What the Human Microbiome Is

The human microbiome is the vast community of microbes that live in and on the human body, together with their combined genes and genomes. It includes bacteria, viruses and single-celled organisms, with bacteria the most numerous and best studied. Far from being passive passengers, these microbes take part in digestion, immunity, nutrition and other processes, which is why the U.S. National Institutes of Health invested heavily in mapping them through the Human Microbiome Project.

This article is general information, not medical advice. It summarises how the microbiome is described by scientific institutions and does not offer guidance on diet, supplements or treatment.

What exactly is the microbiome?

The word microbiome refers to the collective genomes of all the microorganisms present in or on the body. A closely related word, microbiota, usually refers to the microorganisms themselves as a living community. In practice the two terms overlap and are sometimes used interchangeably, but the distinction is useful: microbiota is the population of microbes, while microbiome emphasises the population plus its genetic material.

These microbes are not limited to bacteria. The community also includes viruses and single-celled eukaryotes, a group of more complex microorganisms. Together they form ecosystems that differ from one part of the body to another, so the mix of microbes on the skin is not the same as the mix in the gut.

How many microbes are we talking about?

The scale is striking. The human body hosts trillions of microorganisms. An often-quoted early estimate suggested that microbial cells outnumber human cells by roughly ten to one, though later research revised the ratio closer to one to one. Either way, the numbers are enormous.

Despite their vast quantity, microbes account for only a small fraction of body weight. Because each microbe is so tiny, all of them combined make up only about 1 to 3 percent of the body’s total mass. In genetic terms, however, their contribution is huge, because the microbial genes vastly outnumber human genes.

What was the NIH Human Microbiome Project?

In 2007 the National Institutes of Health launched the Human Microbiome Project, or HMP, as a conceptual extension of the earlier Human Genome Project. Where the Human Genome Project mapped human DNA, the HMP set out to characterise the microbes that normally inhabit the healthy human body and to understand what they do.

The project served as a road map for discovering the roles these microorganisms play in human health, nutrition, immunity and disease. A key early achievement was defining what a normal, healthy microbial makeup looks like, since researchers first needed a baseline before they could study how changes in the microbiome relate to illness.

Where in the body does the microbiome live?

Microbes colonise many surfaces of the body, but the Human Microbiome Project concentrated on five main sites. Each supports its own distinctive community.

Body site	Notable feature
Skin	Exposed surface with varied microbial zones
Mouth	Rich oral community involved in early digestion
Nose	Part of the respiratory tract’s microbial defences
Colon (gut)	Densest and most diverse community in the body
Vagina	Community linked to reproductive and urinary health

The gut is the most intensively studied of these, because it holds a particularly dense and diverse population of microbes and is closely involved in digesting food and interacting with the immune system.

Why does the microbiome matter?

Scientists connect the microbiome to a wide range of body functions. Gut microbes help break down components of food that human cells cannot digest on their own, and they contribute to producing certain vitamins and other useful molecules. The microbiome also helps train and support the immune system, and a healthy, balanced community can make it harder for harmful microbes to gain a foothold.

Research has associated imbalances in the microbiome with various health conditions, spanning digestion, metabolism and immunity. It is important to be cautious here: many of these links are associations, and science is still working out which changes cause disease and which are simply consequences of it. The field is active and evolving, and firm conclusions are still being established.

How did scientists study the microbiome?

Studying the microbiome became practical thanks to advances in DNA sequencing. Many of the microbes that live in and on the body are difficult or impossible to grow in a laboratory dish, which for a long time made them hard to study. Modern techniques get around this by reading the genetic material of microbes directly from a sample, without needing to culture them first.

This is why the microbiome is defined partly in genetic terms. By sequencing the collective DNA present in a sample from the gut, mouth or skin, researchers can identify which types of microbes are present and estimate how abundant each is. The Human Microbiome Project used this approach to build its baseline map of the healthy human microbiome, generating a large public resource for other scientists to draw on.

What does a healthy microbiome look like?

One of the surprising findings of microbiome research is that there is no single healthy microbiome shared by everyone. The specific mix of microbes varies considerably from person to person, and even between different sites on the same body. Two healthy people can host quite different communities, yet both can be normal.

Researchers therefore often focus on diversity and function rather than a fixed list of species. A community with a rich variety of microbes performing a broad range of useful functions is generally regarded as a sign of a healthy ecosystem, though the details are still being worked out. This individuality is part of why microbiome science is complex and why broad claims should be treated with care. It also means that comparing one person’s microbiome directly against another’s is rarely straightforward, and that findings from small studies do not always generalise to everyone. Researchers increasingly look at the microbiome as a dynamic system that shifts over time rather than a fixed snapshot, since diet, illness and medication can all change its balance from week to week.

How is the microbiome shaped?

An individual’s microbiome is shaped by many factors over a lifetime. These include early events such as how a person is born and fed as an infant, along with diet, environment, medications such as antibiotics, and age. Because these influences vary so much, each person’s microbiome is highly individual, which is part of what makes it both fascinating and difficult to study.

Understanding the human microbiome reframes the body as an ecosystem rather than a single organism. The trillions of microbes we carry are a normal, working part of human biology, and mapping them, as the NIH Human Microbiome Project set out to do, has opened a broad new field exploring how these tiny inhabitants relate to human health.

Frequently Asked Questions

What is the difference between microbiome and microbiota?

The terms are related but not identical. Microbiota usually refers to the microorganisms themselves, the living community of bacteria, viruses and other microbes. Microbiome often refers to that community together with their collective genes and genomes. In everyday use the two words are sometimes used interchangeably.

How many microbes live in the human body?

The human body hosts trillions of microorganisms. Earlier estimates suggested they outnumber human cells by around ten to one, and although later research put the ratio closer to one to one, the numbers remain enormous. Because the microbes are so small, they make up only about 1 to 3 percent of total body mass.

What was the NIH Human Microbiome Project?

The Human Microbiome Project was launched by the U.S. National Institutes of Health in 2007 as a conceptual extension of the Human Genome Project. It aimed to map the microbes that normally live in the healthy human body and to explore their roles in health, nutrition, immunity and disease across different body sites.

Where in the body does the microbiome live?

Microbes live across many surfaces of the body. The Human Microbiome Project focused on five main areas: the skin, mouth, nose, colon or gut, and vagina. The gut is home to an especially dense and diverse community, which is why it receives much of the research attention.

Why does the microbiome matter for health?

Research links the microbiome to many body functions, including digesting food, producing certain vitamins, training and supporting the immune system, and resisting harmful microbes. Imbalances have been associated with various conditions, though science is still working out which links are causes and which are effects.

Sources

• National Human Genome Research Institute (NIH) - Human Microbiome Project defines normal bacterial makeup
• NIH Common Fund - Human Microbiome Project (HMP)
• NIH Human Microbiome Project Data Analysis and Coordination Center - About the Human Microbiome
• National Human Genome Research Institute (NIH) - NIH Launches Human Microbiome Project

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