The care and feeding of your microbiome – a quick guide

If you follow me on Facebook (you really should, I post lots of interesting things there) you’ll know that I post a lot of articles that tout the connection between a healthy gut microbiome and our health. Often, there’s an explanation of how we came to have the particular microbial makeup that we do. Whether we were born by c-section, if we were breastfed and for how long, whether or not we had pets, how dirty our childhood kitchen floor was, and the frequency of ear infections for which we were prescribed antibiotics all come into play. Of course, these are things over which we have absolutely no control and we must now play the hand we were dealt when it comes to cultivating our own microbial garden.

As every gardener knows, the closer you can come to providing the perfect environment for a plant, the easier it is to grow, and the healthier and more robust it will be. So it is with your gut. You can change the microbial composition of your gut in a day or two by simply changing the food you eat. So even if you didn’t spend your early years crawling around a dirt-floor yurt, gnawing on sourdough crusts while your hippie parents brewed sauerkraut and tempeh, you can still cultivate the good bacteria and starve the bad.

Even after a bout of antibiotics or severe diarrhea, your body retains a seed vault of bacteria to repopulate your colon. The appendix appears to be one of the sources of this beneficial bacteria, though it appears not to be the only one, as even people without an appendix can recover a healthy microbiome.

Many of the news articles about the connection between the microbiome and disease insinuate that this information will someday be used to create some kind of pill or capsule that will protect us from horrible diseases. They’ll go on to say that at the moment there isn’t really anything that can be done because it’s almost impossible to create the same conditions as exist in a large intestine in a lab, and no one can really figure out what happens to those probiotic capsules once they are swallowed.

The good news is that in almost every case, the good bacteria are already there and just need the right conditions to flourish. And the right conditions exist when you eat a lot of dietary fibre. When you consume a lot of fibre, you feed the beneficial bacteria which appear to be strongly associated with lower risk of inflammatory diseases, diabetes, and cardiovascular disease. In addition, the colon itself is protected from damage which reduces the incidence of colon cancer and other bowel diseases.

So, although it may be true that it is not currently possible to create a pill that can improve your gut’s microbiome, it is not true that there is nothing you can do to create a healthy microbiome. Eating a whole food, plant-based diet is all that is required to cultivate a diverse and healthy intestinal ecosystem.

How can you tell if your microbial garden is healthy? It’s simple, really. It turns out that the largest percentage of matter in a turd is dead bacteria. They live fast and die young, so every day, billions of them die and their tiny little bodies are transported out the back door. If you are having regular (yesterday’s corn shows up today), big (you gotta be a bit nervous when you flush), satisfying (you know what I’m talking about) dumps, you’re probably good. I realize for many people, that’s an elusive state, but being plant-based dramatically improves your odds. If vegan facebook groups are anything to go by, anyway. But you don’t have to become an insufferable, poo-oversharer – that’s optional.

Here are a few things you can do to grow your microbiome:

  1. Choose more intact grains over refined grains. Whole wheat groats, oat groats, and brown rice take longer to break down than flours. This means they are more intact when they hit the large intestine and provide food for the beneficial bacteria there. White flours are the worst, but even whole wheat flour is broken down more completely than flaked grains or intact grains.
  2. Eat more beans! Not only do they have lots of fibre, but some of the starch they contain is considered resistant starch. It’s resistant to digestion and acts like dietary fibre which makes it down to the large intestine where it feeds our good bacteria.
  3. Opt for a smoothie instead of juicing. I know lots of the wfpb gurus aren’t on board with smoothies because of the pulverization of fibre that occurs, but I haven’t seen any evidence that the fibre is destroyed or inactivated. Juicing, on the other hand, removes the fibre altogether. Do make sure your smoothie is more than half veggie, and don’t add any juice, protein powders or sweeteners.
  4. Keep in mind that refined oils and sweeteners and animal products contain no fibre whatsoever, though they are very calorie-dense. Replace those foods with whole plant foods and your fibre intake will increase automatically.
  5. Don’t take antibiotics any more than necessary. One of the benefits of a plant-based diet is a reduced incidence of urinary tract infections in women, due to a lack of exposure to common bacteria found in meat. Eliminating meat from your diet can have the effect of reducing the requirement for antibiotics.

Notice that I haven’t talked about probiotics or fermented foods. I haven’t seen much evidence that probiotics do much to enhance your gut microflora, but I have seen them recommended for people who are taking antibiotics, or who have had a bout of serious diarrhea. Keep in mind that if you aren’t consuming lots of fibre, they’ll simply starve if they even made it into the large intestine alive in the first place. Fermented foods may also be a way of enhancing your microbiome, but keep in mind that many of the fermented vegetables like sauerkraut and kimchi are made in salt brines and contain high levels of sodium. They probably won’t hurt (mind the salt) but their benefit may be limited, especially if your fibre intake isn’t high. The take home message is that you probably already have a store of all the bacteria you need, it’s just a matter of cultivating them.

I’ve tried to keep it simple for this blog, but check out these resources if you want to know more:

A fantastic book on the subject is Gut: The Inside Story of Our Body’s Most Underrated Organ by Giulia Ender. It’s a fascinating and somewhat irreverent read.

Dr. Greger at has many videos and articles on the subject.




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