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Evidence based
Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument.

This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

8 Best Microbiome Supplements for a Happier, Healthier Gut

Written by Michael Ruscio on June 6, 2024

Our Favorite Microbiome Supplements Backed by Science and Clinical Experience

When you have gastrointestinal issues, it’s tempting to buy every new supplement you can get your hands on to try to fix the problem and get your microbiome back to a good place. But it’s much better (and more cost-effective) to choose a combination of supplements based on your individual needs rather than what’s trendy in the wellness world right now. The resulting supplement “stack” might not be what’s popular, but it will be tailored to you. 

This article is about eight supplements we’ve found to be useful in clinical practice for healing the gut and restoring a balanced microbiome, listed in order of importance at the clinic. I’ll also talk about a couple popular supplements that could set back your healing unless you have the right approach.

1. Probiotic Supplements

Dozens of clinical trials and large-scale meta-analyses show that probiotics are consistently better than placebos at improving leaky gut, reducing inflammation, increasing beneficial bacteria, and correcting gut dysbiosis (imbalanced gut microbes) [1].

Probiotics can also be just as effective as antibiotics for treating small intestinal bacterial overgrowth (SIBO) [2] and Giardia infections [3]. They may work by attacking the bacteria or parasites directly, or by making the gut environment less hospitable so the bad guys don’t stick around [4].

best microbiome supplements

In both research and my clinical experience, probiotics are an excellent treatment for common gut ailments, like irritable bowel syndrome (IBS) [5], inflammatory bowel disease (IBD) [6], and constipation [7, 8]. They’re also great for preventing the side effects of antibiotics [9].

This is why we use probiotics as foundational gut support at The Ruscio Institute for Functional Health. While many people believe they need antibiotics or antimicrobial herbs first to kill off pathogens in the gut, often all they need is to reintroduce some good bacteria.

From helping hundreds of people improve their gut health over the last decade, we’ve developed an evidence-based probiotic therapy protocol called Probiotic Triple Therapy. Triple Therapy combines the three main types of probiotics—a blend of Lactobacillus and Bifidobacterium species, soil-based probiotic strains, and a probiotic yeast called Saccharomyces boulardii—to provide a full spectrum of beneficial bacteria and encourage a happy, healthy gut microbiome. 

Our Triple Therapy Sticks offer a convenient way to get all three of these probiotic types in one effective supplement. As a powder, you can easily mix your probiotics in a beverage or food, and increase or decrease as needed.

best microbiome supplements

2. Herbal Antimicrobials

Our next microbiome recommendation is actually a category of supplements. Antimicrobial herbs can be effective against many underlying gut infections, including: 

In a small clinical trial our team conducted, herbal antimicrobials, with or without enzymes that dissolve biofilms, eradicated SIBO in about 40% of patients. That’s close to the 50–60% eradication rate of antibiotics [33, 34]. When combined with probiotics, herbal antimicrobials may be almost as effective (86%) as antibiotics plus probiotics [2].

One big caveat here: It’s important to always use herbal antimicrobials with the guidance of a knowledgeable healthcare professional. People with compromised immunity should take extra caution. Just because herbal antimicrobials are natural doesn’t mean they aren’t potent and can’t cause problems if used incorrectly [35]. 

But in general, they tend to be gentler on the gut microbiome and don’t seem to contribute to bacterial resistance, such as methicillin-resistant Staphylococcus aureus, aka MRSA [36].

Want to learn more about herbal medicine and how it can support your health and well-being? Check out my conversation with herbalist Olivia Amitrano: 

3. Elemental Diet

Maybe an elemental diet counts as more than just a supplement (it’s more of a therapeutic meal replacement), but it can be an enormously helpful tool to reset your gut and recalibrate the microbes in it. (That said, if your gut is already healthy, it’s also a great high-protein option to keep it that way!)

The following are a few mechanisms behind why an elemental diet may help people with microbiome-disrupting conditions, such as SIBO, eosinophilic esophagitis, and Crohn’s disease.

  • It gives your digestive tract a break and a chance to rest, heal, and then repair itself [37, 38].
  • It reduces inflammation [37, 39].
  • It starves SIBO and other overgrowths [40].

In terms of how to use an elemental diet for gut microbiome health, here are a few options: 

  • As a gut-healing meal replacement, you can use it instead of one or more meals daily.
  • As a gut reset, you can use it for 1–4 days on your own (without clinical supervision).
  • As a remedy for potential overgrowths, you can use it for 1–3 weeks with clinical supervision.

We even have this Dosing Calculator for our elemental diet formula, Elemental Heal, to make it easy to find your best personal dose (especially if you want to use it for multiple days).

4. Glutamine

Maybe you’ve heard of this microbiome supplement. Glutamine is the most abundant free amino acid in human blood and the main energy source for intestinal cells [41]. Glutamine may reduce inflammation and leaky gut by supporting the integrity of the tight junctions that hold intestinal cells together [41, 42, 43, 44]. One study found that glutamine was better than a placebo for reducing leaky gut and improving IBS symptoms [42].

You’ll often see glutamine labeled as L-glutamine [45, 46]. L-glutamine is the molecular form found in foods and commonly used in supplements.

I talk more in this video about using a glutamine supplement (along with probiotics and bovine colostrum) as part of a gut healing protocol.

5. Zinc Carnosine

Let’s switch our focus now to an important nutrient for the gut and immune system: zinc. Zinc is an essential mineral in meat, eggs, shellfish, cheese, legumes, and tofu that enables enzyme activity and cell production, particularly in the gut lining and skin [47]. 

Another nutrient in meat is L-carnosine, an antioxidant that may play a role in wound healing, immune function, diabetes, and vision [47].

As you’ve probably figured, the compound zinc carnosine is a combo of these two nutrients that’s more effective than zinc alone. This is because carnosine can enhance the body’s absorption of zinc and deliver it more efficiently to the tissues, especially in the stomach and intestines [47]. 

Randomized controlled trials have shown that zinc carnosine can improve stomach ulcers and leaky gut [48, 49, 50, 51]. Adding this nutrient may therefore improve the gut terrain to support a healthy microbiome. 

At the risk of starting to sound salesy, this is another key supplement we include in Gut Rebuild Nutrients for intestinal support and leaky gut. We’ve seen great results with 75 mg in the clinic, but consult your provider for guidance on dosing.

6. Immunoglobulins

In the clinic, we have found immunoglobulins to be very effective for treating stubborn gut issues that don’t resolve completely with diet changes, probiotics, and other therapies. That makes them solid microbiome supplements in our book.

Serum-derived bovine immunoglobulins are a mix of protein and immunoglobulin G (IgG) that exist naturally in the gut lining. A randomized clinical trial and a later assessment of the same study showed that immunoglobulins may reduce bloating, loose stools, and urgency in people with diarrhea-predominant or mixed-type IBS [52, 53]. Similarly, other studies found that immunoglobulin therapy was associated with reductions in IBS symptoms [54, 55, 56, 57].

We typically use our immunoglobulin supplement, Intestinal Support Formula, at the clinic. Adding an immunoglobulin formula can support a healthy immune response in the gut by binding to and fighting harmful bacteria, allowing for a healthier microbiome and gut overall. 

7. Curcumin

Curcumin is an anti-inflammatory compound that comes from the spice turmeric. People started using it medicinally in India at least 4,000 years ago [58]. Human studies have found that curcumin can benefit people with IBS and IBD, and it has the potential to help eradicate H. pylori [59]. In other clinical research, curcumin outperformed placebo at reducing gut pain, diarrhea, constipation, and indigestion [60]. An in vitro study also suggests it has the potential to reduce leaky gut [61].

All of this points to curcumin’s ability to modulate the gut microbiome by reducing systemic inflammation, eradicating pathogenic organisms (like H. pylori) from the digestive tract, and improving digestive health. In the clinic, we use curcumin when someone seems to have a high inflammatory burden, especially in cases of IBD or severe IBS.

8. Vitamin D

Interestingly, we have early evidence suggesting that natural vitamin D (mainly from healthy sun exposure and some from foods, like oily fish) and supplemental vitamin D may regulate the gut bacteria [62, 63, 64, 65, 66, 67]. However, the jury is still out as far as how and to what degree [62, 63, 64, 65, 66, 67]. 

That said, a lack of vitamin D is often associated with gut disorders [68], so it stands to reason that improving your vitamin D status would contribute to gut health. Clinically, we’ve found that supplemental vitamin D can support a healthy gut and microbiome, especially in those with low vitamin D (less than 30 ng/mL). 

In any case, we need vitamin D for overall health: to regulate the immune system, metabolize calcium, grow and develop cells, and keep our bones strong [69, 70, 71]. 

Bonus: Popular Gut Supplements That May Impede Your Progress (When Used Incorrectly)

Two popular supplements often end up causing further gut issues for people with gut dysbiosis, depending on whether their microbes are imbalanced in the small intestine, large intestine, or both. 

Fiber

The first supplement is fiber. Metamucil, Citrucel, psyllium, and acacia fiber are common examples of supplemental fiber, typically used to add bulk to the stool and improve bowel movements. Often, well-meaning gut doctors prescribe fiber supplements to patients with constipation or diarrhea, but fiber can easily become a double-edged sword. 

Although supplemental fiber can be especially great for constipation relief, it can also worsen gut troubles in some people [72, 73, 74]. For people with a sensitive gut, starting with a lower dose (2.5 g, or ½ tsp, of psyllium or pectin) and slowly increasing over time often resolves the issue [72]. Five to 10 grams, or about 1 to 2 teaspoons, a day is the ideal range for most people. 

For those whose symptoms get worse with even low doses of supplemental fiber, more complex gut issues, such as dysbiosis or leaky gut, may be at play. In such cases, other steps, like dietary and lifestyle changes, probiotics, and possibly antimicrobials should likely come in first to curb the underlying problem. Once the roots of chronic gut symptoms have been handled, then adding supplemental fiber should be less of an issue. 

Prebiotics

The second supplement is prebiotics. These commonly include inulin, fructo-oligosaccharides, and galacto-oligosaccharides. Prebiotics in foods and supplements are also a type of fiber, but their primary function is to feed the microbiome so that good bacteria will make byproducts like butyrate, a short-chain fatty acid with health benefits. 

Unfortunately, multiple meta-analyses with thousands of participants have found that prebiotics have no beneficial effect on people with IBS or similar symptoms, even if these supplements increase the numbers of beneficial species, like Bifidobacterium [74, 75, 76, 77, 78, 79, 80].

Typically, for clients with chronic gut symptoms, I recommend avoiding prebiotic supplements (or taking no more than 3–5 mg/day, which is commonly added to probiotics) in the early stages of their gut healing. After we’ve implemented changes to strengthen their gut health, they may tolerate prebiotics and benefit from them. In the clinic, we’ve found well-placed prebiotics especially good for helping some clients beat Candida. 

Choose Dietary Supplements Wisely

When looking for supplements to improve the gut microbiome, a variety of options can support different aspects of gut health. Whether we’re hoping to directly impact our microbes, support their living environment, improve our immune health, or put the brakes on systemic inflammation, a few choice supplements are worth a look. 

When considering the best microbiome supplements, working with an experienced clinician can streamline the process so you don’t waste time or money on supplements that aren’t right for you. If you’re so inclined, check out our clinic, the Ruscio Institute for Functional Health, and schedule a consultation today.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.

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