rather a series of specialized communities, each adapted to its particular location.
Does Everyone Have the Same Microbiome?
No, every person has a microbiome that is at least somewhat unique, shaped by factors such as genetics, diet, environment, and life history[2].
Even close family members living in the same household typically have microbiomes that differ from one another in meaningful ways. While people generally share certain common categories of microorganisms, the exact composition, proportions, and specific strains present can vary substantially from person to person.
How Does the Human Microbiome Develop From Birth?
The human microbiome begins developing at birth, when an infant is first exposed to microorganisms from the mother and the surrounding environment, and it continues to change and mature over the following years[5].
The way a baby is born, whether vaginally or by cesarean delivery, can influence which microorganisms establish themselves first. Feeding method, including breastfeeding versus formula feeding, also plays a meaningful role in shaping the early gut microbiome. This early period is considered especially important, since the developing microbiome interacts closely with the infant's immune system during a critical stage of development[5]. By early childhood, a person's microbiome generally becomes more stable, though it continues to shift gradually throughout life.
What Does the Microbiome Do in the Human Body?
The microbiome supports several essential body functions, including digestion, immune system interaction, and protection against harmful microorganisms[1], [2].
How Does It Affect Digestion and Metabolism?
The microbiome affects digestion and metabolism by breaking down food components, particularly fiber, that human digestive enzymes cannot fully process on their own, producing byproducts the body can use for energy[1].
Gut microbes ferment fiber into short-chain fatty acids, which serve as an important fuel source for the cells lining the intestine and contribute to the body's overall energy balance[4].
How Does It Interact With the Immune System?
The microbiome interacts with the immune system through constant, ongoing exposure that helps the immune system learn to distinguish harmless substances from genuine threats[2].
This interaction begins early in life and continues throughout adulthood, playing a role in maintaining a well-regulated immune response rather than one that is either underactive or excessively reactive.
How Does It Help Resist Harmful Microbes?
The microbiome helps resist harmful microbes mainly by occupying available space and nutrients, leaving little opportunity for harmful organisms to establish themselves, an effect known as colonization resistance[3].
An established, well-balanced microbial community also helps maintain a local environment, including factors such as acidity, that tends to be less favorable for many harmful organisms to grow in.
What Can Change the Human Microbiome?
The human microbiome can change due to factors such as age, diet, environment, and medications, particularly antibiotics[1], [5].
How Do Age, Diet, Environment and Medicines Affect It?
Age, diet, environment, and medicines each influence the microbiome by altering which microorganisms are present, how many of them survive, and how they interact with one another and with the body.
A person's microbiome shifts naturally across different life stages, starting from initial colonization at birth and continuing to change through childhood, adulthood, and older age[5]. Diet has a particularly strong influence, since the food a person eats directly supplies the nutrients that different microorganisms depend on.
A person's environment, including geographic location and household exposures, also shapes which microorganisms they regularly encounter. Antibiotics can significantly reduce both helpful and harmful bacterial populations at the same time, sometimes leading to a prolonged period of disruption before the community stabilizes again.
What Does Dysbiosis Mean?
Dysbiosis means an imbalance in the composition or function of the microbiome, in which the normal, healthy balance between different microorganisms has been disrupted[2].
Dysbiosis does not refer to a single, specific condition, but rather to a general state in which the microbial community has shifted away from what is considered typical or beneficial for a particular body site. This shift can involve a loss of diversity, an overgrowth of certain organisms, or a decline in organisms that would normally provide benefits such as colonization resistance or nutrient production[2].
Is There One Ideal or Healthy Human Microbiome?
No, current scientific understanding does not support the existence of one single ideal or universally healthy human microbiome[2].
Instead, a healthy microbiome is generally understood as one that is diverse, stable, and functioning well for that particular individual, rather than matching one fixed, standard composition shared by everyone. Because microbiomes vary naturally between people due to genetics, diet, and environment, researchers generally focus on function and balance, rather than searching for a single universal benchmark microbiome that everyone should aim to have[2].
Frequently Asked Questions
Can two people with different diets have similarly healthy microbiomes? Yes, since a healthy microbiome depends more on overall diversity, stability, and function than on matching one fixed composition, meaning different diets and lifestyles can support a well-functioning microbiome in different individuals.
Does the microbiome affect anything outside the digestive system? Yes, the microbiome interacts with several body systems beyond digestion, including the immune system and, according to a growing body of research, potentially areas such as mood and metabolism, although many of these connections are still being actively studied.
Can the microbiome fully recover after a major disruption, such as illness or antibiotic treatment? In many cases, the microbiome does recover substantially over time, though the recovered community does not always return to exactly its original composition.
Is it possible to test and know exactly what is in an individual microbiome? Yes, microbiome testing is available and can identify many of the organisms present, though interpreting what a particular test result means for an individual's health is still an evolving area, and results should generally be discussed with a healthcare provider rather than interpreted alone.
Do identical twins have identical microbiomes? No, even identical twins, who share the same genetics, typically develop somewhat different microbiomes over time, reflecting the strong influence of diet, environment, and individual life experiences.
Morais C. What Is the Human Microbiome and What Does It Do? [Internet]. BiologyWithin.com; 2026 Sep 19. Available from: https://www.biologywithin.com/2026/09/what-is-the-human-microbiome-and-what-does-it-do.html
- International Foundation for Gastrointestinal Disorders. The Human Gut Microbiome: An Overview [Internet]. Milwaukee (WI): IFFGD.
- Bäckhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe. 2012;12(5):611-622.
- Centers for Disease Control and Prevention. CDC Supports Microbiome Science to Advance Infection Prevention, Clinical Care, and Public Health [Internet]. Atlanta (GA): CDC.
- Pérez-Reytor D, Puebla C, Karahanian E, García K. Use of short-chain fatty acids for the recovery of the intestinal epithelial barrier affected by bacterial toxins. Front Physiol. 2021;12:650313.
- Houghteling PD, Walker WA. Why is initial bacterial colonization of the intestine important to the infant's and child's health? J Pediatr Gastroenterol Nutr. 2015;60(3):294-307.
Note on External Links: External links were checked and accessible when this article was published. Their content and availability may change over time and are outside the control of BiologyWithin.com.
Disclaimer: This article is for general educational purposes only and does not constitute medical advice, diagnosis, or treatment. Consult a qualified healthcare professional about personal health concerns.
