Carbs 101 – Part 7 The Secret to Managing Your Microbiome


- 23 September

Researchers now believe that our microbiome (the 100s of millions of microbes in our gut) may potentially have as much influence on our health and fitness as our own genes (DNA). That would make sense, considering that more than 50% of the cells in our body aren’t even our own, but instead microorganisms. We may not be able to choose our genes, but to a large extent we have the ability to make choices that affect the health and performance of our microbiome.

The choice is in the foods we eat.

The “Western diet” in particular (which a majority of Americans follow) is a contributor to a bad microbiome. The main culprits here are animal proteins, saturated fats, refined sugars, excessive salt intake, and a lack of dietary fiber.

On the other hand, mother nature provides a perfectly engineered road-map to a healthy microbiome through fruits, vegetables, plant-based proteins, whole grains, and healthy fats.

Why Your Microbiome Hates Low-Carb Diets

Although high-sugar diets contribute to poor microbiome, eliminating carbohydrates altogether (ie, keto diet and other strict low-carb diets) is problematic as well. Complex carbs contribute to “microbial richness” (in other words, a diverse microbiome), and low-carb diets have been linked to less total good gut bacteria. One 2018 study even linked ketogenic diets specifically to unfavorable gut microbiome in mice, including an increase in a certain disease-promoting bacteria.

Including carbohydrates in your diet is important, but if those carbs are “simple” (sugar), heavily processed, and absent of fiber, your microbiome will likely suffer.

When non- or low-fiber carbs are consumed, the sugars go straight to the bloodstream, which elevates insulin and can lead to increased fat storage and diabetes-related symptoms.

For a healthy microbiome, your best bet is a diet that includes a carb conscious approach, focusing on quality low-glycemic carbs that are rich in natural fiber. This can be very difficult to achieve on extremely low-carb diets like keto. Even the popular “Paleo diet,” which excludes grains and legumes, has been linked to issues with microbiome health.

Your Microbiome Also Hates Artificial Sweeteners

If your gut loves natural foods (and it does), it only makes sense that it would loathe artificial, ultra-processed foods and ingredients. Exhibit A: Artificial sweeteners, which are found in nearly all processed foods to improve taste, texture, and even shelf-life. While these ingredients may help our sweet tooth, while on low-carb diets, they end up wreaking havoc in your microbiome.

Multiple scientific reports have shown increased risk of metabolic disease (specifically elevated glucose levels) in individuals consuming artificial sweeteners like saccharin, aspartame, and sucralose. These types of artificial ingredients appear to negatively affect gut bacteria and microbial diversity, possibly leading to gut inflammation and conditions like colitis and metabolic syndrome.

Sterile Isn’t Always a Good Thing

Anything we put in our body (food, medications, liquids, etc) can either positively or negatively affect our microbiome (gut bacteria). For instance, studies have linked high salt intake with a decrease in healthy gut bacteria, possibly leading to conditions like colitis and increasing gastric cancer risk. It makes sense, right? Before refrigerators, people used salt as a food preservative – to literally kill bacteria.

Don’t think you’re eating too much salt? Might want to think again. Recent statistics from the CDC say that 9 out of 10 Americans are getting too much salt, with most getting more than double the recommended daily amount. It’s usually not from the salt-shaker on the table, but rather the ultra-processed foods we eat. There’s not enough studies to confirm it yet, but it’s very probable that excessive alcohol consumption could have a similar effect (think about what we use to sterilize things from microbes).

Then there’s the fact that Western medicine has a tendency to over-prescribes antibiotics. Think about the name. There’s probiotics, and then there’s antibiotics. The latter serve an important role in medicine, but the potential negative effects have to be taken into consideration. Not every common bug needs to be treated with antibiotics. An overuse of these medications can adversely affect our overall health and, more importantly, our immune system – which is tied to, you guessed it… the microbiome.

The More Natural, the Better Your Microbiome

All this may seem complicated, or a lot of work, but actually mother nature has made it very simple by giving us the answer: Unprocessed, high-fiber carbohydrates (roughage) that are “alive” with natural, “good” bacteria. Unfortunately, natural eating has been disrupted by processed foods, causing an imbalance in the microbiome between good and bad bacteria.

The Best Foods and Nutrients for a Healthy Gut

Here are some things your microbiome loves:

  • A diverse array of vitamins and minerals (micronutrients).
  • Dietary fiber (both soluble and insoluble fiber).
  • Plant-based proteins.
  • Low-glycemic carbohydrates.
  • Healthy unsaturated fats – polyunsaturated and monounsaturated fats from food sources like extra virgin olive oil, fatty fish and almonds.
  • Fruits and vegetables, particularly colorful ones (yellow, orange, red).
  • Polyphenols, not only from fruits and veggies, but also herbs, seeds and grains.
The Bottom Line on Microbiome and Gut Health
  • A healthy gut can help you feel better immediately by increasing your energy. But your mood can be dramatically enhanced as well, as gut bacteria directly affect “feel good” neurotransmitters like serotonin. Poor gut health has been linked to depression.
  • A healthy gut will help you sleep better, have more energy during the day, improve brain health, and boost your immune system. An unhealthy gut will leave you tired, exhausted, and craving unhealthy foods throughout the day.
  • Good gut health equals a lower risk of chronic disease. Bad gut health can increase your risk for heart disease, serious infections, pneumonia, and other illnesses – not to mention ongoing bowel disorders like constipation and diarrhea.

So we may not be able to alter our genes, but we can certainly change how we look, how we feel, and how healthy we are – all by going back to a more natural approach to eating, which will in turn improve the health of our microbiome.

Simply put, a healthy gut makes for a happy and healthier individual.


​​Fetissov SO. Role of the gut microbiota in host appetite control: bacterial growth to animal feeding behaviour. Nat Rev Endocrinol. 2017 Jan;13(1):11-25. doi: 10.1038/nrendo.2016.150. Epub 2016 Sep 12. PMID: 27616451.

Rinninella E, Cintoni M, Raoul P, Lopetuso LR, Scaldaferri F, Pulcini G, Miggiano GAD, Gasbarrini A, Mele MC. Food Components and Dietary Habits: Keys for a Healthy Gut Microbiota Composition. Nutrients. 2019; 11(10):2393.


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