I Contain Multitudes: The Microbes Within Us and a Grander View of Life

by Ed Yong

As palaeontologist Andrew Knoll once said, “Animals might be evolution’s icing, but bacteria are really the cake.”

For roughly the first 2.5 billion years of life on Earth, bacteria and archaea charted largely separate evolutionary courses. Then, on one fateful occasion, a bacterium somehow merged with an archaeon, losing its free-living existence and becoming entrapped forever within its new host. That is how many scientists believe eukaryotes came to be. It’s our creation story: two great domains of life merging to create a third, in the greatest symbiosis of all time. The archaeon provided the chassis of the eukaryotic cell while the bacterium eventually transformed into the mitochondria.

Most microbes are not pathogens. They do not make us sick. There are fewer than 100 species of bacteria that cause infectious diseases in humans;

They help to digest our food, releasing otherwise inaccessible nutrients. They produce vitamins and minerals that are missing from our diet. They break down toxins and hazardous chemicals. They protect us from disease by crowding out more dangerous microbes or killing them directly with antimicrobial chemicals. They produce substances that affect the way we smell. They are such an inevitable presence that we have outsourced surprising aspects of our lives to them. They guide the construction of our bodies, releasing molecules and signals that steer the growth of our organs. They educate our immune system, teaching it to tell friend from foe. They affect the development of the nervous system, and perhaps even influence our behaviour. They contribute to our lives in profound and wide-ranging ways; no corner of our biology is untouched. If we ignore them, we are looking at our lives through a keyhole.

When microbiologists first started cataloguing the human microbiome in its entirety they hoped to discover a “core” microbiome: a group of species that everyone shares. It’s now debatable if that core exists.18 Some species are common, but none is everywhere. If there is a core, it exists at the level of functions, not organisms. There are certain jobs, like digesting a certain nutrient or carrying out a specific metabolic trick, that are always filled by some microbe – just not always the same one. You see the same trend on a bigger scale. In New Zealand, kiwis root through leaf litter in search of worms, doing what a badger might do in England.

Speaking of palms, your right hand shares just a sixth of its microbial species with your left hand.19 The variations that exist between body parts dwarf those that exist between people. Put simply, the bacteria on your forearm are more similar to those on my forearm than to those in your mouth.

When each baby is born, it leaves the sterile world of its mother’s womb and is immediately colonised by her vaginal microbes; almost three-quarters of a newborn’s strains can be traced directly back to its mother. Then follows an age of expansion. As the baby picks up new species from its parents and environment, its gut microbiome becomes gradually more diverse.

Many conditions, including obesity, asthma, colon cancer, diabetes, and autism, are accompanied by changes in the microbiome, suggesting that these microbes are at the very least a sign of illness, and at most a cause of it.

When we look at the animal kingdom through a microbial lens, even the most familiar parts of our lives take on a wondrous new air. When a hyena rubs its scent glands on a blade of grass, its microbes write its autobiography for other hyenas to read. When a meerkat mother breastfeeds its pups, it builds worlds within their guts. When an armadillo slurps down a mouthful of ants, it feeds a community of trillions that, in turn, provide it with energy. When a langur or human gets sick, its problems are akin to a lake that’s smothered by algae or a meadow that’s overrun with weeds – ecosystems gone awry. Our lives are heavily influenced by external forces that are actually inside us, by trillions of things that are separate from us and yet very much a part of us. Scent, health, digestion, development, and dozens of other traits that are supposedly the province of individuals are really the result of a complex negotiation between host and microbes.

Knowing what we know, how would we even define an individual?25 If you define an individual anatomically, as the owner of a particular body, then you must acknowledge that microbes share the same space. You could try for a developmental definition, in which an individual is everything that grows from a single fertilised egg. But that doesn’t work either because several animals, from squids to mice to zebrafish, build their bodies using instructions encoded by both their genes and their microbes. In a sterile bubble, they wouldn’t grow up normally. You could moot a physiological definition, in which the individual is composed of parts – tissues and organs – that cooperate for the good of the whole. Sure, but what about insects in which bacterial and host enzymes work together to manufacture essential nutrients? Those microbes are absolutely part of the whole, and an indispensable part at that. A genetic definition, in which an individual consists of cells that share the same genome, runs into the same problem. Any single animal contains its own genome, but also many microbial ones that influence its life and development. In some cases, microbial genes can permanently infiltrate the genomes of their hosts. Does it really make sense to view them as separate entities? With your options running out, you could pass the buck to the immune system, since it supposedly exists to distinguish our own cells from those of intruders, to tell self from non-self. That’s not quite true, eit...

Individual Definition

As historian Douglas Anderson later wrote, “Almost everything he saw, he was the first human ever to see.” And more to the point, why did he look at the water in the first place? What on earth possessed this man to scrutinise rain that had collected in a pot? A similar question could be asked of many people throughout the entire history of microbiome research: they were the ones who thought to look.

Leehuwenhoek

The narrative of disease and death still dominates our view of microbiology.

In 1994, after her first wave of squid studies was complete, she wrote, “The results of these studies are the first experimental data demonstrating that a specific bacterial symbiont can play an inductive role in animal development.” In other words, microbes sculpt animal bodies.

The weird biology of germ-free animals is most obvious in the gut. A well-functioning gut needs a big surface area for absorbing nutrients, which is why its walls are densely lined with long, finger-like pillars. It needs to constantly regenerate the cells at its surface, which get sloughed off by the passing tide of food. It needs a rich network of underlying blood vessels to carry nutrients to and fro. And it needs to be sealed – its cells must stick tightly to each other to prevent foreign molecules (and microbes) from leaking into those blood vessels. All of these essential properties are compromised without microbes. If zebrafish or mice grow up in the absence of bacteria their guts don’t develop fully, their pillars are shorter, their walls leakier, their blood vessels look more like sparse country lanes than a dense urban grid, and their cycle of regeneration pedals in a lower gear. Many of these glitches can be rectified simply by giving the animals a normal complement of microbes or even isolated microbial molecules.6 The bacteria don’t physically reshape the gut themselves. Instead, they work via their hosts. They are more management than labour.

In other words, the microbe told the mice how to use their own genes to make a healthy gut.

Why? Why have animals effectively outsourced parts of their development to other species? Why not just do everything in-house? “I think it’s unavoidable,” says John Rawls, Who has worked with germ-free mice and squid. “Microbes are a necessary part of animal life. There’s no getting rid of them.” Remember that animals emerged in a world that had already been teeming with microbes for billions of years. They were the rulers of the planet long before we arrived. And when we did arrive, of course we evolved ways of interacting with the microbes around us. It would be absurd not to, like moving into a new city wearing a blindfold, earplugs, and a muzzle. Besides, microbes weren’t just unavoidable: they were useful. They fed the pioneering animals. Their presence also provided valuable cues to areas rich in nutrients, to temperatures conducive to life, or flat surfaces upon which to settle. By sensing these cues, pioneering animals gained valuable information about the world around them. And as we shall see, hints of those ancient interactions still abound today.

This tells us that an animal’s genome doesn’t provide everything it needs to create a mature immune system. It also needs input from a microbiome.

Take inflammation: a defensive response, where immune cells rush to the site of an injury or infection, leading to swelling, redness, and heat. It’s important for protecting the body against threats; without it, we’d be riddled with infections. But it becomes a problem if it spreads throughout the body, lasts too long, or launches at the slightest provocation: that leads to asthma, arthritis, and other inflammatory and autoimmune diseases. So, inflammation must be triggered at the right time, and controlled appropriately. Suppressing it is as important as activating it. Microbes do both. Some species stimulate the production of hawkish pro-inflammatory immune cells, while others induce dove-like anti-inflammatory cells.24 Between them, they allow us to react to threats without overreacting. Without them, this balance disappears, which is why germ-free mice are prone to both infections and autoimmune diseases: they can neither mount an appropriate immune response when one is needed, nor fend off an inappropriate one during quieter times.

At the very least, Patterson and Mazmanian showed that tweaking a mouse’s gut microbes – or even a single microbial molecule, 4EPS – could change its behaviour. So far, we have seen that microbes can influence the development of guts and bones, blood vessels and T cells. Now we’ve seen that they can sway the brain too – the organ that, more than any other, makes us who we are. It is a disquieting thought. We put such a premium on our free will that the prospect of losing independence to unseen forces informs many of our deepest societal fears. Our darkest fiction is full of Orwellian dystopias, shadowy cabals, and mind-controlling supervillains. But it turns out that the brainless, microscopic, single-celled organisms that live inside us have been pulling on our strings all along.

Collins then worked with two common strains of lab mice, one of which is naturally more timid and anxious than the other. If he colonised germ-free versions of the bolder strain with microbes from the timid strain, they became more timid themselves. The opposite was also true: germ-free versions of the timid mice were emboldened by the microbes of their more intrepid cousins. It was as dramatic a result as Collins could have hoped for: by swapping the bacteria in the animals’ guts, he had also swapped part of their personalities.

So it was important that John Cryan and Ted Dinan from the University of Cork in Ireland found similar results, but in normal mice with complete microbiomes. They worked with the same strain of timid mice that Collins studied, and managed to change the animals’ behaviour by feeding them with a single strain of Lactobacillus rhamnosus – a bacterium commonly used in yoghurts and dairy products. After the mice ingested this strain, known as JB-1, they were better able to overcome anxiety: they spent more time in the exposed parts of a maze, or the centre of an open field. They were also better at resisting negative moods: when dropped into a bottle of water, they spent more time paddling away than floating aimlessly.42 These kinds of test are commonly used to test the effectiveness of psychiatric drugs, and JB-1 was behaving rather like substances with anti-anxiety and antidepressant properties. “It was like the mice were on low doses of Prozac or Valium,” says Cryan.

From your perspective, choosing the right item on a menu is the difference between a good meal and a bad one. But for your gut bacteria, the choice is more important. Different microbes fare better on certain diets. Some are peerless at digesting plant fibres. Others thrive on fats. When you choose your meals, you are also choosing which bacteria get fed, and which get an advantage over their peers. But they don’t have to sit there and graciously await your decision. As we have seen, bacteria have ways of hacking into the nervous system. If they released dopamine, a chemical involved in feelings of pleasure and reward, when you ate the ‘right’ things, could they potentially train you to choose certain foods over others? Do they get a say in your menu picks?48

there is no such thing as a “good microbe” or a “bad microbe”. These terms belong in children’s stories. They are ill-suited for describing the messy, fractious, contextual relationships

These principles are easy to forget. We like our black-and-white narratives, with clear heroes and villains. In the last few years, I’ve seen the viewpoint that “all bacteria must be killed” slowly give ground to “bacteria are our friends and want to help us”, even though the latter is just as wrong as the former. We cannot simply assume that a particular microbe is “good” just because it lives inside us. Even scientists forget this. The very term symbiosis has been twisted so that its original neutral meaning – “living together” – has been infused with positive spin, and almost flaky connotations of cooperation and harmony. But evolution doesn’t work that way. It doesn’t necessarily favour cooperation, even if that’s in everyone’s interests. And it saddles even the most harmonious relationships with conflict.

in South America, acacia trees rely on ants to defend them from weeds, pests, and grazers. In return, they give their bodyguards sugary snacks to eat and hollow thorns to live in. It looks like an equitable relationship, until you realise that the tree laces its food with an enzyme that stops the ants from digesting other sources of sugar. The ants are indentured servants. All of these are iconic examples of cooperation, found in textbooks and wildlife documentaries. And each of them is tinged with conflict, manipulation, and deceit.

Acacia

“We need to separate important from harmonious. The microbiome is incredibly important but it doesn’t mean that it’s harmonious,” says evolutionary biologist Toby Kiers.15 A well-functioning partnership could easily be seen as a case of reciprocal exploitation. “Both partners may benefit but there’s this inherent tension. Symbiosis is conflict – conflict that can never be totally resolved.”

Just think about your gut. It’s a long and heavily folded tube that, if spread out fully, would cover the surface of a football field.

Take the mammalian gut. The mucus that covers it comes in two layers: a dense inner one that sits directly on top of the epithelial cells, and a loose outer one beyond that. The outer layer is full of phages, but it’s also a place where microbes can anchor themselves and build thriving communities. They abound here. By comparison, very few of them exist in the dense inner layer. That’s because the epithelial cells liberally spray this zone with antimicrobial peptides (AMPs) – small molecular bullets that take out any encroaching microbes. They create what Lora Hooper calls a demilitarised zone: a region immediately in front of the lining of the gut, where microbes cannot settle.25 If any microbes successfully weave their way through the mucus, run the gauntlet of phages and AMPs, and sneak through the epithelium, there’s a battalion of immune cells on the other side to swallow and destroy them. These cells aren’t just sitting around, waiting for the worst to happen. They are surprisingly proactive. Some reach through the epithelium to check for microbes on the other side, as if feeling around through the slats of a fence. If they find bacteria in the demilitarised zone, they capture them and bring them back across. By taking these prisoners, the immune system gets regular intel about the species that dominate the mucus, and can prepare antibodies and other appropriate countermeasures.

To many scientists, however, warding off pathogens is just a bonus trick. The immune system’s main function is to manage our relationships with our resident microbes. It’s more about balance and good management than defence and destruction.

Immune system more about microbe management than fighting off attacks

Think back to the previous chapter, in which I portrayed the immune system as a team of rangers carefully managing a national park. If microbes breach the park’s fences – the mucus – the rangers push them back and fortify the barrier. They cull any species that becomes too dominant in the park, and they chuck out any pathogens that invade from the outside world. They keep equilibrium within the community, and constantly defend this balance from threats both foreign and domestic. The rangers only get time off at the very start of our lives, when in microbiological terms we are blank slates. To allow our first microbes to colonise our newborn bodies, a special class of immune cells suppresses the rest of the body’s defensive ensemble, which is why babies are vulnerable to infections for their first six months of life.30 It’s not because their immune system is immature, as is commonly believed: it’s because it is deliberately stifled to give microbes a free-for-all window during which they can establish themselves.

Human breast milk stands out among that of other mammals: it has five times as many types of HMO as cow’s milk, and several hundred times the quantity. Even chimp milk is impoverished compared to ours. No one knows why this difference exists, but Mills offers a couple of good guesses. One involves our brains, which are famously large for a primate of our size, and which grow incredibly quickly in our first year of life. This fast growth partly depends on a nutrient called sialic acid, which also happens to be one of the chemicals that B. infantis releases while it eats HMOs.

Every time scientists have pitted a pathogen against cultured cells in the presence of HMOs, the cells have come out smiling. This helps to explain both why breast-fed babies have fewer gut infections than bottle-fed ones and why there are so many HMOs.

They have already found something weird: phages are great at sticking to mucus, but they do so ten times more efficiently if there’s breast milk around. Something in the milk helps them anchor in place.

It means that the measures by which we shape and control our microbiome – the phages, the mucus, the various arms of the immune system, and the ingredients in milk – are all connected. I’ve discussed them as if they were separate tools, but they are all part of a huge interwoven system for stabilising our relationships with our microbes. In this counter-intuitive reality, viruses can be allies, immune systems can support microbes, and a breastfeeding mother isn’t just feeding a baby but also setting up an entire world. And breast milk? German was right: it’s far more than a bag of chemicals. It nourishes baby and bacteria, infant and infantis alike. It’s a preliminary immune system that thwarts more malevolent microbes. It is the means by which a mother ensures that her children have the right companions, from their first days of life.39 And it prepares the baby for life ahead.

Next, the team showed that obese people (and mice) have different communities of microbes in their guts.10 The most obvious difference lay in the ratio of the two major groups of gut bacteria: obese people had more Firmicutes and fewer Bacteroidetes than their leaner counterparts. This raised an obvious question: does extra body fat tilt the Bacteroidetes/Firmicutes see-saw or, more tantalisingly, does the tilt make individuals fatter? The team couldn’t answer that question by relying on simple comparisons. They needed experiments. That’s where Peter Turnbaugh came in. Then a graduate student in the lab, he harvested microbes from fat and lean mice, and then fed them to germ-free rodents. Those that got microbes from lean donors put on 27 per cent more fat, while those with obese donors packed on 47 per cent more fat. It was a stunning result: Turnbaugh had effectively transferred obesity from one animal to another, simply by moving their microbes across.

Connection between gut bacteria and obesity

So, when obese communities colonised lean guts, they found that every morsel of food was already being devoured and every niche had been filled. By contrast, when the lean communities entered obese guts, they found a glut of uneaten fibre – and flourished. Their success only evaporated when Ridaura fed the mice with fatty, low-fibre chow, designed to represent the worst extremes of the Western diet. Without fibre, the lean communities couldn’t establish themselves or stop the mice from putting on weight. They could only infiltrate the guts of mice that ate healthily. The old dietary advice still stands, overenthusiastic headlines be damned.

The hypothesis, as it now stands, contends that children in developed countries no longer run the gauntlet of infectious diseases that they used to, and so grow up with inexperienced, jumpy immune systems.21 They are healthier in the short term, but they launch panicked immune responses to harmless triggers, like pollen. This concept delineated an unenviable trade-off between infectious and allergic disease, as if we were destined to suffer one or the other. Later versions of the hygiene hypothesis shifted the emphasis away from pathogens and more towards benevolent microbes that educate our immune systems, or environmental species that lurk in mud and dust, and even parasites that establish long-lasting but tolerable infections. They have been christened ‘old friends’.22 They have been part of our lives throughout our evolutionary history, but their tenure has become shakier of late. Their disappearance isn’t just due to stricter personal cleanliness, as the word ‘hygiene’ unhelpfully implies. It’s also due to the various trappings of urbanisation: smaller families; a move from muddy countryside to concrete cities; a preference for chlorinated water and sanitised food; and a growing distance from livestock, pets and other animals. All of these changes have been consistently linked to a higher risk of allergic and inflammatory diseases, and all of them reduce the range of microbes that we are exposed to. A single dog can have a huge effect. When Susan Lynch hoovered up the...

Allergies. Having a pet give kids stronger microbiomes

But pets are not our most important sources of old microbial friends. That honour goes to our mothers. When babies emerge from the womb they are colonised by mum’s vaginal microbes – an endowment that creates chains of transmission which cascade through generations. This, too, is changing. Around a quarter of babies in the UK and a third of those in the USA are now born by Caesarean section, many of which are elective. Maria Gloria Dominguez-Bello found that if babies are born through a cut in their mother’s abdomen, their starter microbes come from her skin and the hospital environment, instead of her vagina.24 It’s not clear what these differences mean in the long term, but just as an island’s first colonists influence the species that eventually settle upon it, the effects of a child’s first microbes could ripple through future communities. This might explain why C-section babies are more likely to develop allergies, asthma, coeliac disease, and obesity later in life.

What are the consequences of c sections?

“if you go for a C-section and bottle-feeding, I’d certainly say that [your baby] is on a different trajectory,” says milk expert David Mills. Once we are weaned onto solids, that trajectory can veer even further astray if we fail to feed our microbial friends with the right foods. Saturated fats can nourish inflammatory microbes. So can two common food additives, CMC and P80, used to lengthen the shelf life of ice cream, frozen desserts, and other processed foods; they also suppress anti-inflammatory bugs.25 Dietary fibre has the opposite effects. This is a catch-all term for various complex plant carbohydrates that our microbes can digest.

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Without fibre, we dial our immunostats to higher settings, predisposing us to inflammatory disease. To make matters worse, when fibre is absent, our starving bacteria react by devouring whatever else they can find – including the mucus layer that covers the gut.

Regularly eating fiber is so important

Lack of fibre also reshapes the gut microbiome. As we have seen, fibre is so complex that it creates openings for a wide range of microbes with the right digestive enzymes. If those openings close for long enough, the pool of applicants shrinks. Erica Sonnenburg, Justin’s wife and colleague, demonstrated this by putting mice on a low-fibre diet for a few months.28 The diversity in their gut microbiome crashed. It rebounded when the mice ate fibre again, but not fully; many species had gone AWOL and never returned. When these mice bred, they gave birth to pups that started off with a slightly impoverished microbiome. And if those pups ate more low-fibre food too, even more microbes fell off the radar. As the generations ticked by, more and more old friends broke contact. This could explain why Westerners carry a much lower diversity of gut microbes than rural villagers from Burkina Faso, Malawi, and Venezuela.29 We not only eat fewer plants, we also heavily process the ones we do eat. For example, the milling process that converts wheat into flour removes most of the fibre in the kernels. We are, in the words of the Sonnenburgs, “starving our microbial self”.

Impoverished gut microbiomes (from lack of eating enough fiber) can be inherited!!

But antibiotics are shock-and-awe weapons. They kill the bacteria we want as well as those we don’t – an approach that’s like nuking a city to deal with a rat.

Antibiotics

even short courses of antibiotics can change the human microbiome. Some species temporarily disappear. The overall diversity plummets. Once we stop taking the drugs, our communities bounce back to something that’s largely, but not entirely, like their original state. As in Sonnenburg’s fibre experiment, each knock leaves the ecosystem slightly dented. As more knocks land, the dents deepen.

Ironically, this collateral damage can pave the way for more disease. Remember that a rich, thriving microbiome acts as a barrier to invasive pathogens. When our old friends vanish, that barrier disappears. In their absence, more dangerous species can exploit the uneaten nutrients and ecological vacancies that remain.

Killing bacteria actually puts you at MORE risk of infection

It is the unintended consequence of an indiscriminate approach to killing microbes, akin to blitzing a weed-infested garden with pesticides and hoping that flowers will grow in their stead; often, you just get more weeds.

Even subtler doses of antibiotics can have unforeseen consequences. In 2012, Martin Blaser gave antibiotics to young mice, at doses too low to treat any disease. Still, the drugs changed the rodents’ gut microbes, fostering communities that were better at harvesting energy from food. The mice became fatter.

This tells us a couple of important things. First, there’s a critical window in early life during which antibiotics can have particularly potent effects. Second, those effects depend on changes in the microbiome, but endure even when it largely returns to normal. The second point is important; the first is arguably old news. Farmers have been inadvertently doing the same experiment since the 1950s, by fattening their livestock with low doses of antibiotics. No matter the drug or the species, the result is always the same: the animals grow faster and end up heavier. Everyone knew that these “growth promoters” worked but no one really understood why. Blaser’s work suggests one possible explanation: the drugs disrupt the microbiome, leading to weight gain.

Much of modern medicine is built upon the foundations that antibiotics provide, and those foundations are now crumbling. We have used these drugs so indiscriminately that many bacteria have evolved to resist them, and some nigh-invincible strains can now shrug off every medicine we throw at them.36 At the same time, we have utterly failed to develop new drugs to replace the ones that are becoming obsolete. We are heading into a terrifying post-antibiotic era.

The problem with antibiotics is less their use than their overuse, which both disrupts our microbiome and foments the rise of antibiotic-resistant bacteria. The solution is not to demonise these drugs but to deploy them judiciously, in situations when they are actually needed and in full knowledge of the risks and benefits.

We have taken cleanliness to mean a world without microbes, without realising the consequences of such a world. We have been tilting at microbes for too long, and created a world that’s hostile to the ones we need.