How to Help Your Gut Microbiome Heal from Inflammatory Bowel Disease

Although it’s still unclear whether the unhealthy microbiome causes inflammatory bowel disease or the other way around, what is clear to me is that once we have IBD, our guts have crossed a threshold. We have entered into a state of microbiome delicacy, and we’ll most likely have that delicacy for the rest of our lives.

This disease makes it harder to retain a healthy microbiome. Forever after getting IBD, we’ll probably need to work harder than most people to cultivate our gut bacteria.

But such cultivation is quite worthwhile. A few people have managed to bring their IBD into remission solely through diet, and it’s arguable that that’s because they succeeded in restoring their microbiomes. Kenny Honnas has focused his own healing on largely raw and fermented foods, and he’s brought his UC into remission without meds. Others have famously achieved remission through diet as well, such as Virginia Harper, whose vegan, macrobiotic diet healed her; or Judy Herod, who healed through the paleo SCD.

While these diets vary widely, Honnas points out that the common element is probably restoration of the microbiome. I agree, although I’m not an expert, as I said in the last post. But it makes sense to me that, because everyone’s composition of gut bacteria is unique, different people need different strains of bacteria and thus different diets to restore their guts. Experimentation is necessary.

(Case in point: while sauerkraut helps me immensely, a close relative who recently developed IBD has found that sauerkraut dramatically worsens her own symptoms.)

Although it’s inspiring to see people like Honnas healing through diet alone, such people are still not “cured”—their microbiomes will probably always be higher maintenance than most. Some of them may disagree with me here, and of course I could be wrong. But I notice that although most of them, once healed, describe the ability to “eat anything,” they also mention largely sticking to the foods that healed them.

Honnas now eats meat daily, departing from his initial raw-and-fermented-foods diet, but he still begins each day with a kefir-and-fruit smoothie.

Herod describes her ability to eat out with her family and to bake whole-grain bread, but she says she still mostly eats SCD food, which she enjoys.

In her book, Harper similarly describes sticking to the macrobiotic diet because she loves it, and adds that she would probably return to illness if she went back to her former meat-based Southern diet.

While most of us won’t be able to reach remission through diet alone like these inspiring folks, restoring the microbiome is still a worthy goal for us, too. It can often get us at least part of the way back to health.

Here are basic ways you can restore and tend to your internal ecosystem. Although I’m not a medical practitioner and can’t give expert advice, these are techniques that have worked for me:

• Add good bacteria by eating truly probiotic foods. Truly probiotic foods are not just any fermented foods, but are those with live, active cultures and which have not been cooked at high temperatures, since cooking kills bacteria. Here’s a list of good probiotic foods. Here’s how to cook miso soup without boiling away the bacteria; the same principle applies to other such foods as well. Experiment with different foods to find the ones that might help you.
• Help the good bacteria multiply by eating prebiotic foods. These are foods with lots of fiber, especially certain types of fiber, which beneficial bacteria feed on. They include legumes, garlic and onions, asparagus, certain whole grains, and more.
• Avoid stunting the growth of good bacteria with added, refined sugar. Learn to enjoy the subtler sweetness of fruit, coconut, cinnamon, and other naturally sweet foods. Discover the joys of savory flavors, such as those in Indian or Thai food. Be countercultural—break from the culture of sugar. Your tastebuds will adjust, you will feel better, and your gut will thank you.
• Keep your gut generally healthy by living a healthy lifestyle. Exercise regularly, manage your stress, get enough rest, and avoid drinking too much alcohol. All of these habits help the microbiome.

You may notice that I don’t specifically recommend taking probiotic supplements. That’s because 1) I haven’t personally benefited from them, 2) scientifically, there’s evidence that they’re largely ineffective and even potentially harmful, and 3) philosophically, I prefer getting my nutrition from food rather than supplements whenever possible.

Probiotic supplements do help some people. If you try them, do your research. But in general, a pill will have just a few, or perhaps a dozen, strains of bacteria that were grown in a lab, while fermented foods contain varied and ever-changing strains of bacteria that come largely from the air and soil.

Until less than one hundred years ago, when refrigeration became widespread, fermentation was a primary way all humans preserved food. It is still widely used in developing countries today. Our guts have evolved to eat fermented foods daily; this is how we’ve been getting probiotics for millennia. I believe it’s how we should continue to get them whenever possible.

There’s one more option I haven’t yet mentioned for restoring the microbiome: fecal microbiota transplant (FMT), in which a healthy person’s poop is administered to a diseased person’s colon. A few small studies have so far found that this method is effective for a small percent of UC patients, at least for inducing remission of a couple of months. (For example: here and here.)

More research is needed, though, and FMT has so far been ineffective for most UC patients. For the time being at least, it seems most effective to restore your gut through diet and lifestyle, rather than through injections of healthy people’s poop!

Finally, one last comment on microbiome restoration: your gut’s needs may change over time. The microbiome evolves, especially if your diet changes. A probiotic food that once helped you may eventually become detrimental, if your microbiome shifts to need other things. Your microbiome may even change seasonally, if your diet or lifestyle does.

The key, as with so much of IBD, is paying attention and becoming attuned to what your body is telling you it needs at any given time.

In conclusion, I don’t know whether I caused my own colitis by messing up my microbiome, although I strongly suspect it was a factor. What I do know, though, is that getting my microbiome into balance is a key to moving forward. And so, as I sculpt my diet and lifestyle for healing, the microbiome is always at the very center of my thinking.