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So far, scientists have had a limited understanding of actionable mechanisms that are key in the regulation and integrity of complex gut bacterial ecosystems. Still, as research on catalysts of healthy gut flora is booming, the importance of maintaining microbiome health with trophic regulators—such as a rich-in-fiber plant-based diet—is coming into focus. So are implications for the future of medicine in a post-antibiotic era.
The Effect of Antibiotics on Your Gut
When antibiotics were developed, no thought was given to how they might affect the composition of the gut microbiota. Antibiotics were designed to be broad-spectrum, i.e., used for many types of infections, without regard to sparing the good bacteria in our gut. This approach is a counter-intuitive strategy outside of a life or a death situation, as both by cell number and gene number we're more microbial than we are human.
For many years, antibiotics were overused without recognition of the associated costs. We're now on the verge of severe antibiotic resistance cropping up, with challenging pathogens to eradicate. More insidious is the harm done to beneficial commensal resident microbes for 4 to 12 months after each round of antibiotics and a negative effect on immunity and biotransformations.
The microbiota is like a rainforest. It houses an extraordinary, complex, and dynamic ecosystem of microorganisms that are key players in our health, metabolism, and immunity, as well as in disease. Our gut microbes dictate so much of our biology. We now know that we can foster a healthy and resilient ecological community of commensal, symbiotic, and pathogenic microorganisms living together harmoniously inside our gut. And we are just beginning to scratch the surface of how we, the hosts, can naturally manipulate the microbiome to reap immunity-boosting benefits.
Probiotics are usually the first port of call to repopulate the gut microbial community. They can be used to good effect as placeholders while the microbiome is recovering from a shot of antibiotics. And over time, probiotics can change the entire ecosystem to be inhospitable to many existing detrimental bacteria as they pass through the gut. But there are a few caveats. The supplement market isn't properly regulated. There are a lot of poor products—whose content hasn't been verified by reliable, independent organizations like the US Pharmacopeial Convention—which either don't have the viable organisms or species mentioned on their labels or in too negligible quantity. Except Ferring Pharmaceutical's VSL#3, which has 90 times what everything else has—with eight species and 450 billion bacteria—many brands only cover one to five probiotic strains, a drop in the ocean of a gut community that relies upon thousands of different species to thrive.
At any rate, it takes at least a month for good probiotics to proffer their best benefits, with a risk of dependence, to then keep detrimental bacteria in check. A much faster and more profitable route to determine the mix of gut bacteria is controlling the food to sustain it. The capacity of different diets to create different gut microbial equilibriums is well-established in mouse models. Still, the parallel with human biology was unclear until recent studies found that changes in the microbiome can happen within only three or four days of a big shift in what one eats. And researchers not only observed a variation in the abundance of different kinds of bacteria, but in the kinds of genes they were expressing too.
Thanks to advances in nutrigenomics, the scientific study of the interaction of nutrition and genes to prevent and treat disease, we can change how genes express themselves by adapting our lifestyle and diet. The recommendations are based on clever genetic polymorphism testing and health reports that companies like 23andMe and Promethease respectively offer. We're learning that we can boost or down-regulate specific biologic markers from the data. These markers tell us how our body digests fat, how well we inactivate carcinogens and how efficiently we convert folate from dark leafy greens with a diet promoting certain types of gut bacteria genotypes, of which fiber is the centerpiece.
Diet and Gut Microbiota
The population of gut microbes is located in the colon, and the GI tract at large hosts the largest number of immune cells. Unless these gut microbes receive fiber, they can't make essential chemical compounds called short-chain fatty acids (SCFAs) that are signaling molecules for the regulation of the immune system, promoting the growth of T-regulatory cells and soothing inflammation.
But why can't other food groups feed the gut microbes, you ask? For logistic and physiologic reasons. Much of the food we eat in the Western world is laden in simple, refined carbohydrates (sugar), protein and fats, and all of those things get absorbed and digested early on in the upper part of our intestine. They don't make it to the end of the digestive tract, where all gut microbes primarily live. Without fiber-rich foods like whole grains, fruits and vegetables—that the human microbiome is not very good at degrading, thus making its way down to the colon so that our microbes can ferment them and produce the SCFAs—the whole gut microbial community is essentially starving.
People worry about protein deficiency when they should focus on fiber or lack thereof, which sets off a snowball effect with gut microbes forced to cannibalize themselves. When we don't eat enough complex carbohydrates, the bacteria eat away the gut barrier preventing infection known as mucin instead and get closer to the epithelial cells lining the gut. These cells rely on SCFAs—extracted from fiber by the bacteria—for energy, so starving the bacteria is equivalent to starving the epithelial cells in charge of secreting mucin, which impairs its production to regenerate the part that the bacteria have disintegrated. All because of a low-fiber diet.
Different Types of Fiber
Putting an end to this vicious circle is as simple as increasing the number of plants in the diet to an ancestral level. Hunter-gatherer societies consumed 200 grams of fiber daily. Although numbers dropped to a record low of 15 grams a day in our modern world, having a more vegetarian-like diet is a real strength in that respect. The American Gut Project found that vegans, who eat the most fiber and vegetarians the second most significant amount, are much better off than people subscribing to a version of a Paleo diet and end up eating less than the 20 grams of fiber per day recommended by the USDA. As a rule of thumb, we should aim to eat 25 to 30 different plant species each week to get our fiber intake covered.
When it comes to dietary fiber, though, there are two schools of thought: the eat-as-much-fiber-as-you-can camp and the SIBO-(Small Intestine Bacterial Overgrowth) obsessed camp. The latter fails to understand that SIBO comes about when one consumes only one single type of complex carbohydrates. This way of eating inevitably sustains a handful of strain-specific bacteria that are good at metabolizing or fermenting that exact type of fiber and so become very abundant at the expense of other gut microbes. We can largely avoid this issue by increasing the diversity and quantity of soluble or insoluble fiber in the diet, which improves the bacterial profile.
Indeed, to carry the rainforest metaphor outlined earlier further, the microbiome is a micro-ecosystem that constantly changes. There is a very complex interaction between gut microbes and immune cells, linked to each other through energy transfer and nutritional flow. In ecological micro-ecosystems, species are also not independent from each other; most form a "guild" or functional group that grows together and thrives together or declines together. Similarly, different microbial species within the gut form bacterial guilds and the members of a guild increase or decrease, causing a shift in the microbiota.
In nature, micro-ecosystems tend to be more stable when there are many complexities of life on them. Adding new species at a high number leads to an entirely different chain of interactions and ecology flourishing over a certain period. Research suggests the same thing holds for the microbiome. Eating various types of carbohydrates can foster a gut-bacterial community that is more rich and robust. It has to do with how different fiber-rich foods are broken down, a process known as metabolic specialization in the assembly of microbial communities.
We're learning that environmental conditions in our gut influence various metabolic processes whereby different types of fiber—Cellulose, Lignin, Inulin, Pectin, Hexosan, Pentosan and many more—feed different bacteria. Each group of bacteria specializes in metabolizing the fiber into specific and equally critical chemical byproducts like SCFAs rather than all of them. Any dietary intervention at our level should thus aim to influence the microbiome quantitatively and qualitatively, with fiber at the top of the food pyramid.
This content is for informational purposes only and does not substitute for formal and individualized diagnosis, prognosis, treatment, prescription, and/or dietary advice from a licensed medical professional. Do not stop or alter your current course of treatment. If pregnant or nursing, consult with a qualified provider on an individual basis. Seek immediate help if you are experiencing a medical emergency.
© 2022 Camille Bienvenu