What is the microbiome?

Health, agriculture, and food all depend on microbiomes.

You live with microbes and encounter them daily without even knowing it. Your countertop is covered in microbes. Don’t be grossed out — that is part of your house microbiome. When you re-pot your plants and dig your fingers into the soil, it is full of microbes. But it’s fine. Many of those microbes actually make our antibiotics. Soil, too, has a microbiome.

But what is the microbiome? This word appears in conversation regularly these days, but what’s all the fuss about? 

So, this post is an introduction to microbiomes, which are everywhere and affect us daily in numerous ways. You’ll learn the answers to the following questions: What is a microbiome? Why do we study microbiomes? And why does microbial diversity in microbiomes matter?

What is a microbiome?

If you’ve heard the word “microbiome” before, what was it referencing? Most likely, it was the human microbiome. 

But the word microbiome serves a broader purpose. 

A microbiome is a collection of microorganisms (bacteria, fungi, viruses, archaea, algae, and protozoa) living in a specific habitat.

Sidenote: The microbiome can also refer to the genes and genomes of these microbes. For a great resource explaining the definitions of “microbiome” and related terms like “microbiota,” “microflora,” go read the blog post by Kristina Campbell “Microbiome quick guide series: Microbiome definitions.”

The habitats these microbes live in can be an entire organism (human, cow, ant), specific parts of an organism’s body (gut, skin, mouth), or outside of an organism in the soil, ocean, and even in our homes. Foods also have their own microbiomes (read my article for the American Society for Microbiology about the sourdough microbiome).

Microbes within a habitat interact with other organisms and with the environment itself. Often these activities lead to certain effects on the host, environment, or both.

For instance, microbes live in the soil and help maintain soil health. They also make nutrients in the soil available for plants to use, which ultimately affects the health of our crops. 

Similarly, in the human microbiome, you have organisms that help digest your food. They can break down complex chemicals, making more nutrients available for you to absorb.

Researchers have even studied the home microbiome to figure out which microbes people live with and how the home microbiome changes based on people being present or absent, their geographic location, whether they have pets, and whether they open the windows or not. If you think about it, one way you can be exposed to a variety of microbes is by having a dog. Your dog friend runs around, rolls in the grass (and other things), and picks up microbes. Those microbes then hitchhike inside.

Why do we study microbiomes?

Studying microbiomes matters because, when we understand them, we can devise strategies to harness the power of microbes to improve our lives and the environment.

For example, studying gut and home microbiomes can potentially help us better understand how to alleviate allergies. Remember the dog rolling around outside and then coming inside accompanied by the microbial hitchhikers? Those microbes end up in the dust of homes with pets. Researchers looked at the microbiomes of this home dust to see how those microbes affected mice. They found that when mice were exposed to that dust, their allergies were less severe, and it changed the composition of their gut microbiomes. Let me emphasize, this study was in mice. However, as for any study in mice, it is still potentially applicable to humans, but conclusions must be understood with caution. 

Digging into the soil microbiome can reveal which microbes are responsible for making nutrients available, which could, in turn, help improve crop yield and improve overall soil health. 

The strategies to improve health based on the microbiome, whether it be human or soil health, can be approached in similar ways: adding beneficial microbes (probiotics), promoting the growth of beneficial microbes (prebiotics), and using certain microbes as indicators of health or disease. Likely, combining all three approaches will work better than any one on its own.

Why does microbial diversity in microbiomes matter?

Diversity in microbiomes is generally a sign of health. With diversity, many different microbes provide their unique sets of skills. Think about the workplace: it’s beneficial to hire people that contribute diverse sets of skills and have distinct personality types. That’s why you have different employees that work in departments. And if everyone is detail-oriented, then no one may see the big picture, and nothing ever gets done. The same idea goes for microbial diversity. Microbiomes need many different microbes providing different “skills” to aid in digestion in the human gut or provide nutrients to plants in the soil.

Numerous microbial species make up the gut microbiome. However, when you lose diversity from antibiotic treatment, you could end up with just one resistant pathogen — C. difficile — that dominates and makes you extremely sick, sometimes to the point of death. Not all microbes in a microbiome are beneficial. So, the variety of microbes in the gut keep each other in check.

Microbial diversity can even improve our food. When it comes to sourdough bread, diversity is delicious. If you have many different lactic acid bacteria and yeasts in the sourdough starter, they all contribute to the flavor and texture, and you end up with this amazing, unique sourdough bread. This bread is unlike any store-bought bread made with one of three strains of one species of yeast, Saccharomyces cerevisiae. And so microbial diversity gives us better tasting foods.

Summary

• Microbiomes are everywhere
• Microbiomes are collections of microbes living in a particular environment
• The location of a microbiome can be whole organisms or environments or parts of organisms or environments (human microbiome vs. gut microbiome)
• Studying microbiomes can help improve our lives and the environment
• Microbial diversity, on the whole, is better in microbiomes because more microbial “skills” are available and the microbes in the population keep each other in check

Read more about the microbiome in some fantastic books that I shared in a previous post: 11 Audiobooks About Microbes. Not sure which one to start with? I especially recommend I Contain Multitudes by Ed Yong and Whole-Body Microbiome by B. Brett Finlay PhD, Jessica M. Finlay PhD.