Welcome to the Jungle

Human biology is so much grander—and more fragile—than we ever suspected.

There is a jungle of bacteria inside you. Hundreds of species, half of them variable from person to person; most unique to the human gut. We inherit them, largely from our parents, early in life; many of the bacteria in your gut are descended from ones that lived in the gut of an ancestor, tens of thousands of years ago. We have coevolved with our gut bacteria so intimately that we depend on them for essential components of our biology—things you’d be really surprised we can’t do on our own. Half of your functional genome is stored in this mess of biochemistry that’s only loosely under your control, the metagenome. It's an ecosystem as complex as any macroscopic one.

Consider: Bacteria is a whole kingdom of life, and not even in the sense that the “animal kingdom” is a kingdom. The kingdom Eukarya, of which animals are a part, also includes plants, fungi, and all the weird little guys like protozoa. That’s the kind of diversity we’re talking about; two bacteria in your gut can be as different from one another as a salmon is from a pear tree.

In a jungle, you’ve got fungi that turn leaf litter into soil, insects that subsist on the fungi, birds that eat the insects—and eventually die and become ant food. Ferns wafting their spores, fish spawning in the streams, trees producing fruit. Monkeys eating bananas and shitting out the seeds, planting new banana trees. You’ve got leopards eating the monkeys…and maybe, when the leopard takes a shit, it plants the banana tree anyway, from the fruit that was the monkey’s last meal.

Every aspect of every creature in that jungle has a purpose, shaped by millennia of interactions. Birds pick food from between hippos’ teeth. The banana’s seeds have hard coats, to let them pass through the GI tract unharmed. The hot pepper, which has no such seedcoat, has spice in its fruits instead, dissuading all but the birds, who can pass its seeds through unharmed. Even the whining mosquito, which does little besides feed itself and make others sick, plays its part: The diseases it carries keep herbivore populations in check, preventing over-grazing. Too few plants, and the land becomes swampy with rain. Mosquitos proliferate, and whatever’s been eating the plants dies off from disease, or leaves that area for a while to give the plants a chance to grow back. Once the trees start pulling enough water up through their roots, the land dries out a bit, and the mosquito population diminishes.

This is the key feature of the ecosystem: everyone, in feeding themselves, works for someone else in a weird way. And all these interactions and feedback loops seem, as if by magic, to encourage the growth and stability of the jungle as a whole. The source of this magic is the commonality of biology; the fact that we all need basically the same things to thrive, and the fact that anything which is too detrimental to its environment eventually kills itself off.

The oak needs to put a certain amount of carbohydrates into its acorn, to give the sprout a chance to take root. But, unlike fruits, acorns aren’t meant to be eaten—so it produces tannins, to make the acorn bitter and discourage herbivores. They can’t be too bitter, though, or else no squirrel would bother taking them away and stashing them, which is how oaks spread. So the oak strikes a bittersweet balance, knowing that some of its seeds will be eaten—but that this sacrifice gives the ones that survive a chance to grow up far from its shadow. The fact that the squirrel and the seed both need sugars is what enables both the competition and the cooperation. And whether you’re looking at the macroscopic or the microscopic, the story is the same: All these interactions have their analogues in the microcosm of your gut.

A jungle isn’t the trees, or the land, or even the sum of all the species that live in it; it’s the web of interactions among them, and with their environment, which serve to stabilize and propagate the ecosystem.  Your anatomy, your body, the bits you typically think of when I say “human”—that’s the land.

But the jungle, in this analogy, is you.

And taking antibiotics is like burning down the jungle.

Many things will survive, and things will regrow. But it won’t come back quite the same as before. Where you once had a stand of oaks, fast-growing bamboo might take over, the way Clostridium difficile crops up in the wake of a course of antibiotics.

Often, species will go extinct. When this happens, it’s as if a piece of your genome has been deleted; the chain of stewardship of these biological heirlooms, broken. Genes that were present in every single one of your ancestors, stretching back millennia, suddenly gone in less than a week.

If they were important genes, like those that help you assimilate dietary iron, or produce serotonin and other neurotransmitters, things can go very wrong very quickly; there’s a reason that antibiotic use is associated with increased risk of depression, multiple sclerosis, and other diseases.

Existing probiotics can’t replace those missing pieces; nearly all the currently available ones are either Lactobacillus or Bifidobacterium, the occasional Streptococcus. These are like the cats and dogs of the microbial world: pretty safe, good for certain things like keeping the place clear of mice—but such a small component of the biosphere as to be useless in most cases.  If an ecosystem is floundering for a lack of birds or beetles, there’s no breed of dog that can fix the problem.

And because a lot of those important species are found uniquely in human guts, there’s no easy way at present to replace them. (There are ways, and we’ll get into them in later posts, but they’re not pretty and you’ve got to be pretty desperate to try them.)

There’s been a lot of talk in the public health sector about how to discourage people from taking antibiotics when they don’t need to, and these discussions usually center around the nebulous somebody-else’s-problem of rising rates of antibiotic resistance. We need to reframe that discussion: every course of antibiotics is a roll of the dice, which stands a good chance of giving you a chronic, debilitating disease that’s currently incurable. The more we learn about Alzheimer’s, Parkinson’s, schizophrenia, autism—the more it becomes clear that these maladies are the result of treating our internal ecosystem like we’ve treated the external one: carelessly, not recognizing its fragility until one day we look around and go “huh, I haven’t seen a monarch butterfly in a while”.

It's scary—even scarier when you realize that kids born today won’t even know the butterflies are missing, won’t know the beauty that we lost when the milkweed was driven from our fields by agrochemical advancements.

But it’s also the most hopeful hypothesis you’ll ever hear. These diseases might be curable, and the cure might be as simple as a fecal transplant from a healthy person. That’s a hard sell for most people, part of why we need probiotics that represent the microbial equivalents of the birds, bees, and beasts of the jungle.

We are not doomed to ever-rising rates of psychiatric, developmental, and neurodegenerative diseases. There’s a way out, and it starts with recognizing that there’s no such thing as “clean”—only the right kind of dirty. Come along for the ride.