Ruminating on Microbes and Enzymes

Everybody eats, large and small.

And, it seems, there may be no such thing as dining alone. As I previously quoted David George Haskell in The Self Is a Society: The fundamental unit of biology is therefore not the "self," but the network. A maple tree is a plurality, its individuality a temporary manifestation of relationship. . . . When we gaze at a maple leaf, we now see not an individual made of plant cells, but a thrumming conversation, an embodied network. The "self" is a society. Eating involves the network.

Consider this section from Haskell's book The Forest Unseen, which I reviewed a couple of posts ago:

Freeing the food locked inside the tough cells of twigs and leaves requires a partnership between the very large and the very small. Big multicellular animals can nip off and chew woody material, but they cannot digest cellulose, the molecule that constitutes most plant matter. Microbes, tiny single-celled organisms such as bacteria and protists, are physically puny but chemically powerful. Cellulose does not give them pause. Thus is born a gang of thieves: animals that walk around and grind up plants, paired with microbes that digest pulverized cellulose. Several groups of animals have independently developed this plan. Termites work with protists in their gut; rabbits and their kin harbor microbes in a large chamber at the end of their gut; the hoatzin, an improbable leaf-eating bird from South America, has a fermentation sac in its neck; ruminants, including deer, have a huge bag of helpers in a special stomach, the rumen.

Microbial partnerships allow large animals to use the vast stores of energy locked up in plant tissues. Those animals, including humans, that have not entered into a deal with microbes are limited to eating soft fruits, a few easily digestible seeds, and the milk and flesh of our more versatile animal cousins. . . .

The rumen functions so well that scientists equipped with the most sophisticated test tubes and vats have not been able to replicate, let alone beat, the growth rate or digestive prowess of the rumen's microbes. The rumen's performance is due to the exquisite biological complexity that thrives in its pampered chambers. A million million individual bacteria of at least two hundred species swim through every milliliter of rumen fluid. Some of these microbes have been described; others await description or discovery. Many of the microbes are found only in rumens. . . .

The diversity of life in the rumen makes possible the complete digestion of the plant remains. No single species can fully digest a plant cell. Each species takes a small part of the overall process, chopping up its favorite molecules, harvesting the energy it needs to grow, and then sending back its wastes to the rumen fluid. These wastes become another creature's food, building a cascading web of disassembly. Bacteria destroy most of the cellulose, aided by some fungi. Protists have a special fondness for starch grains, perhaps regarding them as potatoes to accompany their meal of bacterial sausages. Nutrients in the rumen are passed up a miniature food web, then released back into the rumen's fluid, mimicking the nutrient cycles of larger ecosystems. . . .

As the seasons change, the deer's browsing moves from one part of the plant to another. The woody food of winter will change to springtime greenery, then autumn acorns. The rumen adapts to these changes through the gradual waxing and waning of the members of its community. Bacteria suited to digestion of soft leaves increase through the spring, then taper away in winter. No top-down control by the deer is needed to direct this change; competition among the rumen inhabitants automatically matches the rumen's digestive capabilities to the food available. But sudden changes in diet can disrupt this elegant molding of the rumen community to its environment. If a deer is fed corn or leafy greens in the middle of winter, its rumen will be knocked off balance, acidity will rise uncontrollably, and gases will bloat the rumen. Indigestion of this kind can be lethal. . . .

Nature seldom throws rapid dietary change at ruminants, but when humans feed domesticated cows, goats, or sheep, they must address the rumen's needs. These do not necessarily conform to the desires of human commodity markets, so the rumen's balance is the bane of industrial agriculture. when cows are taken from pasture and suddenly confined to feedlots to be fattened on corn, they must be medicated to pacify the rumen community. Only by stamping down the microbial helpers can we try to impose our will on the cow's flesh.

Keeping that in mind, now consider this article:

How the Western Diet Has Derailed Our Evolution
Burgers and fries have nearly killed our ancestral microbiome.

Scientists suspect our intestinal community of microbes, the human microbiota, calibrates our immune and metabolic function, and that its corruption or depletion can increase the risk of chronic diseases, ranging from asthma to obesity. One might think that if we coevolved with our microbes, they’d be more or less the same in healthy humans everywhere. But that’s not what the scientists observed. . . .

Humans can’t digest soluble fiber, so we enlist microbes to dismantle it for us, sopping up their metabolites. The Burkina Faso microbiota produced about twice as much of these fermentation by-products, called short-chain fatty acids, as the Florentine. That gave a strong indication that fiber, the raw material solely fermented by microbes, was somehow boosting microbial diversity in the Africans.

Indeed, when Sonnenburg fed mice plenty of fiber, microbes that specialized in breaking it down bloomed, and the ecosystem became more diverse overall. When he fed mice a fiber-poor, sugary, Western-like diet, diversity plummeted. (Fiber-starved mice were also meaner and more difficult to handle.) But the losses weren’t permanent. Even after weeks on this junk food-like diet, an animal’s microbial diversity would mostly recover if it began consuming fiber again. . . .

Yet then they saw what happened when pregnant mice went on the no-fiber diet: temporary depletions became permanent losses. . . .

When Sonnenburg put these second-generation mice on a fiber-rich diet, their microbes failed to recover. The mice couldn’t regrow what they’d never inherited. And when these second-generation animals went on a fiberless diet in turn, their offspring inherited even fewer microbes. The microbial die-outs compounded across generations. . . .

what the Sonnenburgs’ experiment suggests is that by failing to adequately nourish key microbes, the Western diet may also be starving them out of existence. They call this idea “starving the microbial self.” They suspect that these diet-driven extinctions may have fueled, at least in part, the recent rise of non-communicable diseases. . . .

Whereas North American microbes orient toward degrading fat, simple sugars, and protein, the microbes of subsistence communities so far studied are geared toward fermenting fiber.

Most study subjects live in the tropics; their microbial communities may reflect tropical environments, not an ancestral human state. Yet even “extinct” microbiomes from higher latitudes—including from a frozen European mummy—are similarly configured to break down plant fiber, adding to the sense that the Western microbiome has diverged from what likely prevailed during human evolution. . . .

Scientists studying these communities suspect that while mortality is high from infectious diseases, chronic, non-communicable diseases are far less prevalent. At the same time, researchers since the late 20th century have repeatedly observed that even in the West, people who grow up on farms with livestock, or exposed to certain fecal-oral infections, like Hepatitis A and sundry parasites—environments that, in their relative microbial enrichment, resemble these subsistence communities—have a lower risk of certain Western afflictions, particularly hay fever, asthma, and certain autoimmune disorders. . . .

Years ago, while still a post-doc, Sonnenburg discovered that something very odd occurs when those MAC-loving microbes go hungry. They start eating mucus. “This is the stage where you say, ‘Oh my God. They’re eating me.’ ” Sonnenburg said. “You can see it.”

We need that mucus. It maintains a necessary distance between us and our microbes. And as it erodes with a poor diet, the lining of the gut becomes irritated. Microbial detritus starts leaking through. One of the more striking discoveries in recent years is that you can see this stuff, called endotoxin, increase in the bloodstream immediately after feeding people a sugary, greasy, fast-food meal. The immune system responds as if under threat, leading to the “simmering inflammation” the Sonnenburgs think drives so many Western diseases. . . .

I came away from Sonnenburg’s office with a sense that I’d glimpsed a principle underlying our relationship with microbes. Wringing calories from wild, fibrous fare required a village—microbes specialized in distinct tasks, but each also dependent on its neighbors. The difficulty of the job encouraged cooperation between microbes. When you withheld fiber, though, you removed the need for that close-knit cooperation. The mutually beneficial arrangements began to fray. . . .

Those environments where a relatively prolific sharing of microbes still occurs—daycares, cowsheds, homes with lots of siblings, and homes with dogs—seem to protect against allergies, asthma, some auto-immune diseases, and certain cancers. These observations, often grouped under the rubric of the “hygiene hypothesis,” appear to highlight a phenomenon separate from diet: access to microbial wealth, and possibly to unique microbial heirlooms. . . .

In short, in case you skimmed: Like ruminants, our stomachs can't digest high-fiber plants, so we rely on microbes in our gut to help out with that. The greater the diversity of microbes, the healthier the digestive community, the healthier the person. The less we "dine alone," the better.

On a somewhat related note, here's something else from The Forest Unseen:

The earthstars and mushrooms that ring the mandala's golf balls may devise a way to digest and recycle the balls' plastic. Fungi are masters of decomposition, so natural selection might produce a plastic-munching mushroom. Stupendous quantities of matter and energy are locked up in plastic. Evolutionary triumph awaits the mutant fungus whose digestive juices can free these frozen assets and conjure them to life. Fungi, and their equally versatile partners in the business of rot, bacteria, have already shown themselves capable of thriving on other industrial innovations such as refined oil and factory effluent. Golf balls may be the next breakthrough.

And an article that just came out:

Scientists Accidentally Create Mutant Enzyme That Eats Plastic Bottles

Scientists have created a mutant enzyme that breaks down plastic drinks bottles – by accident. The breakthrough could help solve the global plastic pollution crisis by enabling for the first time the full recycling of bottles.

The new research was spurred by the discovery in 2016 of the first bacterium that had naturally evolved to eat plastic, at a waste dump in Japan. Scientists have now revealed the detailed structure of the crucial enzyme produced by the bug.

The international team then tweaked the enzyme to see how it had evolved, but tests showed they had inadvertently made the molecule even better at breaking down the PET (polyethylene terephthalate) plastic used for soft drink bottles. . . .

“Enzymes are non-toxic, biodegradable and can be produced in large amounts by microorganisms,” he said. “There is still a way to go before you could recycle large amounts of plastic with enzymes, and reducing the amount of plastic produced in the first place might, perhaps, be preferable. [But] this is certainly a step in a positive direction.”