Repairing The Gut Through Prebiotics

The Gut Health Protocol discusses the topic of repairing  the gut in Chapter 2, after the “kill” phase. This chapter shouldn’t be just for someone repairing their gut, but for anyone wanting to strengthen their microbiome.  The human microbiome is a very important part of overall health, immune health, and even cancer prevention. Here I discuss some ways to feed our microbial friends that are not discussed in the book.

The book puts a lot of emphasis put on PREbiotic fibers and foods to feed our beneficial bacteria. Chapter 2 puts less emphasis on PRObiotics as this bacteria isn’t, for the most part, what normally lives in your gut (though some strains do survive there for a time, and probiotics are still beneficial even for the short time they may be there). As I say in the book “Feed them, and  they will come”; providing the gut the prebiotic fiber it expects is what allows the native bacteria to return and thrive. It is a slow process, but one that is far more beneficial than constant “killing” as it attracts and nourishes the bacteria that belong in our gut.

“Circulation of toxic metabolites may contribute to cancer onset or progression at locations distant from where a particular microbe resides. Moreover, microbes may migrate to other locations in the human body and become associated with tumor development. Several case–control metagenomics studies suggest that dysbiosis in the commensal microbiota is also associated with inflammatory disorders and various cancer types throughout the body.” — DOI: 10.1158/1940-6207.CAPR-16-0249 (the journal of Cancer Prevention Research)

The Gut Health Protocol discusses soluble fiber supplements at length, and these are very beneficial to get things started. However it also recommends that people start phasing in a variety of prebiotic foods, starting with those that are the best tolerated (usually those containing little in the way of FODMAP fibers). The key here is variety, do not rely on just one source of soluble fiber, humans need a varied diet, so does our microbiome. Getting your fiber in whole food / whole cell form is also much more beneficial than highly refined supplements; supplements are mostly to get you started and to add some variety that you might not get otherwise.

This article is going to cover some very gut healthy choices for foods that feed the microbiome. Some of these you may not have ever considered gut healthy, such as mushrooms. But after the bad bacteria has been put in its place, medicinal mushrooms can be very beneficial for many people. Besides feeding good bacteria, they tend to normalize the immune system; in ways science doesn’t fully understand yet, but is finally recognizing.

Lower FODMAP Choices

• Mushrooms – all types, all varieties. Focus on those with more medicinal properties, such as: Chaga, Cordyceps, Enoki, Lion’s Mane, Oyster, Reishi, Shiitake, Turkey Tail. But your standard button mushrooms are OK as well. Again, variety is best. Mushrooms contain “resistant sugars”, polysaccharides that feed beneficial bacteria but not us. Some of these polysaccharides, such as beta-glucans, help train, and target, the immune system and are very beneficial for gut health. The medicinal mushrooms also have strong anticancer properties and are immunomodulators; so don’t just stick to button mushrooms when cooking. I love to cook with mushrooms, but I also take a powder supplement with 7 medicinal mushrooms, mixed in with my chaga tea, on a daily basis (chaga is yet another fungus, very similar to the mushroom, and with all the benefits).
• Seaweed – Extraordinary health benefits. Fucoidan is an active ingredient in brown seaweed and fucoidan supplements can also be very useful. Both can serve as a very beneficial prebiotic food for our beneficial bacteria. Research on brown seaweed is showing some pretty significant benefits for the immune system (which can be an important factor in repairing the gut and reducing inflammation). Brown Seaweed can be chopped up and used in soups and stews where it is barely noticeable, it also comes in flakes that can be hidden in many soups, salads, or casseroles.  Brown Seaweed has both immune system enhancing and anticancer properties; it is worth including in your diet.
• Konjac Root – contains a type of fiber called glucomannan. Glucomannan is less likely to cause gut irritation than the FODMAP fibers. Glucomannan can be used as a food ingredient to thicken soups and stews, or you can take it as a supplement. It can add much needed variety to your prebiotic diet.
• Cocoa – Yes, the main ingredient in chocolate is high in soluble fiber. Cocoa is also high in polyphenols which are known to improve the immune system. Be sure to use a natural product with no added sugars or dairy. This the cacao product that I use.
• Flaxseeds – High in soluble fiber. Make sure you use milled flaxseed, otherwise it just passes right through you and the soluble fiber remains unusable.
• Turmeric – can be used in many savory dishes, it doesn’t have to be used just in Indian food. Turmeric imparts very little flavor, most people will only suspect it is in the food due to the yellow / orange color it imparts. Just sprinkle in soups, stews, casseroles, etc., before cooking, until it changes the color of the food. Start slow (light color) and add a little more next time you cook. Turmeric is most beneficial when cooked with a bit of oil/fat and black pepper.
• Cooked Brussels sprouts,  carrots, sweet potatoes, cauliflower are all very good choices (see Chapter 2 in The Gut Health Protocol for more choices). The point of the above is get you to expand the variety of foods you consume

FODMAP Fibers

As you adapt to consuming more prebiotics you can start trying to slowly phasing in foods higher in FODMAP fibers (but avoid some of the other FODMAPs such as sugar alcohols, lactose and fructose). Inulin, chicory, fructans and FOS are all fibers made up of oligofructose. Though not everyone will be able to handle these, you won’t know until you try. Note the word “fructose” is part of oligofructose, that is what can make it problematic for some people; not so much that it bothers us directly, but that it can more easily feed the wrong kinds of bacteria that might be lurking in the gut. Once the gut is better balanced, and these unwanted strains of bacteria are greatly reduced, many people can start tolerating these foods better. Oligofructose is a great prebiotic for beneficial bacteria too, so it is worth it to keep trying to adapt to it. If you can’t tolerate it now, try again every month or so. Again, start slow, with small amounts, and slowly work your way up. Definitely start with small amounts from food sources, not supplements (you can try those later):

• Garlic – an excellent choice to start with as it has many health benefits. Garlic helps to selectively rebalance the microbiome, improves the immune system, and has a lot of evidence showing anticancer properties. Best consumed raw for the medicinal benefits, but cooked garlic is still great for the prebiotic fiber.
• Asparagus – contains inulin. Inulin is not very selective, in other words, if  you have bad bacteria lurking about it may feed them too. Just start slow, eventually your beneficial bacteria will push out the bad.
• Jicama Root – contains inulin
• Onion – again, start slow as it contains both inulin and FOS
• Jerusalem Artichoke – high in inulin
• Chicory Root – high in inulin
• Dandelion Greens – it has inulin, but isn’t overly high in it

Phages: When the phages kill unwanted bacteria in the gut, the cells of those dead bacteria become a delicious prebiotic food for the good bacteria. This has actually been shown in research. This is why Phage Complete is also shown to be a highly beneficial prebiotic, and the food it produces for beneficial bacteria is not a FODMAP and very unlikely to cause discomfort. The main reason for this is that the bacteria food it produces selectively feeds beneficial bacteria.

Beans and Legumes

Though the book somewhat discourages the consumption of beans and legumes, this should be temporary, only lasting through the kill phase and perhaps the first month or two of the repair phase. Beans and legumes are an excellent source of fiber and nutrients. They are also high in carbs, so if you are going low carb just skip this section. It should also be noted that beans can be histamine liberating for some people. Beans are not allowed if you need to remain on a low FODMAP or AIP diet. Beans should only be added if you feel your gut is in pretty good shape, you can tolerate other FODMAP fibers (such as garlic and inulin), and any histamine intolerance is mostly under control. However, for most people, beans are a very healthy choice if prepared properly.  Just like with other FODMAPs your gut may not be happy the first couple of times you try them, but every 6 months or so try again.

Beans contain anti-nutrients (such as phytate / phytic acid and lectin), but this risk can be mostly eliminated  through proper soaking before cooking. Though there are various methods for this, I think some of these methods may not be adequate.  Here are the four most common ways of addressing the anti-nutrient issue:

• Sprout your beans – this is an excellent way to reduce the anti-nutrients and gas producing starches in beans. However, sprouting is more work and requires planning ahead. This is not something I personally have time for. But there are plenty of instructions, and YouTube videos out there if you want to give it a try.
• Overnight soak – this is the traditional way of soaking beans and it does help. It even removes some of the indigestible oligosaccharides, such as raffinose and stachyose. But many experts now believe this doesn’t help as much as we would like.
• Quick soak stove – Bring water to a boil and cook the beans for 1 minute, remove from heat and  soak for 1 hour. Drain the beans and cook as normal. I don’t think this method is very effective as boiling for 1 minute won’t soften the interior of the bean at all, so it is unlikely to change the indigestible starches there.
• Pressure cooker fast soak – This is the method I use. Remove any debris from the beans, rinse, add beans to the pressure cooker (I use this Instant Pot, it is great!). Add water to cover the beans, plus one inch. Pressure cook for 3 minutes, do a quick release when done, drain, rinse well, return to beans to the pressure cooker, and cook as normal (there are many recipes online). I use the following chart and subtract 4 minutes from the “unsoaked” column (mid range) for cook time.

If you keep feeding your microbiome it will keep the bad bugs away and help keep you healthy. It might even help you prevent cancer and other disease (a good microbiome is highly beneficial to our immune system)! There are new studies being released almost daily on the benefits of a healthy microbiome. And just like you and I don’t function well if not fed properly, nor do the microbes in our gut!