The (Very) Early Years and Now

Here at ZOE, we have a deep interest in the gut microbiome, which consists of trillions of microorganisms that reside in your gut. As researchers delve into the science, the importance of gut bacteria in maintaining good health becomes increasingly clear.

Our team of scientists has discovered correlations between certain species of beneficial bacteria and indicators of good health. We have also identified associations between harmful bacteria and markers of poor health.

ZOE is dedicated to exploring how understanding your microbiome today can enhance your health in the future. If you're curious to learn about the bacteria inhabiting your gut, you can begin by taking our complimentary quiz.

While our focus is primarily on improving well-being in the present, we occasionally reflect on the origins of the microbiome.

In this article, we will take a look back at the emergence of life itself and the inception of our relationship with gut bacteria. We will also examine how our microbiome has evolved alongside modern living and provide tips on safeguarding and nurturing your gut bacteria.

The Early Days

Research on the gut microbiome is thriving, yet we are only scratching the surface of the intricate connections between us and our resident microbes.

Although the study of gut bacteria is relatively young, these microbes have been a fundamental part of the human experience since before the existence of animals. Bacteria have been a universal presence for eons.

We did not just evolve from bacteria; we evolved with bacteria.

Compared to humans and other animals, bacteria are simple organisms, consisting of a single cell each.

These single-celled organisms first emerged on Earth over 3 billion years ago. Approximately 1.5 billion years later, individual cells joined together to form the first multicellular life forms.

As multicellular animals became more complex, they maintained enduring relationships with bacteria that continue to this day.

We are familiar with the concept that an animal evolves in response to its environment. In the same way, our constant companions, bacteria, have evolved alongside and within us, as well as with unicellular fungi and various viruses.

You Are a Superorganism

At this moment, your skin is teeming with millions of microorganisms. Your nose, mouth, and gut are also thriving with these tiny bugs. The gut, in particular, is a hub of microbial activity, housing more bacteria than any other part of your body.

And we are not alone in this. To the best of scientific knowledge, all animals with a backbone (and the majority without) host gut bacteria.

Together with your microbiome, you form what scientists refer to as a "holobiont" or a superorganism. These bacteria (as well as fungi, viruses, and other microbes) depend on us for survival, just as we rely on them for good health.

We offer them a secure, warm environment in which to thrive, and in return, they aid in digesting complex foods and combating disease-causing bacteria.

Thus, as evolution shaped the bodies of creatures over geological time, our bacteria were intrinsic to the process: Evolution meticulously honed the superorganism as one.

Due to the rapid evolution of bacteria compared to animals, and their ability to "transfer" among different animals, bacteria could swiftly adapt to support a creature during challenging times as it gradually adjusted.

Conversely, when an animal's microbiome is significantly disrupted, the creature's ability to adapt or evolve efficiently is compromised.

Old Similarities

Your microbiome is distinct to you; however, it shares similarities with all other humans who have ever existed.

If you were to compare your gut microbiome to that of a close animal relative, such as a chimpanzee, the resemblance would be more pronounced than if you compared it to a more distant relative, like a non-primate mammal.

Researchers have observed this concept of phylosymbiosis across various species: As a new species diverges and evolves from another, its gut microbiome also evolves accordingly.

A study revealed that humans, chimpanzees, bonobos, and gorillas share common features in their gut microbiomes that have persisted for 15 million years. This stability in bacterial populations suggests a history of "long-standing co-evolution."

It may seem astounding today that the bacteria residing in our intestines can influence our health and even our mood. Yet, perhaps it should not be so surprising—these single-celled organisms played a pivotal role in shaping our current state.

Mitochondria and Oxygen

Aside from influencing the course of evolution, single-celled organisms have left their mark on multicellular life in other ways.

One prime example is mitochondria, organelles present in nearly every cell of your body. They are renowned for producing the energy required for cell functions.

Experts believe that mitochondria originated as independent microorganisms that established a symbiotic relationship with other cells. The host cell benefitted from the energy produced by the mitochondria, and in turn, the soon-to-be-mitochondria likely received some advantage.

This relationship endured, leading to the host organism engulfing the energy-producing microbe, resulting in a single, integrated organism.

Consequently, almost all cells in your body (and in the bodies of other animals and plants) bear evidence of an ancient association with a microorganism.

While this may be a digression, it is noteworthy: one of the earliest forms of bacteria—blue-green algae—exerted a distinct yet profound influence on life.

These bacteria conducted photosynthesis, producing oxygen, and likely played a role in the Great Oxygenation Event, which occurred around 2.3 billion years ago.

Without the surge in oxygen levels, life would have persisted but in a markedly different form—once again, bacteria played a crucial role in shaping life as we know it. One could argue that Earth is co-evolving with bacteria.

The Modern World

This remarkable narrative of human-bacteria co-evolution over vast time periods encountered a hurdle a few centuries ago. Humanity's advancements led to large-scale changes that disrupted the idyllic environment of the gut microbiome.

Many of us understand that genetic material is passed down from parents to children and further down the line. Similarly, a similar process occurs with the microbiome.

Each generation of humans transmits a portion of its microbiome to their offspring through childbirth, breastfeeding, and close cohabitation. Other sources, such as pets, food, soil, and fellow humans, also contribute to the microbiome, but parental influence remains significant.

Two significant contributors to this change were likely cesarean sections and the introduction of infant formula, which hindered the microbiome's transmission across generations.

It is crucial to acknowledge that despite their impact on the microbiome, these innovations continue to save lives today.

Other factors include an increased awareness of the importance of sanitation and the use of chlorine—a potent antibacterial agent—to maintain clean drinking water.

More recently, the widespread use of antibiotics, while lifesaving, has had a detrimental impact on our beneficial microbes alongside the harmful bacteria they were designed to combat.

The Importance of Diet

Collectively, these modern shifts have extended the human lifespan; however, the finely tuned microbial companions that have accompanied us since the dawn of multicellular life have been altered and diminished.

Nevertheless, the most significant influence stems from the substantial changes in our diet in recent times. The adoption of the Western diet, characterized by processed foods and a scarcity of fresh fruits and vegetables, has displaced beneficial bacteria and fostered harmful bacteria.

In parallel with the surrounding environment, an extinction event is occurring within the human gut.

Examinations of the gut microbiomes of individuals living traditional lifestyles more akin to our ancient ancestors have revealed significantly more diverse microbial populations. Western gut microbiomes have 15–30% fewer species than non-Western populations.

One study scrutinized the gut microbiomes of individuals living 1,000–2,000 years ago using remarkably well-preserved fecal samples. The researchers observed significantly greater diversity in the microbiomes of ancient populations compared to Westernized individuals.

What Can You Do?

At ZOE, we recognize the significance of a flourishing microbiome and understand that enhancing the diversity of your gut bacteria can promote better health.

Through our PREDICT studies, we have amassed a comprehensive database of information on the gut microbiome and its interaction with food.

We have demonstrated that the gut microbiome is linked to markers associated with cardiovascular and metabolic diseases. Certain gut bacteria are associated with positive health indicators, while others are linked to negative health markers.

Critical to our research is the realization that your dietary choices are intricately connected to the composition and abundance of gut microbes within your system.

According to Professor Tim Spector, co-founder of ZOE, there are five actions you can take today to enhance your gut microbiome:

1. Strive to consume 30 or more different plants each week, encompassing nuts, seeds, legumes, whole grains, fruits, and vegetables.

2. Incorporate colorful foods like berries and other fruits, as they are rich in polyphenols that are beneficial for gut bacteria.

3. Integrate fermented foods into your diet, such as kimchi, natural yogurt, and kombucha.

4. Allow your bacteria a reprieve—limit snacking and provide them with a rest overnight.

5. Restrict consumption of ultra-processed foods, as these items are associated with adverse health outcomes and lack the nutrients and fiber necessary to support your gut bacteria.

Although humanity may have relinquished some of its gut microbes, we can now focus on those that remain within us and around us. Concentrating on a varied diet rich in plant-based foods can nurture your gut bacteria, positively influencing your health.

If you are curious to discover the microorganisms inhabiting your gut, you can explore ZOE's at-home testing kit.

We can also reveal how your blood fat and blood sugar levels respond to different foods. As these responses vary among individuals, understanding them is crucial due to their role in dietary inflammation.

Utilizing this information, we can offer personalized nutrition guidance to assist you in selecting the ideal foods to enhance your gut bacteria and achieve your long-term health objectives.

If you wish to uncover how your body responds to food and how to optimize your diet for your unique physiology and microbiome, take our complimentary quiz today.