Updated 24th April 2024

Gut microbiome: Ancient origins and recent extinctions

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At ZOE, we're fascinated by the gut microbiome — the trillions of microorganisms that call your gut home. As researchers dig deeper into the science, the role of gut bacteria in health grows clearer. 

For instance, our scientists have uncovered links between certain species of “good” bacteria and markers of good health. We’ve also identified associations between “bad” bugs and markers of poor health.

ZOE focuses on how understanding your microbiome today can improve your health tomorrow. If you’d like to learn which bugs inhabit your gut, you can start by taking our free quiz.

Although we like to focus on making people feel better today, sometimes we cast our minds further back and wonder how the microbiome began.

In this article, we’ll look back at the dawn of life itself and the start of our relationship with gut bugs. We’ll also look at how our microbiome has changed in step with modern life and give you some tips on how to protect and boost your gut bugs. 

The early days

Research into the gut microbiome is flourishing, but we are still only scratching the surface of the complex relationships between us and our onboard microbes. 

Although the science of gut bacteria is relatively young, your microbes aren’t a late addition to the human experience. Bacteria have been a universal fact of life since before animals were even a thing. 

We evolved from and with bacteria.

Compared with humans (and all other animals, for that matter), bacteria are simple: Each bacterium is just a single cell. 

These single-celled organisms first appeared on earth more than 3 billion years ago. Then, roughly 1.5 billion years later, single cells joined forces to become the first multicellular life.

Because the first creatures “evolved in seas filled with bacteria,” it seems likely that bacteria played a part in their evolution.

And as multicellular animals became increasingly complex, they maintained relationships with bacteria that persist until today. 

We are relatively familiar with the idea that an animal evolves in step with its surroundings. For instance, a small animal that lives alongside larger predators will evolve traits that help it avoid being eaten, like a better sense of smell or longer legs. 

The same applies to our ever-present friends, bacteria — all life evolved while surrounded by and infiltrated by bacteria, as well as unicellular fungi and viruses of all sorts. 

You are a superorganism

As you read this, your skin is covered with millions of microorganisms. Your nose and mouth are also thick with these bugs. And your gut is a microbial hotspot, home to more bacteria than any other part of your body. 

And we’re not alone. As far as scientists can tell, all animals with a backbone (and the vast majority of those without) also host gut bacteria.

Together with your microbiome, you create what scientists call a “holobiont,” or a superorganism. The bacteria (and fungi, viruses, and other microbes) rely on us to survive, and we rely on them for good health.

We provide them a safe, warm place to live, and they repay us by digesting tricky foods and fighting off disease-causing bacteria.

So, as evolution got to work, morphing the bodies of creatures over geological time, our bacteria were there every step of the way: Evolution fine-tuned the superorganism as one.

Because bacteria can evolve much quicker than animals — and can “jump” between different animals — when times were tough for an animal, the bacteria could evolve rapidly, supporting the creature as it took time to adapt.

Conversely, if an animal’s microbiome is severely disrupted, the creature can’t adapt or evolve as efficiently.

Old similarities

Your microbiome is unique. It's distinct from everyone else who has ever lived. However, it shares similarities with all other humans.

If you compared your gut microbiome to a close animal relative, say a chimpanzee, it would be more similar than if you compared it with a more distant relative, like a non-primate mammal.

Scientists have observed this so-called phylosymbiosis across multiple species: As a new species differentiates and evolves from another one, its gut microbiome changes with it.

One study found that humans, chimpanzees, bonobos, and gorillas have shared gut microbiome features that have persisted for 15 million years. This stability in populations of bacteria suggests “long-standing co-evolution.”

Today, it seems incredible that bacteria in our intestines influence our health and even our mood. But perhaps it shouldn’t seem so outlandish — these single-celled organisms helped shape what we are today.

Mitochondria and oxygen

Aside from their influence on how evolution panned out, single-celled organisms put their stamp on multicellular life in other ways. 

Mitochondria are a good example. These organelles are present in nearly every cell in your body. They are probably most famous for generating the energy that cells need to carry out their work. 

Experts believe mitochondria began as free-living microorganisms that developed a relationship with another cell. The host cell benefited from the energy, and no doubt the soon-to-be-mitochondria also benefited in some way. 

The relationship persisted, and eventually, the host organism engulfed the energy-producing microbe, becoming a single organism. 

So, almost all of the cells in your body (and the bodies of other animals and plants) harbor evidence of an ancient relationship with a microorganism.

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This is a bit of a tangent, but it’s worth mentioning: One of the earliest forms of bacteria — blue-green algae — had a very different but profound influence on life.

These bacteria produce oxygen through photosynthesis and were probably responsible for the so-called Great Oxygenation Event. This boost in oxygen levels in Earth’s atmosphere took place around 2.3 billion years ago.

Without the increased oxygen levels, life may have persisted, but it would have looked very different — once again, bacteria were pivotal in the evolution of life as we know it. You might even say that Earth is co-evolving with bacteria.

The modern world

This incredible, utopian story of humans and bacteria co-evolving over deep time hit a roadblock just a few hundred years ago. Humanity got too big for its boots and made large-scale changes that interrupted the gut microbiome's Garden of Eden.

Many of us are familiar with the idea that our parents pass their genetic code on to us, and we pass it on to our children. But a similar thing happens with the microbiome. 

Each generation of humans passes some of its microbiome to its offspring. This happens during birth, breastfeeding, and while living in close quarters. Other sources — for instance, pets, food, soil, and other humans — also add to the microbiome, but the parental influence is sizable

During the 19th century, there was a shift in our microbiome. This was likely for many reasons. 

Two reasons that contributed to the change were probably cesarean sections and infant formula. These interventions reduce the microbiome’s ability to move from generation to generation.

It is important to note, however, that these inventions still save the lives of mothers and babies to this day.

Other factors include humanity’s growing awareness of the importance of good sanitation. Also, humans started using chlorine — a potent antibacterial — to keep drinking water clean.

More recently, the rise of antibiotics, while saving countless lives, severely impacted our friendly microbes alongside the “bad” bugs they were designed to kill.

The importance of diet

Overall, these modern shifts have helped extend the lifespan of humanity. Still, our finely tuned microbial visitors, which have been with us since the dawn of multicellular life, have been altered and reduced. 

However, the factor with the greatest influence is the huge change in our diet over recent years. The rise of the Western diet, rich in processed foods and light on fresh fruit and veg, took its toll by pushing out “good” bacteria and encouraging “bad” bacteria.

Mirroring the environment around us, there is an extinction event going on within the human gut. 

When scientists examined the gut bacteria of people who live traditional lives more similar to our ancient relatives, they found much more diverse gut microbiomes. Western gut microbiomes have around 15–30% fewer species than non-Western populations. 

One study analyzed the gut microbiome of people living 1,000–2,000 years ago using some particularly well-preserved poop. The scientists found that, compared with the microbiomes of Westernized humans, ancient folk had much more diversity.

What can you do?

At ZOE, we appreciate the importance of a thriving microbiome. We also understand that increasing the diversity of your gut bacteria can benefit your health.

Through our PREDICT studies, we’ve collected a vast database of information about the gut microbiome and its relationship with food.

We’ve shown that the gut microbiome is connected with the levels of markers associated with cardiovascular and metabolic diseases. We identified certain gut bacteria that are associated with positive health markers and some associated with negative markers of health.

Importantly, our research has also shown that what you eat is strictly linked with which kind of microbes live in your gut and how abundant they are.

You can’t change the fact that you were born by cesarean section, needed a long course of antibiotics, or were born into an industrialized country, but you can improve your gut microbiome through your diet — within days.

According to ZOE’s scientific co-founder, Prof. Tim Spector, there are five things you can do today to help boost your gut microbiome:

  1. Try to eat 30 or more different plants each week, including nuts, seeds, pulses, whole grains, fruits, and vegetables.

  2. Eat colorful foods like berries and other fruits — these are rich in polyphenols, which gut bugs love.

  3. Add fermented foods to your diet, such as kimchi, natural yogurt, and kombucha.

  4. Give your bacteria a break — limit snacking and let your bugs rest overnight.

  5. Limit ultraprocessed foods — these products are linked to unfavorable health outcomes, and they lack nutrients and fiber to support your gut bugs.

Humanity may have lost some of its gut microbes, but today, we can focus on those that are still in us and around us. Concentrating on a diverse diet rich in plant foods can boost your gut bugs, positively influencing your health.

If you're interested in learning which bugs live in your gut, you can take ZOE’s at-home test.

We can also show you how your blood fat and blood sugar levels respond to food. These measures vary between people and are important because they play a part in dietary inflammation.

From all this information, we can provide you with personalized nutrition advice to help you choose the best foods to boost your gut bacteria and achieve your long-term health goals.

If you're interested in learning how you respond to food and how to eat right for your unique body and bugs, take our free quiz now.


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