What is a microbiome?

Microorganisms dominate all other life everywhere scientists have looked, including the human body

A microbiome is the community of microorganisms—such as bacteria, archaea, fungi, as well as viruses—that inhabit an ecosystem or organism. Microorganisms dominate all other life everywhere scientists have looked, including the human body, the Earth’s soils and sediments, the oceans and fresh waterways, the atmosphere and even extreme environments such as hydrothermal vents and subglacial lakes. Scientists also use the term microbiome to refer to all these genes associated with those lifeforms.

Microbiomes have several things in common. Their inhabitants are plentiful and diverse, varying from place to place and even from person to person. They are also dynamic, changing in response to factors such as diet or climate. Finally, they are interconnected with their host, engaged in a give-and-take relationship that is often beneficial, even essential, to both the host and their resident microorganisms.

Researchers are just beginning to study microbiomes in as systematic way. They are trying to understand what makes a healthy microbiome, including what microbes are present and what those microbes are doing, as well as how microbiomes change over time, how such communities stay balanced and how changes to microbiomes impact human or environmental health. Microbiome research is even important for space exploration and planetary science. Understanding microorganisms here on Earth, especially those that inhabit extreme environments, may help us understand the potential for alternate lifeforms and to search for life on other planets. They may also help us colonize other planets by helping us to create Earth-like, human-friendly environments far, far away.

Where do microbiomes exist?

The Human Microbiome

The human microbiome is the collection of trillions of microbes living in and on the human body. It consists of about a thousand different bacterial species that reside in the mouth, gut and vagina, and on the skin. These microbes, and the genes they express, make us a “superorganism” composed of human and microbial cells. (It’s estimated that one person’s microbiome may include as many as 8,000,000 genes in addition to the 20,000 to 25,000 that our genome is estimated to contain.) The microbiome varies greatly among different body sites. Indeed the differences between a person’s gut and oral microbes have been likened to the differences between the microbes found in soil and the oceans.

We begin to pick up microbes when we are born. That process continues over the next three years of life until we’ve developed a mature microbiome. The results aren't random: The human microbiome is composed of specific kinds of microorganisms that complement each other and their host, fulfilling functions that are essential to life. For example, some gut bacteria synthesize vitamins and neurochemicals; others aid digestion and strengthen the immune system; some may even guide how the brain develops. Though everyone’s microbiome is similar, it varies from one individual to the next. Scientists are still trying to explain how this microbial diversity comes about, but it is likely influenced by factors including diet, environment, host genetics and exposure to microbes early in life.

Researchers are continuing to study the identities and activities of our microbial passengers and the connections between the human microbiome, health and disease. Their ultimate goal is to understand what constitutes a healthy human microbial ecosystem and then to develop ways to keep it healthy and repair it when necessary.

Since 2005, at least eight programs have been established to study the human microbiome, including the US Human Microbiome Project, the Canadian Microbiome Initiative, MetaHIT (EU and China) and the Human Metagenome Consortium in Japan.

The Earth Microbiome

The Earth’s soils and sediments also host microbial communities. Diversity in these underground habitats is tremendously high, with estimates of the soil microbial census exceeding 40,000 species per gram. In the soil, researchers have found that microbes are essential for supporting plant life, mediating uptake and entry of nutrients into the food chain, cycling carbon and nitrogen, breaking down pollutants and much more. However, their understanding of the soil microbiome lags behind the human microbiome, partly because of its vastness and complexity. A handful of large-scale coordinated efforts are underway to characterize the soil microbiome, including the Earth Microbiome Project, TerraGenome, the Brazilian Microbiome Project, the China Soil Microbiome Initiative, EcoFINDERS and MicroBlitz. The eventual goal is to predict how microbial communities will react to environmental conditions such as droughts and to manage these communities to improve the yields, nutritional content or the carbon storing capacity of plants, for example.

The Ocean Microbiome

Oceans cover about 70 percent of the planet, yet we’re only just beginning to know their microbial inhabitants and what they do for us and for the planet. Together, the extremely small organisms, or “nanoplankton” that perform these essential services form the “nanobiome.” These tiny microbes are highly specialized and optimized for their environment, where they provide energy and chemical building blocks to larger life forms. They also produce half of the oxygen we breathe, and recycle about the same proportion of carbon dioxide from the atmosphere. They also remove most of the methane from the world’s oceans. Research cruises such as Tara Oceans and the Global Ocean Sampling Expedition have begun to sample, sequence and analyze the ocean microbiome, from the sunlit surface waters that are mixed by the wind to dark deep layers that relatively unperturbed. Scientists are trying to understand how the ocean microbiome maintains its balance under such a range of conditions.

The Atmospheric Microbiome

Even the atmosphere has a microbiome, though it is difficult to sample and study. What’s clear is that is that microbes in the atmosphere are everywhere, vary from place to place and can remain suspended for weeks. The atmosphere transports these microbes, either freely or attached to particles such as dust, around the globe, a phenomenon that may impact agriculture, infectious disease, human health, clouds, precipitation and the water supply.

What’s the connection between microbiomes, health and disease?

As researchers begin to understand what constitutes a healthy microbiome, they are also learning how imbalances in microbial communities can cause disease—and how to restore the balance as a means of treatment. There are strong associations between the human gut microbiome and conditions including obesity, type-2 diabetes, cirrhosis, rheumatoid arthritis and inflammatory bowel disease. Researchers have already restored the “normal” human gut microbiome using fecal transplants to cure recurrent infections with the bacterium Clostridium difficile. There are still other associations between the gut microbiome and disorders including anxiety, depression and autism that researchers are still exploring. A major goal of microbiome research is to move microbiome research from correlation to causation and to discover the mechanisms by which microbes influence health and disease.

What's the connection between microbiomes and space?

Even scientists looking to space are interested in microbiomes. That makes sense when you consider how fundamental microbes are to life on Earth. Should we seek to colonize another planet, understanding how microbes help make Earth habitable might allow us to create more Earth-like conditions on other planets—conditions necessary to sustain human life. Researchers are also studying whether microorganisms could help us harvest essential minerals from Martian rocks or synthesize materials to construct or replace equipment in remote places. And NASA has a program to study an astronaut’s microbiome to gauge the impact of space travel on the human health. Finally, scientists searching for habitable planets and extraterrestrial life are studying microbes to guide their search. The microbial communities in the Earth’s most extreme environments help them understand the conditions necessary to support life and what kinds of biosignatures to look for on other planets.

Note: The Kavli Foundation closed work on this initiative in 2019.