Your microbiome and you! How to feed it a healthy diet

Guest post by Emillie
Your microbiome and you! How how to feed it a healthy diet
GIANTmicrobes Health 4-Pack

I have this theory that the goal of a lot of diets is to limit what you eat. Not because avoiding cheese or gluten or whatever is particularly healthy, but because if you have a limited diet you will be so bored of eating that you just won’t overeat. That’s my theory, anyway.

Three years ago, I decided I needed to re-haul my diet. I was slowly gaining weight, no matter how much I exercised. I had a host of health issues, including eczema, vitamin deficiencies, and food sensitivities. I had lots of chronic pain, and caught every single cold and flu that came home from school with my kids. It got to a point where I began to wonder what was wrong with me. Why was my body fighting against me? My diet wasn’t that bad, but it just didn’t seem to be enough to keep me healthy.

That’s when I got interested in feeding my microbiome.


Here’s the truth about our bodies: human cells make up less than half of the cells of our body. The rest of the cells in our body are our microbiome or human microbiota. It is made up of millions of bacteria, fungus, viruses, and yeasts that cover every surface of our body, inside, and out.

The even wilder fact is that not only are our bodies a home for tons of tiny organisms, those micro-organisms actually play a huge role in who WE ARE as people. The research into the role of the human microbiome is only just beginning, but it seems to be important for all sorts of things.

Mood: The health of our microbiome has a huge role in depression, anxiety, and quality of sleep. In fact, the microbes in our intestines actually produce 95% of our body’s serotonin (sorry for the geek out… serotonin is the neurotransmitter involved in the regulation of mood).

Skin protection: Ever gone home from your doctor with a warning to stay out of the sun after a large dose of antibiotics? (Or did that only happen to me?) That is because our microbiome protects our skin from sun damage.

Immunity: The microbiome is your body’s first line of defense against colds, flus, and infections. A kick-butt microbiome kicks the butt of all invaders. So take that e.coli!

Food Preferences: You are what you eat… because the community of organisms in your body like to be fed their favourite foods. So if you are a sweet tooth, then it’s because you have some sweet-loving yeasts and bacteria living in the universe that is your body.

So, how did I kick out the crappy members of my microbiome and get everyone else doing their job? Well, Google gave me a number of websites with complicated microbiome diets… but in the end I followed my gut and went with my own science-based diet. (Sometimes a degree in Neuroscience can be handy!)

Here is my…


1. Eat probiotics: I try to eat something probiotic every day. Personally, I don’t trust probiotics that come in pills, potato chips, or chewing gum. Reach for the yogurt, sauerkraut, and miso instead.

2. Eat fiber: Fiber and resistant starches is what your microbiome gets to eat after your dinner exits the acid bath that is your stomach. So eat whole grains, nuts, seeds, beans, fruit with the skin on, and vegetables.

3. Cut down on sugar: This is the hardest part of a microbiome diet. And I’m the first to admit that I probably have sugar (ahem chocolate) every day. But my goal is to limit myself to one treat a day.

This is particularly tricky because sugar has so many different names, and a bunch of them are considered “healthy” because they aren’t digestible to humans… while still feeding the not-so-healthy yeasts and bacteria in your microbiome. Try to avoid sugar, honey, maple syrup, coconut sugar, xylitol, agave, brown rice syrup, fruit juice. Then there is all the dextrose, maltose, and things that look like a chemical experiment…

It’s pretty tough to avoid sugar because it is probably in your breakfast cereal, pasta sauce, chicken broth, and pretty much everything else. So I put this in the “do your best” category.

However, I also know that part of the reason that sugar is put in so many foods is because so many of us have microbiomes that are sugar-addicted. It took me about two months of a pretty much only one serving of sugar (chocolate) a day to cut the cravings. And I would say it was worth it! My health is so much better. Better than it has been in years. And that makes me so much more happy than a chocolate pecan ice cream sundae.

How are YOU feeding your microbiome?

Comments on Your microbiome and you! How to feed it a healthy diet

  1. Thanks for writing this. The microbiome is just so interesting and it’s nice to see an article on it here. And I’m sending this to my husband now. He’s only just starting to accept that his diet severely affects his mood. Sugar causes huge problems for him, as it does for so many.

    One thing, though. While I don’t doubt that the microbiome on the surface of our skin will have a role in sun protection, I don’t think this is why you’re advised to stay out of the sun when taking certain antibiotics. I think, like for some other drug classes, the active chemical itself is affected by UV and can cause localised damage when skin is exposed to strong light. Just in case anyone thought that adopting a diet that promotes a healthy microbiome might overrule that advice…

    • Thanks for the info! I thought it was because of the microbiome issue… because I had been on IV antibiotics at the hospital (which definitely stripped my system of everything), and was I was off the antibiotics when they released me to the sunshine. 🙂 Regardless, that bout of appendicitis certainly was the start of all my food sensitivities and digestive issues.

      • Isn’t there a theory that your appendix acts like a reservoir for reserves of microbiome bacteria? So say you’ve had a pretty stripping dose of antibiotics, you can replenish your microbiome from the appendix. Having it out would be a sure fire way to mess up what replenishes your microbiome!

        • Well… the whole appendicitis rupturing was definitely the downfall of my digestive system, so that makes sense. I always attributed it to the week of IV antibiotics that came with it.

          Not so fun story… the first GP I saw told me I was just whining about period cramps, even though I knew it wasn’t as simple as that. (honestly… how much time would it have taken that male doctor to push on my abdominum?) I was on a ferry boat to visit my parents when I realized I was probably going to die if I didn’t get to the hospital ASAP. So I was pretty sick by the time I did get to the hospital. Hence all the antibiotics.

  2. I’ve been struggling with worsening chronic fatigue (plus migraines, a host of gut issues, and newly developed host of uterine issues, too) over the past decade, and gone through so many tests and experimental treatments, as all of my doctors and specialists just can’t figure it out. I’ve been seeing a GI and a dietician for a year now, as finally everyone was able to agree that is was *something* to do with my microbiome being out of whack. Unfortunately, Western medical science hasn’t progress very far in understanding our microbiome, but everything I’ve read backs up your assertion- our gut plays a lot of roles in human function. And hey, you’re never alone- you have billions of bacterial colonies within you at all times. Yay!

    Seriously, though, for someone whose gut imbalance means she can’t have cabbage, yeast, dairy, onions, mushrooms, sugar, alcohol (and many other things), I can’t find naturally fermented anything that I can eat. :/ (stinks, because I used to love making my own sauerkraut, and kimchi, and I love the taste of kombucha)

    I’m currently trying the SCD (specific carbohydrate diet), which cuts out all starches, with the exception of some fresh fruit, as well as all sources of sugar. It’s not easy, but the hope is to ‘starve out’ the overgrown “bad” bacteria causing the imbalance, and keep fingers crossed that the underpopulated “good” bacteria grow back to normal levels. I’m wondering, given how many ‘ifs’ are in that plan (it’s my Hail Mary, really), if there’s a country whose understanding of microbiomes is much better than ours, on whose science we can lean.

    • That sounds really tough. I would be sad if I had to give up my kombucha. I hope that you find what works for you and get some relief.

      My own journey: vegan for 11 years, mega sweet tooth, no impulse control so I eat a lot of cookie dough and cookies and ice cream. I’m just realising this sugar bingeing is affecting my mood, and possibly my eczema. I’m trying to cut back on processed sugars and instead have a fruit smoothie or a tea (with leaves, not like a store bought Lipton iced tea) when I feel the crave. It’s really difficult. I’m making my own kombucha now and it is also helping my tummy regulate things. I don’t have GI issues but I find I can get an upset when I eat out and things are especially oily.

      Gonna check out the writers website now! Thanks for this article!

    • I have a friend with a very similar list of issues. It totally sucks to be so out of wack. Would you be ab to haleve some really off-beat ferments? Can you tolerate mold? To be honest… I still can’t do mold, but I can do fermented miso. Another idea is… what about lacto-fermenting other vegetables? You can buy vegetable starters online… just make sure they are yeast free. I would also recommend fermenting in a fido or with an airlock to make sure you don’t get any free-range yeasts.
      And… in a different vein… I read “when the body says no” by Gabor Mate. It has been helping with some of my autoimmune issues, from a psychological standpoint. Take care!

  3. Its great that you found a diet you like. But while eating more fiber is unequivocally good for you, most of the rest of this is still speculation that has yet to be determined by science (ex: it is unknown whether consuming probiotics regularly will improve your health if you are already well. The work suggesting they help is all from people with known diagnosed digestive problems.) And some of it is just incorrect. Like the part about sun sensitivity mentioned already. You even misstate the conclusions of the press release you cite about serotonin. In the future it might be best to talk about how the diet works for you, and avoid making scientific claims or giving advice that might be construed as medical.

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