Your Gut Isn’t Just Home to Bacteria

By Lynn Glenda Pinto

GOOD GUT WEDNESDAY · 01
The Nourishment Edit

When we hear the words gut microbiome, most of us immediately think of bacteria. But that is only part of the story.

Inside the human gastrointestinal tract exists an extraordinarily complex ecosystem. Alongside bacteria are viruses, fungi, archaea and other microorganisms, living and interacting within the same environment. In other words, your gut isn’t simply populated by bacteria. It is home to an entire microbial world.

Meet your microbial community

Different members of this ecosystem are often described as their own microbial communities.

There is the bacteriome — the bacterial community we hear about most often.

There is the virome — the collection of viruses, including bacteriophages, which are viruses that infect bacteria.

There is the mycobiome — the fungal community.

And there is the archaeome — communities of archaea, microorganisms that are biologically distinct from bacteria.

Research increasingly considers these communities together because the gut functions as an interconnected ecosystem. Microorganisms can interact with one another, compete for resources and influence the environment in which other microbes live. That complexity is one reason scientists are increasingly looking beyond bacteria when trying to understand the human gut.

And then there is food

Here is where things become particularly interesting.

What reaches our gut is not relevant only to us. It also becomes part of the environment in which our microorganisms live.

Dietary fibre is an important example.

Unlike many nutrients that are absorbed earlier in digestion, certain fibres and other non-digestible carbohydrates reach the large intestine, where members of the gut microbiota can ferment them.

That fermentation can produce compounds called short-chain fatty acids, including acetate, propionate and butyrate. Research continues to investigate the many ways these microbial metabolites interact with human physiology.

This means food isn’t simply providing nutrients directly to our own cells. Some of what we eat also provides substrates for microbial metabolism.

So, what are you feeding?

This changes the way we can think about nourishment. Instead of seeing food only in terms of calories, protein, carbohydrates or fat, there is another fascinating question we can ask:

What is this food providing to the ecosystem living inside me?

Whole plant foods can provide an extraordinary variety of fibres and other compounds that interact with the gut microbiome. Vegetables. Fruits. Beans. Lentils. Whole grains. Nuts. Seeds. Herbs. Spices.

They aren’t interchangeable, either. Different plant foods contain different fibres and phytochemicals, and microbial responses to diet can vary substantially between individuals.

There is still an enormous amount scientists do not know about this ecosystem. In fact, researchers do not yet have one universal definition of what constitutes a perfectly “healthy” microbiome. And that uncertainty matters.

Gut science should not be reduced to claims that one particular food, supplement or bacterial strain will somehow “fix” everyone’s microbiome. The reality is considerably more complex — and considerably more interesting.

A different way to think about your next meal

Your gut is not an empty digestive tube. It is a living, dynamic ecosystem inhabited by microorganisms from multiple biological kingdoms, interacting with one another and with their human host.

So the next time you look at your plate, perhaps ask yourself two questions:

What am I eating? And… What am I feeding?

That second question is where our Good Gut Wednesday journey begins.

Research & Further Reading

Garcia-Bonete MJ, et al. (2023).
The Underrated Gut Microbiota: Helminths, Bacteriophages, Fungi, and Archaea.
Life, 13(8), 1765.
DOI: 10.3390/life13081765
View the peer-reviewed review

Leonard JM, Del Toro D. (2023).
Defining the Microbiome Components (Bacteria, Viruses, Fungi) and Microbiome Geodiversity.
Surgical Infections, 24(3), 208–212.
DOI: 10.1089/sur.2023.014
View the peer-reviewed review

Ost KS, Round JL. (2023).
Commensal fungi in intestinal health and disease.
Nature Reviews Gastroenterology & Hepatology, 20, 723–734.
DOI: 10.1038/s41575-023-00816-w
View the peer-reviewed review

Mann ER, Lam YK, Uhlig HH. (2024).
Short-chain fatty acids: linking diet, the microbiome and immunity.
Nature Reviews Immunology, 24, 577–595.
DOI: 10.1038/s41577-024-01014-8
View the peer-reviewed review

Delzenne NM, Bindels LB, Neyrinck AM, et al. (2025).
The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.
Nature Reviews Microbiology, 23, 225–238.
DOI: 10.1038/s41579-024-01108-z
View the peer-reviewed review

The Nourishment Edit is Lynn’s exploration of food, nourishment and the science behind how we eat. Our articles are for educational purposes and are not intended as medical advice.

Researched and edited by Lynn Glenda Pinto