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Your Gut Microbiome and How You Could Be Endangering It

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From the time we are little kids and mom is telling us to eat our yoghurt, finish our broccoli and that we “can’t eat just candy for dinner”, we’ve been taught that what we eat can impact our health. Whether we followed our mom’s advice at the time or railed against it, even as adults we still wonder if those basic dietary guidelines hold true.

Since then, more and more science has come to light about the dietary guidelines that we were trying to follow but it actually has gotten harder to know what to avoid and what to increase. In the 90’s we were told to go fat-free and eat margarine and then we were told that some fat was good and that we should avoid sugar. Now it seems that every person has a different idea of what a “healthy diet” looks like. While the jury may be out on what the “perfect diet” may be for your overall health, what we are quickly learning is what diet and lifestyle choices directly impact your gut health.

There is an entire ecosystem within our guts called the microbiome and our current challenge is learning about what keeps that world in balance. We all know that eating clean and avoiding junk food is definitely a good start, but what if that new fad diet or that occasional treat is actually doing more harm than you think? Well, we’re here to help you navigate those tricky waters and here are a few ways that you may have been sabotaging your own gut health without knowing it.

Benefits of restricting saturated fat dairy

1. Not Restricting Saturated Fat

One of the most argued topics in the nutrition community right now is about fat. Everyone agrees that we should be avoiding trans fats but when it comes to fat from oils and grass fed beef, it seems there is just as much disagreement than consensus. However, for the microbes in your gut, the science is clear. The less saturated fat we eat, the healthier it is for our gut microbiome. Saturated fat feeds bad microbes like Clostridioides difficile (C. diff) and some bad Bacteroides species, which can contribute to leaky gut and increase inflammation in the body. So where does this saturated fat hide out in our diet? You may be surprised. Here are the most common sources:

  • Coconut oil, coconut cream
  • Palm oil
  • Butter & Ghee
  • Cakes, toffee, milk chocolate, biscuits, pastry
  • Whole fat dairy products (milk, cream, cheese, ice cream)
  • Red meat (beef, lamb, pork)

Good rule of thumb: if the fat is solid at room temperature, it’s most likely saturated. Alternatively, the more unsaturated fat we eat, especially omega-3 unsaturated fat, the healthier it is for our gut bacteria. Try switching out some of the pork or beef with fatty fish like salmon and substituting out your coconut oil for these:

  • Seed oils (grapeseed oil, canola oil)
  • Olive oil
  • Walnut oil
  • Avocado oil

Eating Too Much Animal Protein and Too Little Plant Protein

If there’s disagreement in the nutrition and medical community about fats, there seems to be even more about what types of protein we should eat and how much of it. Whether we eat only organic beef, pork, or chicken, whether we eat wild or farm-raised fish, or whether we eliminate meat altogether, it seems like it’s getting harder to know what protein source is best for our bodies. The good news is that when it comes to the microbiome, there is a general agreement among the scientific literature that a diet high in vegetables and fruit, high in dietary fiber, and low in saturated fat and red meat, is the healthiest. High amounts of red meat and chicken tend to drive up some of the harmful bacteria like Alistipes finegoldii and C. diff which has been associated with inflammation in the gut.

3. Staying on a restrictive diet long term

While an elimination diet can be useful short term to help identify foods that one might be sensitive to, they can be unhealthy for the microbiome to remain on. Even if a diet like keto, paleo, or low FODMAP diets are strictly adhered to for months or years on end, it can actually contribute to gut microbe imbalance. Avoiding high fibrous veggies, for instance, can lead to a lack of the beneficial Faecalibacterium, bacteria. This fabulous microbe is responsible for maintaining a healthy gut and supporting the immune system. Keeping it at healthy levels can even prevent ulcerative colitis.

Effect of alcohol consumption on your gut microbiome

4. Consuming alcohol

Now, I know this isn’t a diet but it’s definitely a regular part of the diet for most of the people in the world and it has been ever since humans figured out how to brew. So it might come as a surprise to find out how damaging it actually is to the gut microbiome. The irony is certainly clear: the yeast used to make wine and beer, Saccharomyces cerevisiae is actually a probiotic species but is killed off when wine and beer go through pasteurization (in the case of beer) and sulfating (in the case of wine). We’ve been told that 1-2 glasses of wine per day can confer certain health benefits, it turns out that even 1 glass per day of wine, beer or any other alcoholic drink can significantly impact your gut balance. A study done on how gin and red wine affected the gut microbiome found that gin caused the biggest spike in bad bacteria (C. diff and bad Bacteroides) and red wine caused an increase in harmful Firmicutes bacteria. What about the resveratrol in the red wine, you ask? That is still proven to be a fantastic antioxidant with powerful anti-tumor, anti-inflammatory, as well as prebiotic potential. But it isn’t only found in red wine. You can find it in red grapes, peanuts and dark chocolate so keep that in mind the next time you’re grocery shopping!

5. Using Antibiotics to Restore Gut Balance

For as much of a God-send as antibiotics have been for removing the scourge of deadly bacterial infections from the face of the planet, we’re now learning that they come with a high price. No one alive today can remember a time when there were no antibiotics but the truth is that they are such a recent medical phenomenon that it only makes sense that our bodies struggle to recover after getting hit with them. Towards the end of the 20th century, we started gaining an understanding of the dangers of antibiotic overuse but it was mainly related to the growth of antibiotic resistant strains of bacteria. Now that we’re learning more and more about the different microbiomes in and on our bodies, we’re gaining a fresh perspective on how antibiotic use can be so devastating to them. This is especially the case with pregnant mothers, infants, breastfeeding mothers, and children under the age of 3. And if it is so difficult to recover from antibiotics when they might be necessary, as is the case when the immune system is losing the battle with the bacteria, then using antibiotics to try to restore balance once dysbiosis (gut imbalance) is present, is almost impossible. Instead, it’s best to do a comprehensive gut test that uses whole genome sequencing (to capture all the bacteria, yeast, and possible parasites) and then carefully replenish the gut with the beneficial bacteria that’s missing.

Taking care of our gut microbiome is here to stay and it’s come a long way from just having the occasional yoghurt to promote regularity. We went from prescribing antibiotics for everything (even viral infections) to trying out herbal remedies instead like oregano oil and tea tree oil, to testing out almost every diet imaginable. The best news is that we’re learning more and more every day to help us make the right decisions for our gut health and, consequently, for our overall health.



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