How to Tend your Garden: Tips to Cultivate a Healthy Gut Microbiome

In my last article on the microbiome, I discussed the health benefits that your internal ecosystem of bacteria provides, or fails to provide, depending on its composition.

So what factors influence which gut bacteria thrive and which ones die off and disappear?

The first thing that needs to be said is that this is a major area of research and ongoing discovery and there is a lot that we don’t yet know. What we do know is beginning to provide some fascinating and useful insights into how we can encourage our own health through cultivating a healthy microbiome.

Initially each of our microbiomes is seeded during gestation and childbirth by our mother. Subsequently, those bacteria are fertilized by the many beneficial carbohydrates found in breast milk. Through this process, the microbiome is “set”, and some of those species of bacteria can’t be gotten in any other way. (1)

As time passes, the balance gets maintained or disrupted by what you eat, how much and what types of soil microbes you are exposed to, whether you have pets and whether you are exposed to antibiotics or other medications that kill off bacteria. Interestingly, children who live with pets have a lower incidence of allergic disease later in life. (2,3)

Taking probiotics and eating probiotic foods isn’t the whole story:

Currently available research shows that most probiotic bacteria, whether from fermented foods like yogurt or sauerkraut or from probiotic supplements don’t take up residence and survive long term in the gut. To varying degrees depending on the strain, they survive passage through the stomach and small intestine and exert health-promoting effects on their way through, but their benefits only last as long as you are taking the supplement or eating the food. (4,5)

For the purposes of this article, I want to talk about what can be done to take the ecosystem of bacteria that are already present and adapted to life in your digestive tract, and use diet and lifestyle to alter your internal “weather and gardening practices” to encourage the more health-promoting ones to thrive and outcompete the less helpful ones. Obviously, you can't just water your garden once in a while and expect this to lead to long term plant health. Similarly, the diet and lifestyle behaviors that promote microbiome health need to be consistent, long term habits.

How does the microbiome change with diet changes?

The microbiome changes rapidly with conditions, and one of the main conditions is what you eat. These shifts simply reflect the fact that whatever foods you are eating regularly will encourage the growth of bacteria that like those foods and thrive under the conditions created by eating those foods. In some ways, this is a good thing. It means your microbiome is adapting to help you digest and extract nutrition from whatever food you eat. However, these microbial changes have other impacts on your health as well. Switching over to eating a diet high in protein and fat causes rapid changes in the microbiome that trigger your body to become more insulin resistant. This is the state that favors the development of type 2 diabetes. (6)

Insulin is the hormone released in response to states of “plenty” that tells your body to take up excess glucose from the blood and store it.  Insulin resistance is a state where your cells become less responsive to insulin and therefore levels of sugar in the blood remain higher. This state is a precursor to type 2 diabetes and favors fat storage. 

Our ancestors lived with constant cycles of feast and famine. They would primarily live on an enormous variety of gathered, vegetarian foods that varied greatly throughout the year. This was supplemented by hunted game. Some of the meat was likely smoked and dried, but much of it was eaten quickly before it spoiled. These people ate a great variety of foods, and when they ate meat, it was usually over a few days in periods of “feast”.  

The interesting thing is that in the context of a feast and famine lifestyle, temporarily developing insulin resistance when there is plenty of meat and animal fat available makes sense. It is beneficial to pack on some pounds when the calories are available in order to better survive the lean times.

In contrast, many of us in the western world live in a constant state of feast. We are never without access to food, and often snack constantly throughout the day. We also have easy access to meat and many of us eat it at most or every meal. Particularly in the absence of adequate dietary fiber, this pushes our microbiomes in the direction of favoring insulin resistance and weight gain. So you can see that there is some innate biological wisdom or adaptation to this seemingly unhelpful pattern. It's just that this adaptation is not suited to our current way of life.

Current research shows that the diet that favors the greatest diversity in the microbiome is one high in fiber and relatively low in animal protein and fat. (7–9)

As always, I will temper this statement by saying that we do not all thrive on the same type of diet and our ancestors ate massively varied diets depending on where they lived and what was available. In my personal experience and my medical practice, I find that tailoring a diet to the individual is so important, and it can take some experimentation to discover the diet that works best for your body.

The importance of fiber

This understanding that dietary fiber is important is not new, but the more we learn about the microbiome, the better we begin to understand why it is important. First, some background:

Our hunter-gatherer ancestors ate somewhere in the range of 100 grams of fiber daily. Modern day Americans eat on average 12 to 18 grams per day. Current recommendations from the Institute of Medicine state that adult women should be eating around 25 grams of fiber daily, and adult men should eat around 33 grams. (10) These guidelines are based on studies showing that coronary heart disease and type 2 diabetes decrease dramatically at this level of consumption. I don’t think these levels are sufficient however. Studies have found conflicting results on the benefit of “high” vs. low fiber diets on colon cancer and diverticulosis (a condition where pockets develop in the lining of the colon which can become inflamed). However I believe this conflict is because the “high fiber diet” used in these studies consisted of of around 23 grams of fiber per day, so the studies are essentially comparing a low fiber diet with an even lower fiber diet. (7)

Why is it important to eat plenty of fiber?

For one thing, fiber increases the rate at which food passes through the colon, which seems to significantly cut down on colon cancer risk. (7)

Specific types of fiber serve as the preferred food source for the most beneficial strains of gut bacteria. When we eat fiber, we feed these bacteria, which in turn produce substances called short chain fatty acids (SCFAs). SCFAs are the preferred food source that nourishes, heals and feeds the human cells that make up the lining of the colon (enterocytes). The enterocytes metabolize these SCFAs and actually produce 5-7% of our daily energy. (11)

One type of short chain fatty acid called butyrate is also the signal to our gut immune system that all is well. Given how high our ancestors’ diets were in fiber, the only time that SCFAs were in short supply was in situations of dysbiosis, meaning when bad bacteria (that don’t produce butyrate) had taken over. As an adaptive response, when levels of SCFAs are low, the immune system interprets this as a signal that there are not enough good bacteria and too many bad bacteria around, and it initiates an assault to kill off the bad microbes. This cycle of increased inflammation continues until sufficient SCFAs return: a sign that balance has been restored. However, in our western world, it is frequently the case that the reason for the deficiency of SCFAs is due to inadequate fiber consumption, not necessarily to the presence of dangerous dysbiosis. (12,13) Unfortunately, the immune system can’t tell the difference. This type of gut immune response causes massive inflammation in the colon and can be one of the causes of inflammatory bowel diseases like Crohn’s Disease and ulcerative colitis.

So what should you do?

1. For starters, eat more fiber:

  • I recommend working up to eating 50 or more grams of dietary fiber per day.
  • Unfortunately, fiber supplements don’t seem to have the same benefits, so stick to whole food sources.
  • If you don’t currently eat a high fiber diet, don’t jump in all at once. Work up slowly. Your body and your microbiome need time to adjust to this way of eating. 
  • Another way to think about slowly increasing fiber is to add an additional 5 grams of dietary fiber per day to your diet each week.
  • Aim for as much variety as possible.
  • For example: start with 1/4 cup of beans per day for a week, then add another quarter cup, working up to at least 1 cup of beans or lentils per day (about 15-20 grams of fiber). 
  • Add in whole grains like quinoa, amaranth, wild rice, buckwheat, whole grain rice, and whole oats. Whole grain breads, crackers and breakfast cereals are not nearly as high in fiber or as rich in antioxidants.
  • Eat moderate amounts of nuts and seeds.
  • Work up to 5-7 servings of vegetables per day with 2-3 servings of fruit. Increase your daily intake of vegetables by 1 serving each week. You will easily meet or exceed the goal of 50 grams of fiber daily if you eat 1 cup of beans, 1 cup of whole grains, 2 servings of fruit and 5-7 servings of vegetables daily.
  • See here and here for fiber content of different foods and more information about dietary fiber. 

Sources of fiber:

Resistant starches, also known as prebiotics are a type of fiber that our digestive tracts can’t break down, therefore they pass intact into the colon where they provide the preferred food of your friendly gut bugs. Some of these resistant starches are called fructans and galacto-oligosaccharides.

Sources of fructans: Nectarine and other stone fruits, persimmon, watermelon, cabbage, broccoli, artichoke, asparagus, garlic, onion, grains like barley, rye and wheat (obviously avoid these if you have a wheat or gluten intolerance), pistachio, chicory root and inulin.

Sources of galacto-oligosaccharides: Legumes such as beans, lentils and peas as well as pistachios and cashews.

Another form of resistant starch is actually formed during food preparation and depends on how you prepare your meals. When starchy foods like potatoes and rice are cooked and then cooled, some of the digestible starches become resistant and will now pass through the upper intestinal tract undigested so that they can then be fermented by gut bacteria.

Side note: If eating fiber causes or worsens digestive symptoms like bloating, abdominal pain, constipation or diarrhea, you may have small intestine bacterial overgrowth, and should work with a doctor who is trained in treatment of this condition.

2. Avoid medications and chemicals that damage the microbiome

As much as possible, avoid medications that damage the microbiome such as antibiotics and heartburn medications like tums and omeprazole.

Work with a medical provider such as a naturopathic doctor who is trained in the appropriate use of antibiotics, and also knows when they are not necessary. If your doctor does prescribe antibiotics for you, ask if they are truly necessary. There are situations where the safest course is to take antibiotics, so the goal here is not to refuse them point blank, but to avoid taking them unnecessarily.

For example, most coughs, sinus infections and ear infections are caused by viruses and therefore won’t benefit from antibiotics. If the cough, ear infection or sinus infection is particularly severe or is not improving significantly within 2 weeks, it may be bacterial and antibiotics may be warranted.

Stomach acid is one of your body’s defense mechanisms against food poisoning or overgrowth of unhelpful bacteria. If you have heartburn, consider working with an ND to address the root causes rather than suppressing your stomach acid with medications. For more on the problems with longterm use of acid-blocking medications see here.

3. Eat organic:

Meats and animal products that are not organic are often grown with antibiotics, which will disrupt your colon bacteria. Glyphosate, or roundup, which is the most common herbicide used on vegetable and grain crops interferes with gut bacteria as well as impairing the liver’s detoxification mechanisms. (14)

4. Manage your stress

Occasional bursts of stress are unavoidable, but those things in your life that cause a constant low (or high) level of stress are harmful and have been show to decrease microbiome diversity, particularly reducing numbers of lactobacillus species, increase inflammation and increase susceptibility to gut infections with harmful bacteria. (15–19) It is vital to work on addressing the sources of stress in your life that can be remedied (Think cleaning off that messy desk that stresses you out every time you see it), and work on letting go of the things you don’t have control over.

5. Eat dirt

Spore forming bacteria, which generally live in soil are some of the only bacteria that do seem to colonize the gut and survive long term. (20,21) This sheds light on one reason why it's important to let children play in the dirt. You can also purchase organic produce from local farms or grow your own and then don’t be overly meticulous about washing off every last particle of dirt before you eat it.

6. Increase variety in your diet

Perhaps unsurprisingly, increasing dietary variety seems to increase microbiome diversity. (22) Even though we are presented with seemingly endless variety in the grocery store, many of these foods are actually genetically identical or very closely related. For example, kale, cabbage, brussel sprouts, cauliflower and broccoli are all different cultivars of the same species, Brassica oleracea. Similarly, tomatoes, potatoes, eggplant, bell peppers (and all peppers) and tomatillos are also very closely related. Beets and chard plants are the same species and onions and garlic are closely related. Once you realize this, your become aware that your diet may not be as varied as you thought. Adding in more variety when available such as dandelion greens and chickweed from your backyard or from farmers markets can be a helpful part of nurturing a more varied microbiome. Never harvest wild plants for food our medicine unless you are positive of your plant identification skills. To learn more about wild food foraging, see here and here.

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