Gut Check

You are born a blank slate, your ecosystems barren. As you emerge, you’re likely swathed in a mix of vaginal juices, dominated by lactobacillus. Your mother’s body is teeming with colonies—each interaction with it is an opportunity to culture your new body. For the next six months, your immune system is depressed to make room for colonization, especially of your digestive system: your gut microbiome.

These bacteria will help you digest and will protect you against pathogens. Your gut goes through what ecologists call succession—successive generations of organisms that settle into a lasting stability. These now-stable ecosystems comprise about half of your body’s cells and over 10,000 species.

In his book I Contain Multitudes: The Microbes Within Us and a Grander View of Life, Ed Yong compares the human body to an archipelago—each body part is an island that contains its own balanced ecosystem. Some of the islands may be inches apart in terms of space (like the large intestines and the vulva), but they’re worlds apart in terms of microbial diversity, with ecosystems as different as jungle, forest, desert.

We are in the age of disintegration, collapse, extinction, loss of diversity. It’s no less true for the invisible ecosystems of our skin, our stomachs, and our noses. For our invisible ecosystems though, the devastation is fueled by modern medicine. Imagine a terrorist on the loose in NYC, says Mark Smith, CEO at Finch Therapeutics, which develops microbiome therapeutics. “Rather than sending out a SWAT team for them, we’re just going to nuke the whole city.” This is the broad-spectrum antibiotic approach. “It’s important, and it saves peoples’ lives, but there’s a lot of collateral damage, and I think we’re really just starting to understand some of the potential consequences of that.”

In one of the most dramatic immediate consequences of antibiotic use, they can leave behind a devastated landscape ripe for an opportunist called C. Difficile. C. Diff is already present in about a third of people, but when the gut ecosystem is disrupted (through sometimes just a single course of antibiotics), it takes over, wracking the body with diarrhea, abdominal cramping, and ultimately kidney failure. The treatment, ironically, is more antibiotics, which sometimes works, but sometimes leaves patients vulnerable and with recurrent reinfections.

The biotic resistance hypothesis in invasion ecology posits that healthy, diverse ecosystems are much less likely to be vulnerable to an invasive species. The places we see these invaders take over without abandon (see kudzu in the Southeastern U.S.) are often those previously disturbed by humans. Holly Jones, associate professor of conservation biology and restoration ecology at Northern Illinois University, says, “As conservation biologists, the goal is to have the most diversity that you could possibly have, so that when your system gets hit by whatever stressor it is—say it’s like a drought or a flood or a fire or whatever—you have species that are adapted to those things.”

So, what if, instead of targeting these “bad guys” of the microbiotic universe, we tried to crowd them out, reintroducing competitors and restoring balance to a heavily disrupted landscape?

J (who prefers her name be left out due to the topic’s sensitivity) was treated with a series of antibiotics for her tick-borne illnesses. J’s body reeled post-treatment with brain fog, low energy, and gastrointestinal problems. So, she decided to try a fecal transplant.

Fecal Microbiota Transplants (FMT) are a controversial treatment, though they have been approved by the FDA for treating the barren, hostile environment of a digestive system in those with C. Diff infections (but they may be helpful for all sorts of health issues). The (over)simplified process is that doctors take fecal matter from someone with a healthy gut ecosystem and put it in the lower intestines of someone with a compromised ecosystem. Reintroducing a healthy gut microbiome with this method was first practiced in Ancient China and continued throughout history in many medicinal approaches. The procedure can be risky (most acutely if the donor has some kind of pathogen) but the payoffs can be enormous—a restoration of healthy intestinal flora.

J told me the treatment helped her “maintain a level of health [she] hadn’t been able to reach before that.” Her energy levels lifted. She had better gastrointestinal functioning. And she had better emotional functioning. It was the most effective treatment she tried for her illness. She’s had to repeat her treatments to continue their benefit (most fecal transplant treatment plans include multiple sessions).

Although J has taken more than many of us, the average Western doctor is quick to prescribe antibiotics, even for lingering upper respiratory infections (often viruses against which antibiotics can’t help). Yong calls antibiotics “shock-and-awe weapons,” which kill bacteria indiscriminately, whether they’re helpful or not. According to research (much of it on mice), digestive flora do rebound after antibiotics (or periods of low fiber, a prebiotic), but some diversity is always lost.

We don’t understand the long-term effects of this loss of diversity, just as we can’t accurately predict the ripple effects of a larger ecology losing a species to extinction.

Our planet is full of patterns, repeated at different scales. The twists and turns of a river flowing to the sea mirror the branching of a fig tree, just as whorls of a tornado or whirlpool can be seen in the spirals of a fern and a shell. This fractal nature, according to Bernard Geiger, who gathers together multidisciplinary fractal research on the website Fractal Institute, can be found in psychology, neurobiology, ecology, and chemistry. The universe itself has some physical fractal structures as well. Our ecosystems are full of tiny ecosystems and are part of larger planetary ecosystems. Carl Sagan even posits that inside one electron on our planet there could be an entire micro-universe that we can’t yet measure and that our entire universe could be enclosed in one electron of a larger universe.

It’s not surprising then that the ecosystems of our bodies show many of the same patterns as larger ecologies and that Western approaches have caused mirrored damage in both of these realms. We wipe out what we see as the “bad guys,” without anything close to a full understanding of the ecosystems, and we are surprised, shocked even, when we create collapse inside the system.

We’ve got our fair share of collapsed ecosystems—due to farming, burning, poisoning, paving, mining. And we’ve got our fair share of opportunists, too. The ecological trauma is not equally devastating to all. But what if we could introduce the equivalent of a transplant to these ecosystems, taking a swath of a healthy ecosystem and reintroducing it to spots we’ve decimated with agriculture or that have taken the brunt of the damage of flooding or fires?

I asked the ecologist Holly Jones about this possibility. Her focus is prairieland, and she told me about a restoration project in Illinois, where the prairie ecosystems have been torn down to build fields of corn, plants that bring money to communities that need it. Often, the land around the railroads was preserved, since the government didn’t allow development near the tracks. So, for one restoration project, the railroad company literally took patches of that land (rich ecosystems in tow) and used land movers to relocate those patches, in order to preserve them and restore nearby countryside. The patches took and transformed the new ecology (albeit costing $45,000 to move the half acre).

There isn’t a lot of research in the inoculation/transfer realm of restoration ecology, but there have been a few other relevant studies. As part of a student’s master’s degree work, ecologists in Canada experimented with inoculating alpine environments with biocrusts.

These combinations of lichens, bacteria, fungi, and bryophytes are essential to allowing alpine ecosystems to recover from trauma. In both greenhouse and field studies, inoculation increased soil surface nitrogen-fixation rates, an essential part of early succession. Although the results varied for different organisms, the inoculation helped most organisms establish themselves in new soil.

And—addressing the need to transform fields that have been stripped by agriculture and abandoned—transferring even one centimeter thickness of soil from healthy ecosystems helps restore degraded farmland. The seeds, nutrients, and organisms in the soil jump start the ecosystem’s natural succession, so that the type of soil used (say grassland vs. tundra) determines the plants and organisms that will grow there.

As someone concerned about the devastation we are causing, it almost gives me a tranquility to think, If we humans are on our way out, what can we do to reverse as much of the damage as possible before we go? Can we make a few stabs at transfers like these and hope the meticulous order and design of niche ecology wins out? Do we throw seed bombs in all the empty lots in our cities? I discussed this with Jones. I wanted her to say we should infect our cities with all the swaths of nature we can collect. I wanted the metaphor to inform us of a strategy, to be the poetic mirror of our bodies. But, she said, focusing on conservation would be her first priority.

Conservation is the only method that preserves the relationships that have evolved to fill every ecosystem’s niche, and we will never understand the complexities of those relationships, nor be able to recreate them with any true likeness—the same as with our guts. But Jones acknowledged that every bit of effort on our way out would help. Yes, seed bombs. Yes, transplanting ecologies and reintroducing species.

Perhaps if it’s developed more, inoculation and transfers could become a quick and dirty way to do our best to copy nature. Sure, when you make a copy of a copy, the images tend to clump up and lose precision—a loss of information. Certain species may not make it through a transfer. And it may be easy to start the early stages of recovery, but building a prairie from scratch won’t bring back bison from thin air. But when our ecosystems have been stripped, we must begin to culture the vacuum in any way we can.