It's been 34 years since I graduated from medical school, so I’ve seen quite a few ideas come and go. In my opinion, the two most exciting advances in our understanding have been the discovery of the microbiome and of epigenetics.
We now know that bodies change on a daily or even hourly basis via processes that are potentially reversible: the modification of gene expression (epigenetics), and the modification of a factory of organisms living within us. This collection of microscopic organisms is called “microbiota.” The collection of all their genetic material is the “microbiome.” Estimates are that 30-50% of the substances circulating in our bloodstream are made by bacteria. HOW DISEASE DEVELOPS These minute-to-minute changes in our gene expression and microbiota, if they keep going in the same direction over time, result in the symptoms of a variety of conditions. To the extent these changes are reversible, the array of symptoms they result in, which we call “diseases,” are also reversible, unless much damage has been done. This may be easier to understand for anyone who has tried to tend a garden: the same plant in two different spots, say one with direct sun, and one in the shade, will look entirely different. If you notice this within a few weeks of putting your plant in the ground, you can move the plant and save it. If you wait too long, the plant may not survive. It’s easy to see in plants because they have “continuous embryogenesis,” that is, they never stop developing. It’s harder to see in humans because we look fairly unchanged from the outside. But on the inside, our immune system and endocrine system set the tone best suited to the moment. What tells our immune system what the tone should be? It’s done by turning certain genes on , and other genes off. This is also known as modification of gene expression (our genes as well as microbial genes). The signals come from our changing gut bacteria, the food we eat, the activities we engage in, how much sleep we get, the events that occur in our lives and how we interpret them in light of everything that has come before, and the impact of toxins from the environment. Each of these affects all other aspects, and each impacts gut bacteria, which as I just remarked, make 30-50% of the substances in our blood: these substances get to work changing the immune and metabolic characteristics in ways we are barely beginning to understand. Thus the task is to get to the root cause of a problem in order to reverse this problem. We target diet, exercise, sleep, stress, events, and toxins, and in turn that modifies our gut bacteria. Much of conventional medicine uses medications meant to modify our own biochemistry, and that has proven quite useful, but too often does not restore us back to a state of health. HOW TO IMPROVE GUT BACTERIA So the question is how to impact our microbiota, given that they have such broad impacts. Clearly, diet, stress reduction, exercise, sleep, and toxin exposure will play a role. A recent article by leading gut researchers at Stanford (see article by Wastyk et. al. below), including Erika and Justin Sonnenburg, describes a 10 week intervention where subjects were instructed to either double the amount of fiber in their diet, or drastically increase their intake of fermented foods. The researchers thought that if they could modify the microbiota, they might find improvements in the immune system and metabolic markers (glucose regulation for example, or blood pressure and cholesterol). To their surprise, adding fermented foods worked much better overall than increasing fiber. Their conclusions were that too many people don’t have a good enough microbiome (the bacteria in their gut between them do not have enough genes) to make proper use of the added fiber. A few people in the study were indeed able to make use of the fiber (as evidenced by whether there were undigested carbohydrates in their stool, or not) and those people got an anti-inflammatory boost from the fiber. However, in the fermented food section of the study, 10 weeks was sufficient to improve microbiota diversity. The new bacteria acquired were not mostly from the fermented foods themselves. They were from elsewhere in the environment, but the fermented foods were somehow able to help them thrive. The subjects in the study consumed about 6-7 portions of fermented foods each day. One portion is equivalent to 6 oz of kefir, yogurt, fermented cottage cheese, 1/4 cup of kimchi or sauerkraut, or 2 oz of fermented brined vegetable juice. In a side experiment (see video referenced below), the Sonnenburgs gave some people probiotic capsules to see if supplements (like the bacteria in the fermented foods) would result in a more diverse microbiome with anti-inflammatory benefits. They found that this was the case only for a minority of participants. Probiotics were beneficial only in the subset of people already consuming lots of vegetables and fruit. Thankfully, that does describe the majority of our functional medicine patient population, but it doesn’t necessarily fit most of the American public. This second experiment with the probiotics wasn’t published so I can’t comment on which probiotics were used, or how much benefit was derived compared to eating fermented foods. Now that we know this, we can have some fun creating and consuming a wide range of fermented foods. We can circle back to raising the fiber in our diets when we get some better bacteria as a result. FERMENTING The simplest foods to ferment at home are from the cruciferous vegetable family. Many recipes are available online and in books on fermentation (a couple of books I liked are listed in the references below). Cabbage, cauliflower, kohlrabi, turnips, daikon radish, and others just need to be cut up, mixed with salt, and massaged for a few minutes. Liquid will appear as you do that, and you can stuff them into a jar below the level of the liquid if you push hard enough (usually). Then they need to be weighted down, with a glass weight, or a sterilized rock (boil it for 12 minutes). Finally, you want to place a permeable lid (I like airlock lids that let gases out but not in), and keep the mixture at room temperature, 60-75 F, for a few days. Taste them once a while and decide when they are done. You can add other vegetables to the mix, or ferment just carrots, onions, cucumbers, etc., but you’ll have to find recipes that tell you how much salt to use, and which starter culture to add. If you also add hot peppers, you can make kimchi. Fermented drinks are also quite simple to make. You can place grated ginger and raw unprocessed sugar in a jar and leave the mixture at 70-80 F for a few days, feeding it additional sugar and ginger daily. This will create a “ginger bug” and you can use some of the liquid to make bubbly gingery drinks, while keeping the “bug” going over time. If you purchase (or obtain from friends) a “symbiotic colony of bacteria and yeast” (SCOBY), either milk kefir grains, water kefir grains, or a kombucha SCOBY, you can turn milk, water, coconut water, nut milks, or tea into fermented drinks. The first fermentation (1-21 days, depending on the preparation and temperature) isn’t very bubbly, but then you can ferment your drink further in a sealed container (“second fermentation”), at room temperature, for 1-2 days, maybe adding fruit and herbs, to increase the carbonation and flavor. In other words, there is an endless world of creativity out there! The kefir grains and SCOBY are living organisms, so you have to figure out what to do with them to keep them healthy between making batches of fermented drinks. One more option: fermented vegetable tonics. This is vegetable juice such as carrot or tomato juice or a mix, fermented at 65-75 F with the addition of brine from a previous ferment, for 3 days. This produces a highly nutritious drink — just 2 ounces constitutes a portion of fermented foods. There’s also beet kvass, which is cut up beets soaked in salt water for a few days. This can also be secondary-fermented into a more complex and bubbly drink. HUGE VARIETY Of course there is also yogurt, cultured cottage cheese, cultured cream, and butter. A recent report revealed that many commercial products do not contain the probiotics they claim to contain. Making these products at home could be one solution to this problem. Meats can be fermented (salami, corned beef), as well as grains. Soybeans and other legumes, and hot peppers and garlic can be fermented into useful sauces. It’s truly endless. There’s even a book about fermenting wild radish seed pods and cattail stems. With the Holidays almost upon us, we naturally think about all the multiple roles of food, nourishment, tradition, togetherness, celebration, and delight. It can be a good time to venture into learning about the playful art and science of fermentation. REFERENCES Fermented: A Four-Season Approach to Paleo Probiotic Foods — Ciciarelli Mastering Fermentation: Recipes for Making and Cooking with Fermented Foods — Karlin Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Video: https://www.youtube.com/watch?v=s3MZjgtvEQ8 Using Diet as a Lever to Improve Your Microbiome: Erika SonnenburgI
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Blog AuthorDr. Myrto Ashe MD, MPH is a functional medicine family physician. Archives
October 2024
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