Flush

IMAGINE THAT YOU’RE A GIANT short-faced bear living in North America about 20,000 years ago. You would be massive, reaching roughly ten feet in height when standing on your hind legs—no small feat considering that you’d weigh more than a ton. Although paleontologists haven’t fully reconstructed your regular diet, you would likely be an omnivore and devour leafy greens and the carcasses of large animals. And when you shit in the woods? Well, that’s where things get interesting.

Giant short-faced bears, like the continent’s more carnivorous American lions, dire wolves, and saber-toothed cats, were the apex predators in a complex food web during the Pleistocene Epoch. An exotic menagerie of lumbering plant-eaters provided a diverse source of prey. Western camels and large-headed llamas. Long-horned bison and stag-moose with their massive antlers. Harlan’s ground sloths that rivaled the bears in size. Vulnerable young of the Columbian mammoths that towered above them all and swung their curving tusks across most of the continent.

These colossal beasts had diets to match, and their digestive systems transformed the masses of vegetation they consumed into vast piles of manure. When they were eaten themselves, their fats and proteins and other nutrients sustained the lions and wolves and cats. Giant short-faced bears likely sniffed out half-eaten carcasses and helped themselves to the rest, leaving their own scat littered across the landscape.

Plants and trees grew in the fertilized patches, new grazers appeared, and the cycle repeated.

Some 20,000 years later, the process looks rather different for the planet’s second most prolific poopers (after cattle). Many of us send our own output hurtling through a miles-long odyssey from the toilet into a complicated sewer network that connects to a wastewater treatment plant. We screen, filter, and aerate the incoming sewage; digest it with microbes; treat it with chlorine or other disinfectants; and pump the effluent through more pipes until it discharges into a nearby lake or river or sea. We extract the solids and haul much of them off by trucks or trains to be burned in incinerators or buried in landfills.

Modern sanitation is a luxury for much of the world: with a simple flush, our poop disappears. But have you ever wondered what exactly is swirling down the drain? Unlike bears or whales or birds, we expend an inordinate amount of effort to sequester our by-products from the rest of the natural world. And in so doing, we’re effectively wasting one of the planet’s most versatile natural resources.

I know what you’re thinking. Seriously, poop? Yes, the object of disgust, the butt of jokes, the rump of puns—and a dangerous substance to boot—is far more than meets the eye (or nose). To understand what we’re missing out on, though, we need to know why we should care about it, how we make it, and what it contains. One particularly instructive example of why we should give a crap dates back to the heydays of the Pleistocene.

As rocks slowly weather and erode, they release phosphorus into soils, where plant roots can absorb it. Plants use the element—one of the fourteen soil-derived nutrients they require (fifteen if you include cobalt)—to produce and store energy from the sun, and to construct DNA, RNA, and cell membranes. Animals get phosphorus from eating plants and use it to store energy and to make DNA, RNA, membranes, teeth, bones, and shells.

Phosphorus, in other words, is essential for life. To increase its availability, we’ve learned how to mine it and add it to fertilizers. But phosphorus leaches from soils, washes into streams and rivers, and eventually sweeps into the ocean, where it sinks to the bottom and gradually accumulates in sediments. And that presents a big problem: we’ve already tapped most of the accessible deposits and don’t have thousands of years to wait for geological uplifting from the ocean floor to expose more phosphorus-rich rocks. So how else can the element be redistributed to help replenish soils?

Chris Doughty is an earth system scientist who views our planet as one integrated system. In particular, he studies how large-scale ecological patterns such as nutrient cycles are influenced not only by wind, water, and plants, but also by animals. That means he spends a lot of time modeling and calculating how animals help complete the cycling of elements like phosphorus. After taking in nutrients over a lifetime, a bear or whale or elephant can return them to other living things when it dies and its body decomposes. But to Doughty’s surprise, his research has suggested that a much more important contributor—by several orders of magnitude—is the periodic release of nutrient-rich bundles in the form of animal dung. That makes sense when you consider how long and far the producers can roam. For broad distribution by both aquatic and terrestrial fauna, Doughty determined, the bigger the better. “Big animals move more than small animals; they’re key,” he told me. That’s because bigger animals are more likely to move into an area with limited nutrients.

Focusing on Pleistocene megafauna weighing at least ninety-seven pounds, Doughty and colleagues developed a model that suggested they were key players in a complex phosphorus transport chain that moved the element from the deep ocean back up to the vast interior of continents. Whales carried phosphorus from the depths and, upon surfacing to catch their breath, dispersed it in the shallows and across the surface through plumes of floating fecal slurry. Vast flocks of seabirds and schools of migratory fish such as salmon ferried the nutrient to the shore and up rivers and streams. And a succession of carnivores and herbivores completed the relay to forests and plains, mountains, and meadows.

The complex predator-prey interactions created what Doughty and other scientists call “landscapes of fear,” where carnivores relentlessly stalking herbivores kept them both on the move. “That has a huge impact on where they poop and how the elements are incorporated into the ecosystem,” he explained. Over time, the animals re-dispersed phosphorus fairly evenly across the landscape. Those regular deposits, in turn, left behind extensive trails of food for others. Poop, in other words, helped make the living world go ’round.

It still does. Filter-feeding whales in Antarctic waters can convert iron-rich krill into bright orange feces that fertilize the surface for iron-dependent phytoplankton, the microscopic algae that feed a vast array of sea creatures. On the sunbaked African savanna, elephants can disperse seeds up to forty miles from a parent plant and nearly double the amount of soil carbon through their dung, thereby enriching a common grass that feeds other herbivores like gazelles. In North America, research by Canadian ecologist Wes Olson suggests that microbes taken in by a bison’s snuffling nose or mouth help break down the cellulose in grass, while each resulting pile of dung can support more than a hundred insect species. In Beloved Beasts, science journalist Michelle Nijhuis describes the profound impact of this “bison patty ecosystem” and “bison snot ecosystem” on prairies. When bison abounded, the clouds of insects in turn fed a community of birds and small mammals. “Without bison—without bison snot, bison crap, and everything in between—the prairie is a smaller and quieter place,” she writes. It’s no wonder that some researchers call these kinds of habitat-creating animals “ecosystem engineers.”

But Doughty and his collaborators believe a massive die-off of land giants during the Late Pleistocene and early Holocene Epochs—peaking in what other researchers have called “a geologic instant” between 14,000 and 11,000 years ago—decimated the global recycling system. In North America, the collective loss is strikingly apparent at the La Brea Tar Pits in Los Angeles, where I marveled at the jumbles of fossils still being pulled from the bubbling asphalt and reassembled into a ghostly zoo of exquisitely preserved predators and prey. Researchers strongly suspect that human hunters, climate change, or maybe both contributed to these mass extinctions. For the survivors, more recent human roadblocks have sharply limited their ability to travel across ecosystems, whether due to freeways that carve up the habitat of panthers and bison or dams that impede the upstream migration of salmon. As a consequence, Doughty’s group calculated that land mammals in Eurasia, Australia, and the Americas have retained less than 5 percent of their former capacity to distribute nutrients. The nutrient-dispersing ability of whales and migratory fish has plunged as well. “Basically, animals used to be very key conduits of elements across landscapes, and right now they’re not,” Doughty said.

Humans and domestic animals are Earth’s dominant megafauna now. In theory, we’ve taken over many of the ecological roles of the extinct or diminished giants: humans as the carnivores and our livestock as the herbivores. But instead of dispersers, we act as concentrators; animals that no longer live in landscapes of fear tend to poop in the same place. Consequently, the output piles up in some areas and drains from others. Or as Doughty observed, “The rich get richer and the poor get poorer.” Danish businessman and philanthropist Djaffar Shalchi put it even more memorably: “Wealth is like manure: spread it, and it makes everything grow; pile it up, and it stinks.”

Albeit on a smaller scale, we’re not much help in redistributing phosphorus when we die either (it makes up about 1 percent of body mass). Our dead are most often cremated or embalmed and entombed in clusters of wooden or metal boxes. While the nutrients in our poop have mainly ended up in landfills or ocean sediments, those in our remains mainly feed cemetery microfauna or the garden flora that receive a commemorative sprinkling of ashes (the recomposition movement, though, is working to expand the list of beneficiaries).

In her book, Braiding Sweetgrass, Robin Wall Kimmerer writes about how wiingaashk, the sacred sweetgrass of the Anishinaabe Indigenous peoples of North America, can teach us about the necessity and beauty of a balance between taking and giving.

In disrupting ancient cycles, we’re unwittingly dumping vital nutrients where they’re least useful. Whether in life or death, our equilibrium between consumption and production is seriously out of whack. And as the inexperienced arbiters of life in the Anthropocene Epoch, we can create imbalances that have a way of coming back to haunt us. Disorder in our inner ecosystem can harm our health through disease and antibiotic resistance. It shouldn’t be a surprise that on a larger scale the same kind of asymmetries can threaten the health of the entire planet.

Phosphorus, if undeniably vital to Earth’s well-being, is just one of many things that pass through us over a lifetime and retain their utility at the other end. For the giant short-faced bear, the incoming nutrients may have regularly taken the form of a rotting stag-moose or tender greens. I’m far more partial to a medium-rare burger on a sesame seed bun with cheddar cheese, tomato, avocado, and dill pickles from a local burger joint. It may not be the healthiest option, but a burger can provide a useful glimpse into how we as modern omnivores acquire and process a range of carbohydrates, proteins, fats, fibers, vitamins, and minerals from the plants and animals we consume. And just as extinct megafauna have helped us understand how we can disperse useful raw materials over vast distances, more contemporary species are helping us understand how we disassemble complex foods into building blocks that can nourish and harm us, alter the balance of our inner ecosystem, and reshape the flora and fauna all around us.

Digestion really begins when we start grinding up food by chewing it and softening it with enzymes in our saliva. Even here, at the front end of a tube that runs from the mouth to the anus, we still don’t fully understand our inner workings. In 2020, stunned researchers in the Netherlands documented their discovery of a “previously overlooked” set of salivary glands set deep in the back of the throat behind the nose. Their report, in turn, set off a fierce debate about whether nineteenth-century anatomists may have actually discovered the glands and whether they really aid digestion or play a more obscure physiological role. This much we do know: from multiple locations, we can produce up to two wine bottles’ worth of saliva every day. That spit helps us mash up each bite of, say, a sesame seed bun, into a manageable ball, or bolus. Swallowing that compact bolus, in turn, is one of the most complicated actions in the human body. Some experts suggest that about thirty muscle pairs and a half-dozen cranial nerves might be involved, while others say the true number of muscles may be closer to fifty.

Once the bolus moves from the throat into the esophagus, a top-to-bottom contraction of muscles acts like a conveyor belt to carry the mash through a sphincter into the churning vat of acids we know as the stomach. In 1824, a British physician and chemist named William Prout created a stir by isolating hydrochloric acid (also called muriatic acid) from the stomach of a rabbit—the first proof that the gastric juices described by researchers experimenting on animals as varied as kites and bullfrogs contained the potent acid. Prout wrote that he had found the acid “in no small quantity” in the stomach of a hare, horse, calf, and dog.

Nine years later, a US Army surgeon named William Beaumont confirmed Prout’s findings and opened a new window onto the digestive process—literally—when he chanced upon French-Canadian fur trapper Alexis St. Martin. The young man had miraculously survived a grisly musket wound that left him with a hole in his left side that extended into his stomach. Beaumont nursed his patient back to health but then took full advantage of the opening and besieged St. Martin, who became both his live-in servant and his guinea pig, with hundreds of invasive experiments. In one, Beaumont tied multiple pieces of beef, pork, bread, and raw cabbage to a silk string and then coaxed them into the hole in St. Martin’s stomach before fishing them out at regular intervals to time how long it took to digest each morsel. Beaumont’s Experiments and Observations on the Gastric Juice, and the Physiology of Digestion, if a landmark in new gastrointestinal insights, was a low point in medical ethics.

From these and other observations, we know that salivary and pancreatic enzymes, not gastric ones, are responsible for breaking down a bun’s high starch content into sugars like maltose and then glucose, delivering the first burst of energy from a hamburger. White bread lacks many of the nutrients and fiber of wheat’s bran and germ layers, though, which is one reason why it’s often considered a poster child of “empty calories” among dieticians.

Cheddar cheese and ground beef contain abundant calories, too, though almost all in the form of cow-derived proteins and fats. In the stomach, the hydrochloric acid–containing gastric juices begin to denature the proteins like the unfolding of an origami crane. The complicated three-dimensional shapes smooth into simpler forms that can be more easily torn apart. The stomach’s chemicals, in essence, can partially “cook” beef; it’s the same principle behind adding weaker citric acid to milk to form cheese or making ceviche by curing raw fish or shrimp in acidic lime juice.

Cooking our food ahead of time can ease digestion even more. Grilling or frying beef, for instance, can break down proteins like the collagen in connective tissue, making the meat more tender and easier to chew. To understand more about the general physiological process of digestion, a 2007 study used Burmese pythons as human stand-ins (or rather, slither-ins). In the wild, Burmese pythons are solidly in the megafauna category and famous for swallowing things like goats and pigs and even alligators. In a lab at the University of Alabama, sixteen youngsters dined instead on lean eye of round beef from South’s Finest Meats in Tuscaloosa.

For the experiments, the researchers compared the more typical python meal of an adult rat to equivalently sized raw steak, microwaved steak, raw ground beef, and microwaved ground beef. The pythons needed the most energy to digest the raw steak—just as much as they needed to digest the rat. Grinding the meat decreased the digestive energy requirement by about the same amount as cooking it. And the pythons used the least amount of energy to digest beef that was both ground and cooked. We grind meat when we chew it. And for our human ancestors, learning how to outsource more of the digestive effort by cooking meat might have given them an evolutionary leg up on the competition by freeing up more energy for other activities.

Even so, breaking down the fats in beef and cheese requires the additional dissolving power of enzymes made in the pancreas and bile produced by the liver (the latter normally doled out by the gallbladder). Not far from where the stomach empties into the small intestine, the common bile duct and major pancreatic duct converge at a small sphincter that controls the delivery of what German physician and writer Giulia Enders has likened to detergent. “Laundry detergent is effective in removing stains because it ‘digests out’ any fatty, protein-rich, or sugary substances from your laundry, with a little help from the movement of the washing-machine drum, leaving these substances free to be rinsed down the drain with the dirty water,” Enders writes. In the gut, the enzymatic action breaks fats into glycerol and fatty acid building blocks, carbohydrates into simple sugars, and proteins into amino acids to enable their mass absorption into the bloodstream.

Further details of our gastrointestinal tract have come from comparisons with a multitude of lab animals. Pigs, in particular, share similar organ structures and arrangements within the gastrointestinal system, and have become a favored model for intestinal injuries and diseases. In both pigs and humans, the lining of the small intestine is studded with a vast fractal network of villi and microvilli projections that resemble the threads of a shag carpet and collectively act like a huge sponge. Intricate capillaries connected to the villi soak up amino acids, sugars, glycerol, smaller fatty acids, and water-soluble vitamins and minerals, while a mirror web of lymphatic vessels collects larger fatty acids and fat-soluble vitamins. This is how we pluck the nutrients, energy, and building materials we need to fashion our own fats, proteins, and other molecules from liquified food as it flows through the tract.

The regular appearance of undigested food in a stool may suggest that the normally ultra-efficient small intestine is struggling to properly absorb these nutrients. Patients with short bowel syndrome, for example, can lose much of the energy in food through malabsorption, while a foul-smelling and greasy or oily stool may suggest poor fat absorption due to a deficiency in bile or pancreatic enzyme production. Bile can also provide color indicators: after doing its duty to help digest fats, bile’s pigments slowly degrade into a chemical called stercobilin that turns the greenish-yellow intestinal remnants brown on their way toward the exit doors. A rushed departure, though, can prevent the bile from fully breaking down, leaving the output more yellow or green.

In people with lactose intolerance, the small intestine can’t make enough lactase, the enzyme that helps it digest the main sugar in dairy products. Like roughly two-thirds of adults around the world, I’ve become partially lactose intolerant and can get abdominal cramps, gas, and diarrhea after drinking too much milk. People with celiac disease instead mount an abnormal immune response against the gluten protein in wheat, like in that hamburger bun, which can damage the lining of the small intestine and cause either constipation or diarrhea, among other symptoms.

Within the broad range of a typical transit time, about 10 percent of a burger might pass through my stomach within an hour of eating it, while emptying half of it into my small intestine might take upward of two to three hours, on average, and somewhat longer for women. The arrivals to the small intestine might spend another six hours or so wending their way through up to sixteen feet of twists and turns until they reach the large intestine, or colon. And then, through the final five feet of the digestive pathway (shaped like a corkscrew in pigs but a question mark in humans), the pace drops down to a leisurely crawl. That’s a good thing, because the colon has plenty of work to do, such as absorbing some of the remaining minerals like calcium and zinc from the cheddar cheese, breaking down some last bits of food, and regulating the gut’s balance between electrolytes and water.

The colon’s workload, in turn, is made far easier by a dense population of tiny helpers. Based on recent estimates, the trillions of bacterial colonists inhabiting our gastrointestinal tract, mostly in the colon, roughly equal the sum of our own cells. In the human gut, a thriving ecosystem that can support up to several hundred bacterial species—rivaling the complexity of a rain forest—has coevolved with us. This microscopic jungle constantly shifts and adapts in response to what we eat, where we live, whether we’re sick or have taken antibiotics, and other environmental influences. All told, research suggests that several thousand bacterial species have colonized the guts of people around the world.

Scientists have compared the entire community of microbial inhabitants—our inner microbiome—to a “hidden metabolic organ.” So far, they have found that this “organ” aids in tasks like digesting food through breaking down plant fibers and other carbohydrates (like in that avocado and tomato), synthesizing nutrients like vitamin K and all eight B vitamins, and balancing the immune system to recognize genuine external threats without overzealously attacking our own cells. Researchers have linked an out-of-balance microbiome, known as dysbiosis, to everything from inflammatory bowel disease and high blood pressure to diabetes and obesity.

We’re only beginning to understand what the bonanza of bacteria and their products can do, but a few microbial groups have become particularly well-known. The most common genus in both the human gut and human feces in many parts of the world, Bacteroides, feeds its microbial neighbors by breaking down complex carbohydrates and protects us against pathogens; studies have suggested that it’s a major regulator of the human immune system. In the relatively rare instance that it gains access to a vulnerable spot, though, Bacteroides can become an opportunistic pathogen and invade our cells. Escherichia coli is another opportunist. In one form, it’s a relatively benign gut resident that can aid digestion and vitamin production and is a favorite experimental organism of labs like the one where I received my doctoral degree; in more toxic versions, or strains, it can be a deadly assailant that invades through contaminated food or water.

Another widely known genus, Bifidobacterium, includes dozens of species that specialize in fermenting plant fibers and carbohydrates in the gut while those in the genus Lactobacillus release lactic acid as a product of fermenting carbohydrates in foods such as breast milk. By releasing the acid as well as antibacterial peptides and hydrogen peroxide, lactic acid bacteria can aggressively protect their home turf in the gut (and the vagina, where they dominate) by making the surrounding environment inhospitable for pathogenic microbes.

Bifidobacterium and Lactobacillus abound in the infant gut, where they play a critical role in development and infection control. Thousands of years ago, our ancestors learned how to exploit the fermentation strategy used by these bacteria and by yeast cells to convert goat, sheep, camel, cow, horse, and buffalo milk into early versions of kefir and yogurt. Lowering the milk’s pH through fermentation gave the foods a sour but not unpleasant taste while preserving them from spoilage by other microbes. We’ve since branched out to ferment thousands of foods and beverages like kimchi, kombucha, miso, sauerkraut, sourdough, salami, beer, wine, cheese, and some pickles (pickling in acidic brine is a separate process). More natural preservatives are added when the yeast or bacteria produce ethanol and antimicrobial proteins. Many of the fermented foods we love today, in other words, are made with the descendants or variants of microbial specialists that originally thrived in our ancestors’ guts and were expelled in their poop.

When eaten regularly, fermentation expert Robert Hutkins said, the live microbes in fermented yogurts (the focus of most research) can out-compete gut pathogens and shift the balance toward a more favorable intestinal mix by unleashing products that kill off other microbes. They can digest complex fibers and alleviate the gas and bloating from lactose intolerance. Yogurt, Hutkins said, still contains plenty of lactose; the fermenting microbes only consume a fraction of the sugar within each cup. So how does it aid lactose intolerance in those of us who have it? When we eat yogurt, he said, the accompanying microbes effectively supply our small intestine with the missing lactase enzyme and help break the more complex sugar into the more readily absorbed simple sugars glucose and galactose. Little or no intact lactose remains to cause trouble in the large intestine by overfeeding other gas-producing bacteria. Yogurt-derived bacteria contained within a capsule can achieve the same thing if swallowed with a glass of milk.

Perhaps even more impressively, the microbes may help pacify the immune system by continually training it. The immune system regularly conducts friend-or-foe inspections to distinguish between safe and unsafe substances. Incoming fermenters normally pass the test, but by triggering the immune system’s screening process, Hutkins said, they keep it from looking for trouble on its own and inadvertently attacking things it shouldn’t—like the gut.