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When most people think of microbes, the first things that come to mind are disease-causing germs or healthy probiotic yogurts. We go about our lives largely unaware of the trillions of microbes on every surface and throughout our bodies, influencing everything from coral reefs to the physical and mental health of humans. In his debut book, I Contain Multitudes, Ed Yong explores the mysterious and fascinating world of microbes: microscopic organisms with the ability to make sea creatures glow, eradicate diseases, and nudge ecosystems into disarray.

Yong argues that not only are microbes ubiquitous, but they’re also integral to animal bodies (including humans). And by understanding the ways that we’re interdependent with microbes, we can then explore opportunities to use microbes to improve our health.

Yong is a British-American science journalist reporting for The Atlantic. He won a Pulitzer Prize for his coverage of the...

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I Contain Multitudes Summary Defining Microbes and Their Evolutionary Role

To appreciate the role of microbes in the animal world today and the ways we can leverage them to our benefit, we’ll start by defining microbes and explaining their significance in the evolution of living organisms.

What Is a Microbe?

“Microbe” is a catch-all term for microorganisms, living things that are too small to see with the naked eye. Yong explains that microbes exist in many forms, broadly categorized as bacteria, fungi, and viruses. (Shortform note: Protozoa is another scientific category of microbes that Yong doesn’t discuss in detail. Protozoa are single-celled organisms that are sometimes parasitic and cause diseases such as malaria.)

Within these categories, other terms are often used to indicate a microbe’s function. For example, pathogens are disease-causing microbes, probiotics are microbes that produce a health benefit, and bacteriophages (also known as phages) are viruses that eat bacteria.

Although pathogens are generally considered “bad” microbes, Yong asserts that microbes aren’t inherently bad or good. In his analogy of individual people as ecosystems of interacting microbes, Yong compares pathogens to invasive species—plants or...

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I Contain Multitudes Summary Microbes Impact the Initial Development of Animals

Now that we’ve defined microbes and how they came into symbiotic relationships with animals, we’ll discuss Yong’s examples of the ways microbes impact the early development of animals. Through his examples, Yong shows that microbes shape fundamental aspects of animals, such as protection from predators, metamorphosis, and immunity. These microbial factors establish conditions that impact the animal for the rest of its life.

Microbes Shape Animals and Their Protection From Predators

Yong explains that microbes are an integral part of animal defense systems because they can alter an animal’s body and activate specific genes to make it less vulnerable to predation. (Shortform note: Microbes not only defend animals but also attract other organisms. For example, the unique scent produced by microbes in an elephant’s urine signals to other elephants its sex and mating readiness.)

In one of Yong’s examples, a single bacterium species is responsible for the unusual self-defense mechanism of the Hawaiian bobtail squid. The bobtail squid...

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I Contain Multitudes Summary Microbes Form Interdependent Relationships With Animals

While the last section focused on the ways that microbes help shape animals fundamentally, we’ll now explore the ways that microbes influence animal life through long-term interdependent relationships. These relationships are more like conventional symbiosis, where both partners gain a mutual benefit, and they include food symbiosis and co-management of the immune system.

(Shortform note: In The Plant Paradox, Gundry also describes the interdependence between people and microbes, but he focuses on a diet-based strategy to foster beneficial microbes using his Plant Paradox Program. The PPP includes three main phases: a three-day cleanse, adjusting your diet (by eating fewer high-sugar foods, for example), and reducing your consumption of animal protein and beginning a form of fasting.)

Food Symbiosis

Yong explains that microbes enter into food symbiosis with animals by evolving ways to expand the animal’s food options. Animals benefit from increased food access,...

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I Contain Multitudes Summary Human Lifestyles Impact Microbial Ecosystems

Now that we’ve covered how microbes are linked to animal development, as well as how microbes form long-term interdependent relationships with animals through food and immunity, we’ll talk about how humans are altering microbial populations at an unprecedented rate. Yong describes how these changes have catastrophic effects on ecosystems in some environmental contexts, like coral reefs. Within the human body, scientists are not yet sure what the implications are of our changing microbiome.

Shifts in Microbe Populations Contribute to Ecological Collapse

Because of human activity in oceans around the world, ecosystems like coral reefs are declining rapidly due to a shift in microbial populations. Yong asserts that for coral reefs, this decline often starts with the presence of iron from boats and other human-made structures that cause rapid growth of fleshy algae. This fleshy algae growth is also happening in the context of humans overhunting sea animals and polluting oceans, which drastically reduces the population of fish and other sea creatures that would normally eat the fleshy algae and moderate its population.

As a result, the fleshy algae produce an overabundance...

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I Contain Multitudes Summary Potential for Microbes in Medicine

In the previous sections we talked about the ways that microbes are closely linked to living organisms, as well as the ways that human behavior is impacting microbial populations. Now, we’ll dive into the question underlying Yong’s idea that all animals are thoroughly interdependent with microbes: How can we use our knowledge of microbes to manipulate our partnerships with them to our benefit? In this section, we’ll discuss Yong’s argument for why popular probiotics on the market are largely ineffective and explore the promising forms of microbe medicine that may be on the horizon.

How Commercial Probiotics Have Oversold Health Benefits

Despite Yong’s arguments for why microbes can be powerful allies in health, he aims to debunk myths surrounding the health benefits of commercially sold probiotics like Lactobacillus (present mostly in capsules and yogurt products). Food companies advertise wide-ranging and vague benefits including improving bowel regularity, improving digestion, boosting immunity, treating digestive disorders, and more.

(Shortform note: Michael Pollan’s In Defense of Food notes that most...

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Shortform Exercise: Reflect on the Microbiome as an Ecosystem

Yong often uses the analogy of an ecosystem to describe the complex network of relationships between microbes and animals. They occupy every part of us, and in combination with our genes and lifestyle choices, impact our physical and mental well-being.


This idea suggests that there are ecosystems on the microscopic scale, as well as at larger scales, like in a forest, or even zooming out to the planet as a whole. How does your understanding of the relationship between microbes and animals change your perspective on the ways that all living beings are connected?

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