Microbiome Superfoods – Everything You Need To Know

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By Leslie Waterson

Reviewed by Juliana Tamayo, MS, RDN - Last Updated

Microbiome Superfoods

Bacteria overall can get a bad rep, when in reality, there are two groups of bacteria, bad bacteria, and good bacteria. Inside our bodies, we have groups of bacteria, as well as protozoa, fungi, viruses, and more than a hundred trillion microbes. These different things make up the microbiome, where all these microorganisms live.

Your microbiome is a vastly multifaceted unit. The intricacy of its genome is far superior to your own, and it forms an essential part of your existence. The human microbiome has an essential role in the growth of our immunity, regulation of nutrition, metabolism, and it even impacts how we behave. These are just some of its many functions. That’s why feeding our microbiome the right things is essential, and that’s where microbiome superfoods come in. In this guide, we will take a closer look at the microbiome, its functions, and microbiome superfoods. Let’s get started!

Microbiome Superfoods-Bacteria

Function of the Microbiome 

These tiny organisms are contributory to the initiation, training, and maintenance of your immune system. Your friendly cooperation confers defense against other opposing microbes and molecules in optimal conditions.

If you could see your microbiome with your naked eyes, You would soon come to distinguish your microbiome as perhaps the most tightly populated ecosystem in the world if you could see it with your naked eyes. The majority of which is found in your gastrointestinal tract.

Microbiome Functions

Your gastrointestinal tract is believed to be microbe-free just before birth. But, you soon become occupied with your microbial buddies as you go through the birth canal, which is believed to be vital for the lifetime function of your immune system. 

Though, there is separation to avoid unfortunate consequences, like sepsis, which is a life-threatening disease that happens when a massive immune response is caused by the occurrence of bacteria in the bloodstream.

While you do have these innate microorganisms, there are things that can boost or hurt your microbiome. Things like lifestyle choices, exercise, food consumption, etc., play a large role in the health of your microbiome. 

The best way to support your microbiome is by eating a nutrient-rich diet that aids in the growth of healthy, good bacteria. This bacteria will keep your body healthy, able to fight off viruses and bad bacteria. Conversely, highly processed foods, along with emulsifiers and non-natural sweeteners, can do a lot of damage to your microbiome. But for now, let’s discuss items that can help strengthen your microbiome!

Foods That Are Beneficial For The Microbiome

Thankfully, there is good evidence proving that there are many things you can do to preserve a healthy, balanced, committing, and optimally functioning gut microbiota. Examples of happy-gut factors within your control are the way you eat, how frequently you take prescription medicine, and your exercise habits.

The human gut is dependent on the bacteria in our body. Foods that promote harmful bacteria will destroy our good gut bacteria and cause negative effects. Eliminate high-fat foods, refined sugars, and processed items from your diet and focus on meals that promote beneficial bacteria in your gut.

You need to consume an assortment of foods that are beneficial to maintaining a healthy gut. There is an abundance of foods you can choose from that promote the growth of bacteria that are beneficial, improving your overall well-being.

Foods That Are Beneficial For The Microbiome

Foods Rich in Fiber

Foods that are rich in fiber, such as bananas, legumes, peas, beans, leeks, oats, asparagus, and berries, have been proven to be great for gut health. One study found that even a small amount of garlic can have positive effects on immune function. And another study showed that onions have anti-cancer properties and may help with the absorption of some nutrients in the body.

Fermented Foods

Fermented foods have traditionally been considered a healthy source of probiotics. The most well-known ones are sauerkraut, kimchi, miso, yogurt, kefir and tempeh. While the quality of these foods varies widely, the benefits of the gut microbiome are almost universally acknowledged by researchers. The fermentation process itself creates fatty acids that help support both digestion and gut regulation.

Nutrient-Dense Foods

Foods such as salmon, grass-fed beef, and bone broth provide you with essential nutrients that are beneficial for overall health and gut health. Eating these things will help the digestive tract heal and repair itself.


Another great addition to your daily regimen is smoothies. They are a healthy source of fiber while being easy on your stomach. They also provide you with lots of antioxidants and nutrients. The best way to have a smoothie is to make it on your own as you can be sure of its contents. You may add probiotic-rich fruits for more benefits and include leafy greens and fruits, so it is balanced.

Another effective way to cleanse your body is by eating a variety of fruits and vegetables. They’re rich in vitamins, minerals, phytochemicals, fiber, and other nutrients that can help detoxify your system and improve your health. Just be sure you only buy organic produce when it’s produced. A lot of vegetables include inulin, a soluble fibre. Inulin can be found in things like onions, garlic, asparagus, bananas, Jerusalem artichoke, and more.

Foods to Minimize To Support Your Microbiome

Just like there are foods to support your microbiome, there are foods that can hurt your microbiome. Saturated and trans fats (think fatty foods) are related to heart disease, obesity, diabetes, arthritis, and many other health concerns. It is advised to decrease your intake of saturated and trans fats that can be found in processed items or anything labeled with “low fat.” Replacing butter with olive oil, avocados, and nuts for healthier fats is a great way to cleanse your body of harmful saturated and trans fats.

Drinking too much alcohol is known to cause problems for your physical health. Your liver will also be harmed if you consume too much alcohol regularly. It’s important to support your bacteria, but if you drink infrequently, it won’t impact you badly.

Microbiome-Minimize Drinking Alcohol

Lastly, food additives can be found in many processed items. They make the food last longer, make it look better, and make it taste better. Food additives can cause intestinal inflammation and increase the odds of having irritable bowel syndrome.

Many studies have found that artificial sweeteners cause gut issues, including the overgrowth of bad bacteria and other negative metabolic consequences. If avoiding sweets is not an option, try to limit your consumption of them to one small treat a day. 

Microbiome Superfoods


Prebiotics are fibers, commonly called superfoods, that your stomach doesn’t digest, but good bacteria can use them for food. Since your stomach doesn’t digest these plant fibers, they travel to the lower part of your digestive system and are used by the healthy bacteria there. Prebiotics are not the same as probiotics, and indeed there are some differences in their purpose. Nonetheless, both are important to digestive health.

Prebiotics are essential for your health and well-being. However, more research is needed to understand all the ways they can aid you. Prebiotics occur naturally in certain high-fiber foods and are available as a dietary supplement.

Prebiotics can help boost your gut health by providing the “good” bacteria you need to ward off pathogens and keep your digestive tract healthy. They can also help with constipation because they provide the fiber that your intestines need to keep things moving along smoothly. Because of all of these benefits, there are quite a few prebiotic options on the market. Some choices worth considering include PrebioThrive, Dr. Tobia Prebiotics, and Performace Lab Prebiotic.

Microbiome Superfoods- Foods rich in Fiber


A probiotic is a beneficial microorganism that can be found in certain fermented foods, such as yogurt. It may also be added to non-fermented choices like bread, meat, and milk. Probiotics contribute to good health by supporting the immune system, hindering food spoilage, and keeping the stomach healthy.

Your gut microbiome is affected by what you put into it. You can easily support this by eating more probiotic-rich foods like sauerkraut, kimchi, and kefir.

There are lots of healthy choices that you can eat to get probiotics. If you can’t or won’t eat these foods, you can also take a probiotic supplement that contains the same strains of bacteria as those in the foods. These “superfoods” are beneficial bacteria that have been linked to better health.

Like prebiotics, probiotics are quite popular within the health and wellness world. With that comes a large variety of options available for purchase. Some solid probiotic choices include Klean Probiotic, Dr. Mercola Complete Probiotics, and 24 Strain Probiotic.


Iron can alter the bacteria in our gut, which is why the availability of iron can contribute to the growth and survival of pathogens. It has been known for a long time that iron availability can contribute to the increased virulence of pathogens. This has a huge effect on your microbiome and generally good for your gut.

A study suggests that fermented foods may increase iron absorption. The reason behind that is because fermentation increases pH in the intestines, increasing the solubility of iron and decreasing the number of phytates that bind it.

The best way to get the most iron is to eat foods that contain both of the different types of iron. Items like nuts and meat are excellent sources of nonheme iron; whole foods like spinach and beans are good sources of heme iron.

Vitamin C is needed for the stomach to absorb iron from foods. To maximize your absorption of iron, eat meals that are rich in vitamin C along with dark green vegetables and citrus fruits. It’s also important to avoid substances that can limit your iron absorption, such as calcium-rich supplements and zinc.

‘The Microbiome Diet’ by Raphael Kellman, MD

Dr. Raphael Kellman focuses on gut health in his book “The Microbiome Diet” and provides useful information to get started on your gut healing journey. In his book, he provides readers with an actionable plan to heal their gut as well as reset their metabolism and digestion. It also includes meal plans and over fifty recipes to chose from.

You can check out his book here.

The Microbiome Diet by Raphael Kellman MD

Support Your Gut Microbiome

If you are looking to improve your gut bacteria, support your gut microbes, nourish your gut flora, or achieve a healthy gut, there are many things you can eat to do so. When you decide to take charge of your health and seek a healthy gut, there are many different things that are good for your gut.

From what you eat, to how you exercise, to managing stress, and more, there are many factors that play a role in your overall wellness. Some quick things to add into your daily diet include: green tea, dietary fiber (like oats), protein, garlic, fatty acids, and other items that help balance blood sugar levels.

Gut Microbiome

You can also add vitamins (like vitamin a) and minerals (like iron) into your diet, but make sure this comes second to supporting your gut with food. Your gut bacteria will thank you, and your overall wellness will improve dramatically.

Lastly, it’s always important to figure out if you have any food allergies while you are focusing on your health. If you have a health condition, or an allergy, this can help steer you in the right direction with healing. There are many different conditions that can also contribute to food sensitivities or allergies to look at.

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Leslie Waterson

Leslie has been passionately involved in the health and fitness industries for over a decade. She is constantly reviewing the latest scientific research and studies in order to take a research-backed approach to lifestyle optimization. Her main areas of interest include nutrition and supplementation. Leslie shares her findings on Fitness Clone to help other health enthusiasts choose the products and routines that will help them achieve their goals.