PDF Summary:I Contain Multitudes, by Ed Yong

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. In his debut book, science journalist 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.

He argues that not only are microbes ubiquitous, but they’re also integral to animal bodies (including humans)—although we often think of ourselves as individuals, we’re essentially walking ecosystems containing countless species of microbes living in symbiotic partnership with us. He contends that by understanding the ways that we’re interdependent with microbes, we can then explore opportunities to use microbes to improve our health. And since our understanding of microbes is constantly shifting, our guide will also update Yong’s examples and dive deeper into the health implications of microbial phenomena.

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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, and the microbes ensure the survival of animal hosts that provide food, habitat, and future generations of hosts. Microbes increase animals’ access to food by enabling some animals to survive off sap and toxins, enabling others to digest cellulose, and allowing humans to eat a diverse diet.

(Shortform note: Robin Wall Kimmerer’s Braiding Sweetgrass discusses this concept of food symbiosis in the context of plants and humans. Within the plant world, she describes how the different feeding strategies of fungi and algae enable lichens (composite organisms of fungi and algae) to get the nutrients that neither can get alone. Kimmerer also frames food symbiosis between plants and humans as a form of cyclical gift-giving. For example, when humans get nutritious food from a coconut tree, they might return the gift by spreading its seeds and cultivating more trees. Yong might argue that microbes are another component of this symbiotic gift cycle because of the soil nutrients and digestive abilities they provide.)

Microbes Help Animals Eat Sap and Toxins

Throughout the animal kingdom, bacteria enable some animals to eat things they couldn’t eat on their own, like plant sap and toxins. In many cases, the bacteria produce essential nutrients that are missing in sap, as a kind of dietary supplement. In other cases, the bacteria break down toxic substances for the animal. Reindeer, koalas, woodrats, and many more animals co-evolved with specialized bacteria that allow them to take advantage of a niche (generally toxic) food source.

(Shortform note: Bacteria can also reduce toxicity in foods that humans eat. For example, during fermentation, a lactic acid bacteria reduces the naturally occurring cyanide (present in varying amounts, depending on the variety) in cassava root, a staple food of Africa and South America.)

For example, the caffeine in coffee beans (which are really the seeds of the plant) is toxic to most insects and protects coffee plants from pests. However, a caffeine-eating bacteria allows one insect, the coffee berry borer, to subsist solely on coffee beans. (Shortform note: The coffee plant also has lower doses of caffeine in the nectar of its flowers, which creates a different symbiotic connection between the plant and insects. At these smaller doses, the caffeine is non-toxic to insects and gives them an energetic buzz, encouraging insects to pollinate the coffee plant.)

Microbes Allow Animals to Eat Cellulose

Microbes also established food symbiosis in animals by enabling animals to digest plant cellulose (a structural part of plant cells that humans can’t digest). Yong argues that this helped revolutionize life on Earth because it ultimately enabled humans to adopt agriculture based on domesticated livestock. Bacteria formed a symbiotic relationship with grazing animals like goats and cows, which can eat grasses and other vegetation, and humans then began raising the grazers as food.

(Shortform note: In Sapiens, Yuval Noah Harari notes that the shift to an agricultural food system focused on wheat (prior to the use of domesticated animals) wasn’t exactly an improvement for human communities. The first farmers spent more time working to produce food than they did as hunter-gatherers, and their diet was less nutritious due to the lack of variety. Later, the domestication of livestock reduced the burden of labor for farmers (because of draft animals) and added variety to their diet.)

Microbes Enable Diverse Diets in Humans

In humans, a greater amount and diversity of microbes enable us to eat an omnivorous diet. (Shortform note: If humans can’t digest cellulose, then how and why do we eat plants? Although we can’t digest cellulose like other animals can, we can still extract nutrients from plants by chewing and cooking vegetables and greens. The cellulose, also known as “dietary fiber,” is still important because it passes through the colon and feeds gut microbes that regulate bowel movements.)

Since breaking down plants requires more digestive enzymes, plant-eaters have a much larger microbiome than those who predominantly eat meat. And because humans have a wide array of food options, we’re also able to use them to regulate the microbes in our guts. Yong writes that our microbiome can change drastically within 24 hours, depending on what we eat.

(Shortform note: Although we can survive on many different types of food because of microbes, Michael Pollan’s In Defense of Food presents arguments for why humans benefit from a mostly plant-based diet. He writes that vegetarians tend to be healthier and live longer, and the vitamin C in plants helps eliminate toxic and cancer-causing compounds.)

Microbes and Immune Cells Co-Manage Our Immune System

In addition to enabling food symbiosis, microbes form life-long interdependent relationships with humans by co-managing our immune systems with immune cells. Yong argues that the common conception that the immune system’s primary job is to eliminate “bad microbes” is incomplete. Instead, he describes it as a constant fine-tuning process of keeping microbe populations in a healthy balance. (Shortform note: Some people agree with Yong’s idea that militant metaphors that frame the immune system as battling microbes or diseases (the enemies) are inappropriate because it elicits a sense of shame if the patient “loses the battle.” Some people advocate for a more nuanced “journey” metaphor instead.)

Yong describes three examples of how microbes work together with our immune system to keep us healthy:

1. Bacteriophages regulate microbe populations. Although viruses have a bad reputation for causing illness, most viruses are actually bacteriophages, which infect bacteria, kill them, and re-program them to produce more bacteriophages. They help us keep our microbial populations in balance, and we provide them with a steady supply of bacterial hosts. (Shortform note: Bacteriophages are actually the most abundant life form on the planet. Scientists estimate that there are about a trillion bacteriophages for every grain of sand on Earth.)

2. Beneficial microbes outcompete pathogens. Beneficial microbes help keep the population of pathogens in check by competing with them for food and nutrients. Yong claims that this is why people are often more susceptible to bacterial infections after a dose of antibiotics, when the microbial slate is wiped clean and pathogens have an opportunity to fill the vacuum and overwhelm the immune system. (Shortform note: This is the argument that Gundry makes in The Plant Paradox when he warns against the use of broad-spectrum antibiotics. He claims that it can take up to two years for beneficial microbes to return, and some might never be restored.)

3. Microbes mediate inflammatory responses. Microbes moderate both the timing and scale of immune responses by telling our immune cells what to respond to and when. Some species of microbes trigger pro-inflammatory responses (when the immune system ramps up its activity) when they detect something harmful, like a virus. Other species trigger anti-inflammatory responses when they detect a harmless microbe. Without anti-inflammatory responses, the immune system destroys normal cells and we contract inflammatory conditions like inflammatory bowel disease, asthma, and rheumatoid arthritis.

(Shortform note: T. Colin Campbell and Thomas M. Campbell’s The China Study discusses non-microbial factors associated with inflammatory diseases (also known as autoimmune diseases). These include geography, vitamin D deficiency, viruses, and foods such as cow milk.)

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 of a substance called dissolved organic carbon (DOC), and the bacteria that live on coral consume the DOC, grow exponentially, and essentially suffocate the coral. In other words, the disruption of nutrients in the water causes the microbiome of the coral itself to grow uncontrollably and kill the host organism. Other stressors like pollution and the increasing temperature and acidity of oceans further disrupt the microbiome.

(Shortform note: While Yong only briefly mentions the wide range of factors contributing to coral reef decline, Elizabeth Kolbert’s The Sixth Extinction claims that the driving forces are acidification of the oceans and climate change. As human activity increases the amount of carbon dioxide in the atmosphere, more carbon dioxide dissolves in oceans, and acidity increases. In addition, Kolbert writes that one-third of coral species are at risk of extinction, mostly due to rising water temperatures. She also lists overfishing and agricultural runoff (which both promote fleshy algae growth) as immediate threats. Researchers list numerous other factors contributing to coral reef decline, such as reckless tourism and oil leaks.)

Yong explains that this phenomenon has a snowball effect, as the more coral that dies, the more room there is for fleshy algae to grow. And the more the algae throws the microbial community out of balance, the more vulnerable the coral is to disease and pollution.

Yong’s example of coral reefs shows how the sequence of human activity, declining biodiversity, and a change in the diet of coral bacteria led to the rapid collapse of coral reefs around the world, after hundreds of millions of years of stability.

The Implications of Dying Coral Reefs

Research shows that the loss of coral reefs is a massive threat to biodiversity on Earth. Coral reefs are a key part of oceanic ecosystems and provide food and habitat for over 1 million aquatic species.

So what exactly is the impact of this shrinking biodiversity? Scientists explain that biodiversity is important because all species are interconnected. More diverse ecosystems tend to be more resilient to diseases and are better at adapting to changing conditions. As Robin Wall Kimmerer points out in Braiding Sweetgrass, taking care of other species is not just altruistic but also ensures human survival.

In addition, countless industries, including pharmaceuticals, tourism, agriculture, and construction depend on resources from coral reefs. Economically, the damage to coral reefs translates to an estimated global loss of $375 billion in communities that depend on marine activities.

Sanitized Environments Decrease Microbial Diversity

In addition to the microbial changes that humans cause in nature, Yong also describes the ways that human hygiene habits alter microbial diversity indoors. Although modern sanitation practices have largely eliminated diseases like cholera and typhoid in wealthy countries, Yong explains that our tendency to sanitize things to get rid of germs has led to less diverse microbial communities. This occurs because anti-bacterial cleaning products kill all microbes, even if they’re harmless or beneficial.

Scientists don’t agree on the implications of this phenomenon. Some argue that the benefits of disinfection outweigh the downside of decreased microbial diversity, though Yong points out that there are some contexts where it’s clearly detrimental. For example, despite rigorous cleaning and constant disinfection of surfaces, 5-10% of people who are admitted to the hospital in the US get an infection during their stay. Furthermore, research shows that hospital rooms contain fewer pathogens if windows are open to allow outside air to flow in. Otherwise, the hospital is too sterile with no beneficial microbes to compete with pathogens.

Environments Might Be Too Clean or Not Clean Enough

The study discussed in this section was conducted in Oregon, and the same principle may not apply in other settings with more air pollution. For example, a three-year study in California showed almost 30,000 hospitalizations and ER visits as a result of air pollution. These cases included conditions like asthma and other cardiovascular and respiratory illnesses linked to high levels of particulate matter in the air and high ozone levels. More research is needed in diverse geographic locations and during different seasons to determine if the benefits of outdoor ventilation apply in other contexts.

In addition, Bill Bryson’s The Body points out that inadequate hand-washing in hospital settings leads to over a million infections every year. Therefore, we may be going overboard with sanitation in some ways while still needing improvement in other types of personal hygiene and environmental cleanliness.

Western Lifestyles Alter Microbiomes

In addition to our sanitation habits, Western lifestyles are also drastically changing the gut microbiomes of people living in wealthier, developed countries. Yong cites contributing factors like our changing diet, lower exposure to microbes in our environment, and use of antibiotics. As a result of these factors, many species of microbes that were once ubiquitous in humans are going extinct, leading to a decrease in microbiome diversity. Although scientists don’t agree on the implications of this pattern, Yong suggests it may be responsible for the rise in inflammatory conditions (like allergies, asthma, and inflammatory bowel disease) in Western countries.

(Shortform note: This idea that being too clean is increasing the prevalence of inflammatory conditions in the West is called the “Hygiene Hypothesis.” Researchers have also made this observation in populations in high-income, urban areas within poorer countries. A contributing factor to this phenomenon is the fact that children today spend less time outside (and therefore encounter fewer microbes) than previous generations. Some groups are trying to reverse this trend by increasing access to outdoor learning at school and encouraging unstructured outdoor play.)

How Diets Alter the Microbiome

In terms of diet, Americans eat less fiber than people in less developed countries, and they also eat more processed foods. As mentioned earlier in the guide, a plant-based diet (which is higher in fiber) requires more diverse microbes. Processed foods and saturated fats, on the other hand, nourish less diverse microbes, and Yong writes that these foods also tend to nourish inflammatory microbes—microbes that are associated with the immune system’s overactivity, in conditions like asthma and allergies. Chlorinated water, which kills microbes, is another potential contributing factor to our decreased microbial diversity.

(Shortform: Based on this idea that certain foods disrupt the balance of the microbiome, Gundry’s The Plant Paradox recommends eliminating the following foods from your diet: grains, legumes, corn, soybeans, whole grain foods and other saturated fats, sugars, and artificial sweeteners. He also recommends eating more leafy greens, vegetables, tubers, and omega-3 fats like fish oil and olive oil. Given the challenges of eliminating many common staple foods, others recommend simply eating non-processed foods.)

How Our Environments Alter the Microbiome

In terms of lifestyle, Yong suggests that people in wealthier countries are simply exposed to fewer microbes because they generally spend less time outside and less time around livestock. Yong points to research indicating that even having a dog or cat in the house helps bring in more diverse microbe species that suppress allergies in humans. (Shortform note: Even among scientists who support the Hygiene Hypothesis, there’s a consensus that some types of bacteria and viruses can actually cause allergies and asthma. So while lifestyle is an important factor, especially during childhood, it also doesn’t explain all cases of inflammatory illness.)

How Antibiotics Impact the Microbiome

The third factor Yong describes is the use (or overuse, as he suggests) of antibiotics. At the same time that Westerners are eating food that nourishes less diverse microbes and exposing themselves to fewer wild microbes in the environment, they’re also killing the gut microbes they do have when they take antibiotics.

Like antibacterial cleaning products, antibiotics get rid of microbes indiscriminately. A downside of this is evident in Yong’s example of an intestinal infection called C. difficile (also known as C. diff). This bacterial infection is difficult to get rid of and often occurs as a result of taking antibiotics. (Shortform note: Since the book was published, the US Food and Drug Administration approved the first fecal microbiota therapy for recurring cases of C. diff. The drug is manufactured from human stool samples with microbes that restore balance to the gut microbiome.)

Similar to conflicting opinions on sanitizing our environment, Yong admits that there’s no consensus on how to balance the sometimes life-saving effects of antibiotics with their potentially detrimental effects on the microbiome.

(Shortform note: In addition to the impact of antibiotics on beneficial microbes, Gundry’s The Plant Paradox explains the health risks of ingesting antibiotics by eating meat. He writes that antibiotics in meat can make us resistant to similar antibiotics that we may need to treat diseases, and they also increase our fat storage by disrupting our microbiome.)

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 healthy and nutritious foods, like vegetables and other unprocessed foods, don’t have to advertise their health benefits because it’s common sense. When trying to navigate what foods are good for you, Pollan recommends a simple rule of thumb: sticking with foods that don’t have a health label.)

However, Yong identifies several reasons why evidence for these claims is lacking:

1. Many studies were done in a laboratory setting and on animals, so it’s unclear whether the results are applicable to humans. (Shortform note: To Yong’s point, a study reviewing the last several years of promising research on Lactobacillus included only one study on humans and 25 studies using mice. However, it’s common for researchers to focus on animal models first, so they can easily manipulate variables like genetics. Future research may be able to focus more on clinical trials for humans.)

2. Studies that involved humans were likely skewed because of their small sample size and the fact that the subjects were volunteers (Shortform note: Yong doesn’t explain how the factor of volunteer subjects may have skewed the results, but we can infer that volunteers for a probiotic study may be biased toward perceiving benefits from the probiotics).

3. The number of microbes in a probiotic capsule or yogurt serving is negligible compared to the rest of the microbes in our gut. In other words, it’s a drop in a bucket and therefore won’t make much of an impact. (Shortform note: The problem of quantity may be more relevant for yogurt, as opposed to capsules. Probiotics are usually quantified in terms of colony-forming units (CFUs), and a single serving of yogurt contains an average of 6 billion CFUs while probiotic supplement capsules contain anywhere from 1-50 billion CFUs.)

4. Commercial probiotics, such as Lactobacillus, don’t occur naturally in the human gut. Yong points out studies showing that Lactobacillus fails to colonize the human gut or change the microbiome even after the subjects ate twice-daily servings of probiotic yogurt for seven weeks. (Shortform note: Although Lactobacillus doesn’t colonize the gut, studies suggest that some species can still help alleviate symptoms of lactose intolerance when people eat yogurt products.)

(Shortform note: In addition to probiotic capsules and yogurt, fermented foods like kimchi, kombucha, and kefir are other sources of probiotics that are growing in popularity. In The Art of Fermentation, Sandor Katz explains some of the benefits of eating fermented foods, as well as their historical significance in different regions. He writes that fermenting foods pre-digests nutrients into more accessible forms, increases the vitamin B content of some foods, and detoxifies compounds like pesticide residues on food.)

Yong explains that the EU has even banned the use of the word “probiotic” on food products due to the lack of evidence for its claimed health benefits. However, Yong lists a few specific circumstances when Lactobacillus does have a significant medical effect: shortening infectious diarrhea, reducing the risk of diarrhea from antibiotics, and treating a gastrointestinal disease in infants called necrotizing enterocolitis.

(Shortform note: Despite the EU ban on using the term “probiotic,” several European countries continue to use the term for dietary supplements. France classifies probiotics as a type of food product (containing live cultures of microbes) rather than a health benefit. Other countries have developed their own set of standards for specific strains and required quantities of microbes in probiotic dietary supplements.)

Using Microbes to Prevent and Treat Disease

Rather than using a few commercially popular probiotics with limited health benefits, Yong claims that we can tap the full potential of probiotics by using communities of microbes that are naturally occurring in their hosts. His examples of potentially impactful uses of probiotics include adding bacteria to insects to eradicate malaria and dengue, creating bespoke microbial concoctions for individuals, and engineering physical objects full of beneficial microbes to add to buildings.

Inserting Bacteria Into Insects to Eradicate Diseases

Yong describes how researchers can now use a bacteria called Wolbachia, which is present in about half of all insects, as a way to eradicate diseases such as malaria and dengue. This bacteria provides mosquitos with immunity against the microbes that cause these diseases. Scientists inject the bacteria directly into mosquito eggs and then release the immunized insects which can no longer transmit the disease to humans. In addition, they can pass on this immunity to future generations of mosquitos. Yong argues that this has been a risk-free strategy that greatly benefits human health.

(Shortform note: Some researchers consider this method safer and more cost-effective than other methods of eradicating malaria and dengue. For example, spraying toxic insecticides negatively impacts humans and other beneficial insects. Another strategy is to release sterilized mosquitoes, but this method requires costly annual releases to prevent the population from rebounding. In addition, eradicating a species of mosquito would reduce the number of pollinators in an ecosystem.)

Designing Bespoke Microbial Medicine

Yong also advocates using individualized microbial communities as medicine—that is, tailoring a microbial mix to an individual’s unique ecosystem. He explains that determining which species to use would depend on many factors such as the person’s genes, their microbiome, physical symptoms, mental health, medical history, diet, and living environment. Yong explains that scientists are already working on projects like this and not only selecting microbes for certain jobs, but also engineering specialized microbes that can target specific problems, like cancerous cells and viruses.

(Shortform note: Recent research efforts reveal an additional layer to the complexity of microbial medicine: The profile of the microbiome varies within individuals throughout the course of the day. In one study, researchers identified 15 species of bacteria that can potentially diagnose Type 2 diabetes early on, and they found that oscillations in bacteria during the day versus the night are an important aspect of accurate diagnosis.)

Adding Beneficial Microbes to Physical Objects

Yong’s final example of promising ways to use probiotics is to create physical objects that are teeming with beneficial microbes and add them to places like houses, hospitals, offices, and schools. Yong suggests that this would be a form of preventive medicine that might counterbalance the effects of our anti-bacterial cleaning habits. He cites one scientist who is trying to transform the microbiomes of buildings by integrating small probiotic spheres into walls.

Beneficial Microbes in Farming

In the context of agriculture, farmers are already applying this concept of intentionally adding beneficial microbes to the environment. Some farmers use beneficial microbes as an alternative to insecticides and fungicides to prevent crop diseases, and these soil probiotics also increase soil quality and plant growth.

For example, a commercial product called Effective Microorganisms (EM) includes a community of bacteria, yeast, and fungi in the form of a liquid. EM contains isolated beneficial microbes that are naturally present in organic materials such as compost and manure. Using EM also minimizes the risk of potential pathogens and contaminants that could be present in compost and manure.

In a more DIY method called Korean Natural Farming, you first bury an unsealed container of white rice in the ground to attract beneficial indigenous microbes. Placing the rice near specific plant species such as bamboo attracts the ideal microbes for this process. Once the box is full of mycelium (white fungal threads) you mix the rice with grains (as a medium) and a sugar source like molasses (as food for the microbes). Then, you let the microbes multiply and apply this mixture to your growing area, inoculating the soil with local, beneficial microbes.