Understanding the Microbiome
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Understanding the Microbiome

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Did you know that in the average human body, the number of bacterial cells matches the number of human tissue cells at a roughly 1:1 ratio? By cell count, that makes us about 50% bacteria.[*]

It’s no surprise, then, that these bacterial populations can profoundly affect our health.

In this article, you’ll learn about the gut microbiome, how it affects your health, how diet (including Keto) influences gut bacteria and several ways to help your gut microbiota flourish.

Microbiome Definition

So, what is the microbiome?

Your gut microbiome is the unique ecosystem of bacteria and fungi residing in your large intestine. One of the key roles of these bacteria is to digest material that your body isn’t able to (like fiber). In turn, these bacteria produce short-chain fatty acids (SCFAs) that influence the body in several ways.[*]

A number of factors influence your microbial populations. Notably, when a baby is born, their gut is “sterile.” But it quickly becomes populated by the bacteria present during delivery, and from the breast milk or formula they drink. However, what you eat has a profound impact on your gut microbiota for your entire life as well — not just during infancy.[*]

Some other factors that influence your gut bacteria include[*]:

  • Genetics
  • Age
  • Medications, particularly antibiotics
  • Dietary supplements (prebiotics and probiotics)
  • Intermittent fasting

How the Microbiome Affects Health

Your gut bacteria have a direct effect on your digestive health. In fact, many digestive issues — particularly those related to the large intestine, like constipation or diarrhea — are likely related to microbiota imbalances to some degree.[*]

However, the gut microbiome also affects several other critical aspects of your health:

  • Metabolism. One interesting study in over 1,000 people noted that gut bacterial populations could “predict” a number of factors related to metabolic health, including blood sugar control, cholesterol levels, heart health, and markers of inflammation. What’s more, the bacteria associated with a healthy metabolism were those that were also associated with a healthy diet.[*]
  • Cognition and mood. The “gut-brain axis” is a direct line between your gut and brain. Via this pathway, your microbial balance can influence brain function. Additionally,  gut bacteria produce the “feel-good hormone” dopamine and other neurotransmitters.[*]
  • Weight. Researchers have also noted that microbial balance in the gut appears to be a more reliable indicator of abdominal fat (a harmful type of fat distribution associated with obesity) than body mass index.[*]
  • Immunity. SCFAs produced by gut bacteria also play a crucial role in modulating immune health and regulating inflammation, an immune response.[*]
  • Skin. Skin problems like eczema, atopic dermatitis, or acne may be related to diet and microbial balance. Researchers have found that gut microbiota can influence these conditions, especially if they’re caused by inflammation.[*]
  • Bone density. Some early research also suggests that the gut microbiota may also play a role in bone density and strength.[*]
  • Cancer. Research has shown that H.pylori–an invasive gut bacteria that can cause stomach ulcers and inflammation–has also been linked to gastric cancer (Wroblewski LE, Peek RM Jr, Wilson KT. Helicobacter pylori and gastric cancer: factors that modulate disease risk. Clin Microbiol Rev. 2010;23(4):713-739. doi:10.1128/CMR.00011-10)

Your microbiota health may even play a role in longevity. In certain healthy centenarian populations (people over 100 years old), researchers have noted similarities in microbial balance and diversity that may be related to healthy aging.[*]

Diet and Your Microbiome

Gut bacteria are profoundly influenced by what you eat. 

Generally, healthy, minimally processed eating styles allow beneficial bacterial populations to flourish, while diets higher in processed foods may harm healthy bacteria and allow harmful populations to colonize your gut. The following food sources can drastically influence your gut health:

Good for the gut

  • Fermented foods. These foods — like yogurt and sauerkraut — contain live bacteria. When you consume these foods, the bacteria may take up residence in your gut and help promote a healthier bacterial balance.[*]
  • Prebiotic fibers. Prebiotics are food sources for gut bacteria. These fibers are what the bacteria break down in order to create SCFAs. All foods that contain fiber can possess prebiotic properties, but certain types (like inulin) are more beneficial than others.[*]

Bad for the gut

  • Artificial sweeteners. Numerous studies have demonstrated the harmful effects of artificial sweeteners on gut bacteria balance. Unlike natural foods, they can’t be fermented or digested by these bacteria, and they can harm your healthy bacterial populations as a result.[*]
  • Ultra-processed foods. Likewise, ultra-processed foods (like those high in additives, added/refined sugars, and ingredients that are far removed from their natural state) are uncharted territory for your gut microbiota. Eating lots of processed foods may harm your microbial balance.[*]

Keto and the gut microbiome

So, what’s the link between the Keto diet and the microbiome? 

Although little direct research has been done on the topic, a high-quality Keto diet may promote microbiota health. In fact, one study noted that a Keto diet was associated with microbial changes that resulted in reduced inflammation.[*]

On the other hand, a Keto diet full of artificial sweeteners and processed foods — although it may still provide some weight loss and blood sugar management benefits — could ultimately have adverse effects on your gut health.

The key is to limit your consumption of processed foods (yes, even Keto-friendly processed foods) and artificial sweeteners.[*]

Top 10 Keto-Friendly Foods for Microbiome Health

Here are some of our favorite Keto-friendly foods that are loaded with probiotics or prebiotics.

  1. Kimchi. This spicy Korean condiment made from fermented cabbage is phenomenal with other Asian flavors or any meal that needs a spicy, tangy punch. You can find it at the grocery store in the refrigerated section or make your own at home.
  2. Fermented sauerkraut. Traditional fermented sauerkraut (also made from cabbage) is crunchy and pungent, making it an excellent complement to fatty meats like corned beef or bratwursts. Note that shelf-stable canned sauerkraut doesn’t contain any live probiotics, though. Buy it from the refrigerated section or make your own.
  3. Fermented pickles. A fermented dill pickle is the perfect Keto snack with essentially zero calories and tons of probiotic goodness. You can find them in the refrigerated section at most grocery stores, and they’re also easy to make at home using whole cucumbers.
  4. Dandelion greens. Although not commonly eaten in the US, dandelion greens are a popular food worldwide. They’re rich in inulin, a favored food source of healthy gut bacteria. Try this Keto-friendly dandelion and blueberry salad.
  5. Garlic. Like dandelion greens, garlic is also a good source of inulin. Use it to season your cooking, and your prebiotic intake will add up. Garlic also provides some immune benefits, so it’s a great regular addition to your diet.[*]
  6. Seaweed. Seaweed is a crisp and briny snack with essentially zero carbs or calories, and it’s a rich source of prebiotic fibers. You can use it to make Keto-friendly sushi wraps or add it to salads.
  7. Asparagus. Asparagus is rich in fiber (to the point where it can be described as “woody”) and serves as a great low-carb source of prebiotics. Try roasted as a simple side. 
  8. Jicama. A mild tasting root vegetable, jicama can be used to make Keto-friendly fries. It’s loaded with prebiotic fiber.
  9. Flax seeds. Flax seeds are loaded with fiber and anti-inflammatory omega-3 fats, giving them a one-two punch of benefits. You can use them in Keto-baking, as a warming breakfast cereal or as a nutty topping for almost any meal.
  10. Chia seeds. Chia seeds are mostly fiber, so they’re an excellent prebiotic. Dry, they add great texture to meals, and when you add water, they gel. For a Keto-friendly dessert, make sugar-free chia pudding with a sweetener like allulose or erythritol.

5 Ways to Create a Healthy Microbiome

  1. Learn about your gut bacteria. Microbiome testing from Viome delivers a comprehensive report about your gut microbiome health. Getting this test is a great starting point, especially if you’re experiencing some digestive discomfort and want to see if your microbiome may be playing a role.
  2. Consider probiotic and prebiotic supplements. Probiotic supplements contain living colonies of beneficial bacteria. When you take them, they can help bring balance to an imbalanced gut microbiome — potentially providing some relief from digestive issues. Likewise, prebiotics are indigestible material that can be used to feed your gut bacteria. We like Ancient Nutrition Ultimate SBO Probiotics because they contain both pro- and prebiotics. You can also purchase custom probiotics from Viome after your microbiome testing.[*] If you’d like to skip a supplement altogether, a low carbohydrate yogurt is probably the easiest way to ensure adequate prebiotics in your diet.
  3. Eat fermented foods. Fermented foods like traditionally prepared kimchi, sauerkraut, and pickles are Keto-friendly and loaded with probiotic strains. Fermenting is also a satisfying hobby that’s really simple with the help of tools like Nourished Essentials Easy Fermenter Starter Kit. Yogurt and kefir - fermented dairy products -are other good choices, but they tend to be higher in carbs. If you do include these, choose plain versions with no added sugar or artificial sweeteners, or make your own and enjoy them in moderation.
  4. Eat fiber-rich foods. Although your body can’t digest fiber, the bacteria living in your gut can. When they break down fiber, they produce beneficial SCFAs that provide a number of positive health effects. Enjoy nuts, seeds, avocados and cruciferous veggies.
  5. Limit artificial sweeteners and ultra-processed foods. These foods can harm your microbial populations, so it’s best to limit them as much as possible — even if they’re otherwise Keto-friendly. 


For optimal health, your gut microbiome shouldn’t be ignored. It influences your health in a multitude of ways by affecting metabolism, weight control, bone health, cognition, mood, and more. 

Diet plays a huge role in gut health, and the Keto diet can be a gut microbiota-friendly choice as long as it’s not high in processed foods and artificial sweeteners. Incorporating probiotic and prebiotic foods and supplements into your low-carb lifestyle can also help to encourage healthy microbial balance.

Start by including various low-carb vegetables to help feed your healthy gut bacteria plenty of prebiotic fiber. Add in probiotic foods like kimchi, sauerkraut, pickles, or plain yogurt, and this will go a long way to help populate or repopulate your gut with healthy bacteria.

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Comments 3

  • Alexandria444

    Alexandria444 2 years ago

    This is fantastic- Before starting keto I followed a gut health diet but unfortunately gained weight (but my gut was happy!) so I appreciate you highlighting the fermented and prebiotic foods still available to the keto community. Thank you!

    • StellarRadish317670

      StellarRadish317670 2 years ago

      Awesome article! Thank you for this info!

      • RemarkableKetone833626

        RemarkableKetone833626 2 years ago

        Thank you