by Andy Gricevich, Newsletter Writer
Microbes have been around since well before the rest of us were a twinkle in evolution’s eye. Unimaginably diverse and adaptively rapid, they’ve found ways to live on and in every conceivable environment, from vents of hot volcanic gas at the ocean’s bottom to the core of ice shelves—and they feed on or make their home inside every living creature. Many plants, animals, and fungi can’t survive at all without the bacteria and viruses they host, and the ones who can are very different without them.
Invisible for so long, microbes have moved powerfully into the public eye. Freed from a longstanding phobia about “germs,” a new science of tiny critters has been exploring uncharted territory. As a young field, it’s full of enticing, hard-to-test theories, as well as good hyphotheses and solid experimental observation. Unsurprisingly, the human microbiome gets a lot of attention, especially with regard to the role of microbes, helpful and hostile, in our immune system.
Microbes populate every surface of our bodies, outnumbering human cells ten-to-one, and each part of us hosts a unique, specialized community. Over millennia, some microbes have helped create a bodily environment that makes us good hosts, and a good host has to stay healthy. As many as 99% of these native bacteria make their home in one major bodily organ, one that we don’t intuitively think of as “outside:” the gut.
THE GUT AS ECOSYSTEM
The gut is more than the stomach; it includes the whole folded tube running from the mouth down through the intestines and the colon. The majority of gut microbes live at the lower end, where—when things are going well—they form complex systems of interrelationships. Such systems are best understood ecologically, in terms of microbial communities.
Both a healthy forest and a thriving salt marsh feature organisms that house and feed all the others (like big trees or large cattail mats), peak predators (wolves or large fish), smaller plants (shrubs, duckweeds), etc. Each ecosystem may feature different species, but there are always the same roles to fill in order to keep the system in balance. A well-functioning gut works in exactly the same way, with a parallel distribution of roles. Different bacteria prefer different foods, and the byproducts of one microbe can be the nourishment of another; their populations are managed by bacteria-eating viruses and other larger microorganisms.
The “ground” of this complex community is the gut lining. The gut is bounded by a very thin layer of cells, protected by a double layer of mucus. The thicker layer, on the inside of the gut tube, is the preferred home for our gut bacteria. The thinner layer is kept mostly unpopulated by antibacterial compounds produced in the adjacent lining. Beyond the lining itself reside seventy percent of our immune cells. When microbes do make it to the inner mucus layer, these cells grab them, pull them through, and perform a genetic analysis to determine whether the organism is friend or foe, distributing that information to the immune system before assaulting the invader with antibodies.
CHALLENGE AND BREAKDOWN
Ideally, our gut contains around fifteen percent hostile microbes, ensuring short-term stresses that keep the system well-informed, responsive and able to return to a normal, relaxed state once a threat has passed; that’s positive inflammation. When the system has to handle too much, for too long, it can get stuck in overdrive, ultimately attacking beneficial microbes and even the body’s own cells. That kind of inflammation often springs from a damaged gut, and it plays a major role in many of the diseases of the “developed world,” including food sensitivities, irritable bowel syndrome, autoimmune disorders, cancer, and even mood disorders.
In a healthy gut, a high population of beneficial or neutral microbes takes up space that could otherwise be filled by hostile organisms. In addition, microbes stay where they belong. A damaged gut lining lets microbes and other particles escape into the bloodstream, where they can overstimulate the immune system. Excess stress, lack of sleep, and overconsumption of alcohol can lead to a leaky gut, but the most damaging factors in modern western society are our overreliance on antibiotics and our diet.
Antibiotics are life-savers, but they’re also prescribed excessively (and often needlessly). These substances (and the antibacterial products we use so enthusiastically) kill microbes indiscriminately, and every dose wipes out some of our native bacteria. Some species may recover from the blow, while others weaken or never return. As space opens up, hostile microbes move in. For example, salmonella infections skyrocket after antibiotic treatment in humans and in heavily medicated livestock. Surviving bacteria can give birth to “super-germs,” resistant to medications, just as herbicides encourage the rise of resistant weeds.
Speaking of herbicides, our food and water supplies are now broadly tainted with glyphosate, the main ingredient in the widely used herbicide Roundup. Glyphosate treats our microbes like weeds, wreaking havoc on our gut. Even without chemicals, our modern diet tends toward poor gut health. What we eat determines which microbes thrive and form our internal communities.
Some of our most valuable microbes are the fiber-digesters, which break down materials we can’t process ourselves; they probably first allowed us to glean significant nutrition from plant foods. As they eat what we can’t, they excrete crucial short-chain fatty acids that reduce inflammation by letting immune cells know they can settle down.
Our fiber-poor diet, rich in processed foods, leaves those microbes hungry, so they feed instead on our thick mucus lining, perforating it so that other bacteria and various particles can pass through. Eventually their population dwindles as they starve.
Of more profound consequence, this situation is heritable. We’re given our foundational microbiome by our mothers, and then it develops as we come into contact with the wider world. Ideally, our immune system learns from exposure to a wide variety of microbes, preparing us for a resilient existence. If we inherit a microbial community that’s already poor in fiber-digesters, and continue with modern dietary practices and chemical exposure, our collective microbiome will be gradually impoverished, and we’ll likely see a continued increase in the health problems that plague our culture.
TOOLS FOR RESILIENCE
To reverse this trend, a good diet is foundational. If we want to maximize the contributions of our microbial partners and minimize our exposure to factors that damage our gut and make room for more pathogens, the basic solutions are pretty simple. Above all, we need to increase our consumption of prebiotics.
Prebiotics are starchy fibers that only our beneficial microbes can digest; harmful bacteria prefer other food sources. We get them from all kinds of fruits and vegetables, including sweet potatoes, barley, flax, bananas, apples, and greens. Particularly beneficial are the vegetables with high amounts of inulin: especially jerusalem artichokes, asparagus, dandelion, burdock, garlic, and onions. These foods give us the basic ground in which a healthy microbiome can take root.
Many otherwise healthy plant foods contain antinutrients, compounds that can interfere with our ability to absorb vitamins and minerals. Lectins in beans and nightshades, as well as tannins and phytates in seeds and nuts, can also damage our gut walls. Traditional processing can help. We can soak beans, seeds, and nuts, and cook tomatoes and peppers, and boil greens and brassicas like broccoli to deactivate or remove antinutrients.
We don’t need to do those things religiously, though. A seasonal diet gives our bodies time to process or flush out antinutrients. It also supports natural cycles of microbial ecology, in which different strains become dominant at different times, providing us with a wider variety of useful byproducts. Organic, fiber-rich foods, changing with the seasons, are the best medicine for our microbiome.
PROBIOTICS
Probiotics are all the rage in the natural foods world. They fall into two basic categories: fermented foods containing live microbial cultures, and supplements composed of a range of potentially beneficial microbes. Probiotics are widely recommended to boost immunity, increase the diversity of gut microbes, and more. Research suggests a range of reliability for these such claims.
It’s often said that the living organisms in products like sauerkraut, yogurt, and kimchi can increase the quantity and diversity of gut flora. Most studies, however, have found that these microbes rarely survive the saliva and stomach acids they encounter on the way to the colon, and claims that we can “repopulate” gut bacteria with probiotics should probably be viewed with skepticism. This doesn’t, however, mean that fermented foods don’t benefit us and our bacterial partners.
Some lactobacillus cultures found in live-culture yogurt have a close relation to our native gut bacteria, and—when present in sufficient quantities, and in some hosts—have been shown to make their way successfully through the digestive system, alleviating diarrhea in the wake of antibiotic treatments and even indicating positive effects on mood and mental clarity. It’s also likely that the bacteria in ferments convey genetic information about microbes outside to our immune system, helping it respond to potential threats and benefits from foreign visitors.
In any case, fermented foods have some definite dietary benefits. Bacteria responsible for fermenting vegetables and milk do work similar to that of our gut flora, digesting compounds we can’t deal with on our own and producing essential nutrients (like certain B vitamins) we can’t access otherwise. Fermentation also reduces or negates antinutrients, and has even been shown to lower pesticide residues. It’s another traditional processing method that makes food more usable and allows us to eat nourishing foods out of season while minimizing the disadvantages of doing so.
Probiotic supplements are based less in tradition than in the cutting edge of microbial science. Conscientious researchers are developing products based on a holistic understanding of bacterial communities, using their knowledge of what organisms can survive in our gut and what effects they have when present in particular proportions. Research is focused on the potential to treat highly specific physiological and psychological conditions with well-formulated cultures.
One exciting area of study concerns soil-based microorganisms, or SBOs. Dirt plays an important role in the development of our native microbiomes. Compared to earlier populations, hunter-gatherers, and traditional farmers, who regularly come into contact with dirt and other animals, our typical microbial communities are much weaker and less diverse (and our soils less alive). Manufacturers of SBO-based supplements try to make up for our lack of exposure by sampling and cultivating microbes from undisturbed soil, and they’re showing some promising results for supporting gut health.
Before purchasing any expensive supplement, we’ll ideally want to do some independent research. Which producers provide the most specific information about the bacterial strains included in their products? What’s solidly known about the effects of different combinations of species when introduced into our gut? It’s a delightfully deep rabbit hole for the curious researcher. Those without the drive to dive into that hole can still stick with tradition.
LIVING IN THE ECOSYSTEM
Though we may want to consult nutritionists, scientists and doctors to help us recover from serious conditions, we can ordinarily cultivate a diverse, strong, well-informed immune system in ways that require no research or complicated dietary plans. Seasonal, produce-heavy diets feed our most desirable bacteria, while also providing essential, immune-supporting antioxidants like those found especially in greens and berries. Fresh, locally grown produce provides diverse microbes (including SBOs); ingesting them helps calibrate our system for our own region.
Time outdoors helps as well. Even in winter, contact with nature exposes us to beneficial microbes of all kinds. We’re used to thinking about cold as inclining us toward illness, but—as long as we’re not freezing—the open air does our microbial community a world of good. One study, conducted in a hospital, found a high number of pathogens inside the sealed building full of antibiotic-dosed patients and sterilized surfaces. Just opening windows for a short time and letting cold outside air in quickly shifted the microbial population indoors toward a more positive state.
Adopting some simple ways of living can bring us more in line with the long-evolved partnership between our microbes and ourselves. We can do a lot to stay well through harsh climates and new strains of flu just by eating well, resting enough, and spending time outside. Our world definitely presents novel threats in the form of chemical exposure and unprecedented stresses. The good news is that microbes change and adapt much more quickly than we do! If we take care of our microbiome, it may help us thrive in circumstances we may feel are changing so fast that we can’t keep up.