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How to Improve Your Gut Microbiome for Better Health

By Rachel Link, RD, MS

January 21, 2025

There’s a reason the gut microbiome gets so much attention: It’s within someone’s gut where many bodily functions take place every day that are essential for survival and overall health. For example, the vast majority of the immune system is located inside one’s gut.

How can you improve your gut microbiome? If you’re looking to learn how to increase good bacteria in your gut naturally, you’ve come to the right place. We’ll show you how to eat in a way that supports growth of healthy gut microbes, plus explain “gut disruptors” you’ll want to avoid.

Of course, you should always consult your healthcare professional prior to beginning any new dietary or lifestyle regimen, including dietary supplementation. 

What is your gut microbiome?

Your gut microbiome is the community of organisms (or microbes) living inside your gut. There are actually trillions of these microbes populating your gastrointestinal tract as we speak, including various types of bacteria and yeast.

This may sound scary, but it’s actually a very good thing — considering many microbes have positive effects on digestive function, a healthy immune system, energy production and much more.

You can actually thank the microorganisms in your gut, as well as other parts of your body such as your mouth, for helping to keep you alive. 

You need them to help promote a healthy immune system, to absorb and produce nutrients, and to eliminate waste. They even help to manage your appetite, a healthy weight and your overall outlook or mindset.

In addition, gut health affects skin health, for a healthy gut microbiome is important for maintaining a healthy skin microbiome — which plays a crucial role in supporting the skin, helping to keep it populated with beneficial  microorganisms and maintaining its barrier function. 

How to improve your gut microbiome

1. Eat a gut-friendly diet

Wondering what you can eat to improve your gut microbiome? The goal is to include plenty of the best foods for gut health in your daily diet, such as probiotic and prebiotic foods. These also are one of the ways for how to reduce bloating.

How to improve gut health? Here are some of the top foods for a healthy gut microbiome:

• Probiotic foods — This includes things like yogurt, kefir, kombucha, sauerkraut, kimchi and fermented soy products. What do probiotic foods do to your gut? They contain a wide range of “live and active cultures” plus other nutrients that support digestion and overall health. Eating them promotes a healthy balance of microbes in the gut, which is useful for keeping you healthy and reducing occasional constipation, gas and bloating. You can even learn how to ferment foods at home.

• Prebiotic foods — Some of the best sources include: leafy greens, onions, garlic, artichokes, asparagus, broccoli, underripe bananas, berries, seeds, nuts, whole grains and legumes. These help to provide “fuel” that probiotic bacteria thrive off of, allowing them to flourish.

• High-fiber foods — Fiber supports a healthy gut microbiome, with a balanced and diverse gut microbiota. It also promotes the health of the colon and surrounding digestive areas — and reduces the likelihood of occasional constipation. High-fiber foods include broccoli, legumes, apples and pears, berries, sweet potatoes and avocados.

• Antioxidant-rich foods — Antioxidant foods, such as berries, leafy greens, cruciferous veggies, herbs and spices, cocoa, red wine and green tea function as beneficial foods that contribute to general health. If you find it hard to squeeze enough of these into your meals, try Ancient Nutrition’s Organic SuperGreens powder, in which you'll find superfoods like wheatgrass, spirulina, beatroot, oat grass and more that contribute to healthy digestion, energy and detoxification as well as reducing occasional constipation, gas, and bloating.

• Vitamin C and magnesium foods — These nutrients help to nourish the gut lining, fight free radicals, and aid in elimination by supporting normal muscular functions. Some of the top sources are: kiwi, citrus fruits, spinach, kale, pineapple, mango, bell peppers, dark chocolate, yogurt and cruciferous veggies like Brussel sprouts, sweet potatoes, whole grains and bananas.

• Bone broth (which provides collagen) — Collagen is a type of structural protein that helps to form and support a healthy gut lining and gut, which is where the majority of your immune system is located. Consuming more collagen, both from supplements such as our Multi Collagen Protein and from bone broth, can support gut lining integrity which is essential for functions such as nutrient absorption.

These foods are also what should be on any gut health grocery list.

What can you eat to balance your gut microbiome after taking antibiotics? 

All of the foods listed above are great choices, especially those with probiotics such as yogurt and sauerkraut. Since antibiotics can kill off both good and bad bacteria living in your gut, you want to replenish the good types ASAP by eating probiotic-rich fermented foods. As always, you should consult your healthcare professional. 

2. Supplement with SBO probiotics

While certain gut supplements shouldn’t replace a healthy diet that includes a variety of nutrient-dense gut-friendly foods, taking a probiotic supplement is still a smart way to support gut health.

Probiotic supplements, usually in capsule form, serve as a convenient way to obtain strains of microbes that are known to benefit overall gut health.

Ancient Nutrition’s SBO Probiotics provide not only special types of soil-based organism (SBO) probiotics, but also prebiotics and postbiotics for even more positive effects on your microbiome. Together, these three — called the “trifecta” for gut health — support your digestive system and help keep gut function on track.

SBOs are a particular type of probiotic found in soil that are considered “hardy” and tolerant to the harsh conditions of the stomach, which helps with their absorption. Taking SBO probiotics regularly can help reduce occasional constipation, bloating and flatulence/gassiness, and can support healthy immune system function. An added benefit: They don’t need to be refrigerated like many other types of probiotics. 

Ancient Nutrition offers several types of SBO Probiotics based on individual needs, including SBO Probiotics Gut Restore (provides 25 billion CFUs per serving at time of manufacture) and SBO Probiotics Ultimate (provides 50 billion CFUs per serving at time of manufacture). There's also SBO probiotic formulas for women and men.

SBO Probiotics Trinity are a new entry to this category. They contain a proprietary, clinically studied blend of postbiotics and parabiotics to bring you our most well-rounded probiotic yet. What are parabiotics? They contain inactivated unused parts of probiotics. Some studies show that parabiotics can create a favorable environment for good bacteria to grow. They’re believed to help nourish and positively influence the microbiome.

If you're new to the probiotic supplement category, consider starting with Ancient Nutrition's SBO Probiotics Once Dailies, as you only need to remember to take one capsule per day.

In addition, consider adding digestive enzymes to your routine in order to make sure your foods are being properly digested, an issue that can crop up as one ages.

3. “Leaky Gut” supplement formulation

Ancient Nutrition’s Leaky Gut capsules are formulated with a powerful blend of botanicals as well as adaptogenic mushrooms and 2 billion CFUs* (*at the time of manufacture) of probiotics. They promote a healthy gut lining and gut integrity, support healthy gut function and healthy gut microflora, plus reduce occasional constipation, gas and bloating.

This multifaceted formula features the key ingredients licorice root, astragalus, marshmallow, lion’s mane mushroom and L-glutamine. Marshmallow root acts as an antioxidant and can help to generally soothe the lining of the gut while supporting overall gastrointestinal health.

L-glutamine is the most abundant free amino acid in the body and supports gut integrity and a healthy gut lining.

Licorice root is considered an adaptogenic herb that supports normal absorption of nutrients. It contains the active compound called glycyrrhizin that is generally known to help support the health of the mucosal lining of the gut, which assists in a healthy response to inflammation.

For the best results, try taking Leaky Gut capsules on an empty stomach, either first thing in the morning or right before bed, at the same time each day. Please refer to the label directions for suggested use.

(You may also be interested in Ancient Nutrition’s Leaky Gut Bundle, which includes Leaky Gut capsules, SBO Probiotics Gut Restore capsules and Digestive Enzymes capsules.)

4. Collagen protein

Collagen is the main type of protein in the body that gives connective tissues, including those that form the gut lining, their health and strength. It's why collagen for gut health can be so effective.

Using a collagen powder supplement each day is a convenient and effective way to help give your body the building blocks, in the form of amino acids, that it needs to make its own collagen.

Ancient Nutrition’s Multi Collagen Protein powder features 10 types of collagen from four real food sources, plus it contains no fillers, sugar, artificial flavors or artificial preservatives, ensuring you get the highest quality collagen available. Multi Collagen Protein specifically features hydrolyzed collagen, meaning the protein molecules are broken into smaller molecules, making them easier for your body to digest, absorb and use.

Aim to consume between 1–3 servings daily, or about 10 to 30 grams of collagen protein. (Note: Please read and follow label directions for use.)

In addition to providing you with collagen protein, Ancient Nutrition’s Multi Collagen Protein Gut Restore Powder formula provides you with 2 billion CFUs of soil-based organism (SBO) probiotics, powerful prebiotics and two kinds of glutamine for overall gut support.

One serving contains 9 grams of protein from 10 types of collagen, all derived from sustainable sources, along with botanicals like ginger root, licorice root and peppermint leaf extract which have general digestive-soothing effects.

Together, collagen plus probiotics, glutamine and botanicals help promote healthy gut microflora, support integrity of the gut lining, reduce occasional bloating, and more, such as supporting healthy joints and skin. Try mixing one heaping scoop, which has a light lemon/ginger flavor, with 8 ounces of water, juice, tea or your favorite smoothie.

Otherwise, the Multi Collagen Protein Gut Restore Capsules use traditionally gut-supporting ingredients to support gut microflora, gut lining and gut integrity. They include 5 billion CFUs Bacillus coagulans and Bacillus subtilis.

5. Avoid gut disruptors

A number of foods and lifestyle habits ("gut disruptors" like too much sugar and stress) can take a toll on gut function, including that they can disrupt the balance of “gut bugs” in your microbiome. 

Things to avoid in order to support your microbiome include:

• Consuming too much sugar, including from sweetened drinks, desserts, sweetened dairy products, cereals and snack bars. Sugar can feed unhealthy bacteria in your gut, which is the opposite of what you want. Instead, opt for complex carbs and foods with natural sugar plus fiber, such as low-sugar fruit.

• High consumption of alcohol and smoking cigarettes, both of which can trigger over-the-top inflammation and hinder healthy immune system function.

• Chronic stress, which impacts hormonal health and may even negatively impact the gut lining (where many hormones and neurotransmitters are made). To keep it under control, try things like exercise, deep breathing, meditation and mindfulness exercises like yoga, reading and journaling.

• Sleep deprivation, another source of bodily stress. Aim for 7 to 9 hours of quality sleep per night.

• Being too sedentary. Your body requires movement to stay healthy and to detoxify itself, so build exercise into your daily routine.

• Taking antibiotics when not necessary (use of antibiotics should ideally be limited to when you really need them). Consult your healthcare professional about this.