I Contain Multitudes

“Each of us has our own distinctive microbiome, sculpted by the genes we inherited, the places we’ve lived in, the drugs we’ve taken, the food we’ve eaten, the years we’ve lived, the hands we’ve shaken.” 

Our microbiome is unique and shaped by the world around us. These facts account for why evolution can act on not just us but our bacteria. We are constantly shaping our microbiome with our everyday actions.

“‘The history of warfare always looks more glamorous than accounts of co-operation.’” 

The French scientist Rene Dubos said these words. Yong uses this quote in discussing how much of the history of microbial research was conducted to figure out how to kill microbes, and Dubos was one of few at that time not to view microbes as enemies. This viewpoint was critical in shifting research from killing microbes to learning about them.

“‘The germ free animal is, by and large, a miserable creature, seeming at nearly every point to require an artificial substitute for the germs he lacks,’ wrote Theodor Rosebury. ‘He is as a child might be if we could keep him under glass, entirely protected against the buffest of the outside world.’” 

Germ-free animals are important to studying the impact of microbes on an animal. Germ-free mice and zebrafish are two common lab animals used in these studies. These animals have been critical for the expansion of microbiology.

“I think it’s more accurate to see the immune system as a team of rangers in charge of a national park—as ecosystem managers. They must carefully control the numbers of the resident species, and expel problematic invaders. But here’s the twist: the creatures of the park hired the rangers in the first place. They taught their guardians which species to care for and which to evict. And they’re constantly producing chemicals like PSA that affect how alert and responsive the rangers are.” 

The immune system is more than just a defense system; it actually partakes in more of a balancing act. This act has been carefully crafted over time by our genes and the bacteria that inhabit our bodies. This process is critical to understanding how our immune system functions on a disease level and how bacteria may play a role in determining when we get sick.

“It’s highly unlikely that we’ll come up with a cocktail of probiotics that will treat severe depression. But there’s potential at the milder end of the spectrum. There are lots of people who don’t want to take antidepressants or find therapy to expensive, and if we can give them an effective probiotics, that would be a major advance in psychiatry.” 

It may be an exaggeration to believe that bacteria will be able to solve psychiatric issues or any other health issue. However, there might be a connection between our bacteria and our health. There is a good possibility that we will end up seeing bacteria in healthcare in the future.

“Every symbiosis is, in its degree, underlain with hostility, and only by proper regulation and often elaborate adjustment can the state of mutual benefit be maintained. Even in human affairs, the partnerships for mutual benefit are not so easily kept up, in spite of me being endowed with intelligence and so being able to grasp the meaning of such a relation. But in lower organisms, there is no such comprehension to help keep the relationship going. Mutual partnerships are adaptations and blindly entered into and unconsciously brought about as any others.”

Symbiosis is a neutral act because partnerships involve maintaining a balance. Bacteria and their hosts have their own needs, and those will take priority. If they are not met, hostility can arise.

“I’ve seen the viewpoint that ‘all bacteria 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.” 

Just as the previous quote, this quotation lays out how we have taken symbiosis to be positive, rather than as the neutral term it actually is. Cooperation and harmony are just as present as hostility and disease.

“To begin with, every body part on every species has its own zoological terroir—its unique combination of temperature, acidity, oxygen levels, and other factors that dictate what kinds of microbe can grow there.” 

Each person has a different environment in which to harbor bacteria, which means that the bacteria that live on each of us are different. This difference creates variation on which natural selection can act.

“The immune system’s main function is to manage our relationships with our resident microbes. It’s more about balance and good management than defense and destruction.” 

The immune system isn’t just for defense, but for management and balance of the microbes that are within us. This is crucial for understanding the relationship between our microbes and selves.

“That’s dysbiosis. It’s not about individuals failing to repel pathogens, but about breakdowns in communication between different species—host and symbiont—that live together.” 

Dysbiosis, the opposite of symbiosis, is when our microbes fall into a state of disarray. This can cause a great deal of problems for the host’s health and the health of the microbial ecosystem. 

“The immune system, for all its intricacy, […] works like an ‘immunostat’, which, rather than stabilizing temperature, stabilizes our relationships with our microbes. It manages the benign trillions that live with us, while thwarting invasions by an infectious minority. If it is set too low, it becomes relaxed, missing threats and leaving us open to infections. If it is set to high, it becomes jumpy, falsely attacking our own microbes and triggering chronic inflammation.” 

The immune system defends against infections, but if it reacts too often it will attack not only our own microbes but also non-disease-causing molecules (like peanuts). It can also cause autoimmune disorders when it begins to attack needlessly. The immune system is a system of balance.

“The problem with antibiotics is less their use than their overuse, which both disrupts our microbiome and foments the rise of antibiotic-resistant bacteria.” 

While antibiotics have been highly effective at managing disease, we have come to rely too heavily on them, causing a rise in antibiotic resistance. Even today, we are chasing new compounds to attack the bacteria that we have caused to be resistant to all that we can attack them with.

“But despite his zeal, Eisen practices a modest restraint and recognizes that there is still a phenomenal amount to learn about our microbial companions. And he is concerned that the pendulum of scientific attitudes is swinging from germophobia, where all microbes must be vanquished, toward microbomania, where microbes are heralded as the explanation for—and the solution to—all our ills.” 

Our history with microbes has been one of extremes. Yong argues that finding a medium ground will be the best course of action to understand the role they play in our lives. 

“It’s likely that many symbioses started this way, with random environmental microbes—some parasites and other more benign— that somehow sneaked into animal hosts. Such incursions are common and inevitable. The ubiquity of bacteria means that almost everything we do brings us into contact with new species.” 

Just as random as evolution, symbiosis is typically a random event, too. The meeting of a microbe in a host happens by chance, and these meetings don’t always end in symbiosis. Sometimes the right microbe meets the right host in the right environment, and then symbiosis results. 

“The hologenome idea isn’t necessarily about togetherness and cooperation, as its critics (and some of its proponents) suggest. It merely says that microbes and their genes are part of the picture. They affect their hosts in ways that matter to natural selection, and in ways we can’t ignore when thinking about animal evolution.” 

The hologenome is still a contentious topic in science and will likely remain so until there is a better understanding of how integral bacteria are to our evolution. 

“There’s no denying that microbes help to build the bodies of their hosts, or that they are involved in the most personal aspects of our lives from immunity to smell to behavior, or that their presence can make the difference between health and disease. To me, that is extraordinary enough.” 

Bacteria are influential in the lives of their hosts, no matter how you look at it. Yong suggests that the fact these small, single-celled organisms can have such a large impact on our lives is astounding.

“Time and time again, bacteria and other microbes have allowed animals to transcend their basic animalness and wheedle their way into ecological nooks and crannies that would be otherwise inaccessible; to settle into lifestyles that would be otherwise intolerable; to eat what they could not otherwise stomach; to succeed against their fundamental nature.” 

Bacteria have been influential in our evolution since we were single-celled organisms, and they will continue to be. With their help, we are able to access more variation and more parts of our environment. 

“In other words, microbes shaped the evolution of the mammalian gut, and the shape of the mammalian gut influenced the evolution of microbes.” 

We give our microbes a home, just as our microbes give us additional nutrients or other bits of their genome that we normally would not have access to. We are in a partnership that has lasted generations.

“Excitable journalists sometimes like to claim that HGT challenges Darwin’s view of evolution, by allowing organisms to escape the tyranny of vertical inheritance […] This is not true. HGT adds new variation into an animal’s genome but once these jumping genes arrive in their new homes, they are still subject to good ol’ natural selection.” 

HGT represents a new aspect to Darwin’s evolution that was not previously known. While HGT doesn’t change Darwinian evolution, it does speed up the process of evolution. Natural selection its role, just as it always was. HGT is just a new aspect of evolution. 

“These changes are all fundamentally Darwinian. This point is worth repeating: taking any fast or instant evolutionary shifts as a refutation of the slow, gradual changes we associate with Darwin’s vision is a fatal mistake because these quick shifts are still powered by gradualism.” 

People consider evolution to be a slow-moving process, but that is not always the case. The addition of HGT to the Darwinian toolkit still supports the idea of gradualism; the changes aren’t occurring so rapidly that they refute Darwin.

“The world around us is a gigantic reservoir of potential microbial partners. Every mouthful could bring in new microbes that digest a previously unbreakable part of our meals, or that detoxify the poisons in a previously inedible food, or that kill a parasite that previously suppressed our numbers. Each new partner might help its host to eat a little more, travel a little further, survive a little longer.” 

Symbiosis happens randomly, as does every encounter of new microbes. The partnerships that have lasted eons happened the exact same way and will continue to happen. Only time will tell what microbes we will encounter in the future.

“There is still no clear evidence that probiotics help people with allergies, asthma, eczema, obesity, diabetes, more common types of IBD, autism, or any other disorder in which the microbiome has been implicated. And it’s still not clear if the documented benefits happen because of changes in the microbiome.” 

It is very easy for clinical studies to be manipulated to show correlations or to be conducted using small pools of volunteers. It is important to vet these studies and determine if they are showing a real connection to the disease. Currently, there isn’t a clear connection between these health issues and bacteria. More studies need to be done.

“Yet despite the excessive hype, the concept behind probiotics is still sound. Given all the important roles that bacteria play in our bodies, it should be possible to improve our health by swallowing or applying the right microbes.” 

Conceptually probiotics should work, but concept and practice are worlds away from each other. It will take more time and more science to determine whether probiotics can function successfully.