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8 Best Microbiome Supplements for a Happier, Healthier Gut

Skip the trendy gut stack. Here are eight microbiome supplements that earn their place in clinical practice, and how to use them without making symptoms worse.

Written by Michael Ruscio

on January 16, 2026

Reviewed by Hannah Wright Hannah Wright

Key Takeaways:
  • More supplements rarely equal better results. The goal is choosing the right tools for your gut, in the right order, at the right dose.
  • Probiotics are often the foundation. When used at therapeutic doses and for long enough, they may help improve dysbiosis, reduce inflammation, and alleviate common gut symptoms.
  • Herbal antimicrobials can be powerful, but timing matters. They may help when infections or overgrowth are driving symptoms, and are best used with guidance.
  • For stubborn symptoms, the “gut terrain” often needs support. Tools like an elemental diet, glutamine, zinc carnosine, and immunoglobulins may help restore resilience.
  • Some popular gut supplements can slow progress when used too early. Fiber and prebiotics may be helpful later, but they may worsen bloating or irritable bowel syndrome (IBS) symptoms for sensitive guts.

When gut symptoms don’t improve, it is easy to assume the answer is another supplement. And another. And another. The microbiome space is crowded, persuasive, and very good at making each new product sound like the missing piece.

But in practice, that approach rarely works.

It’s not about how many microbiome supplements you take, but which ones make sense for your gut, at the right time. A well-chosen combination can support balance and healing. A poorly timed or overly aggressive gut stack can slow progress or even worsen symptoms.

In this article, I’ll walk through eight supplements we’ve found most useful in clinical practice for supporting gut health and the microbiome. They will be listed in the order we typically prioritize them at the Ruscio Clinic. I’ll also touch on a few popular options that can be counterproductive unless the right foundation is in place.

1. Probiotic Supplements

There’s a large body of evidence showing 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 may be just as effective as antibiotics for treating small intestinal bacterial overgrowth (SIBO) 2 and help eliminate Giardia infections when used alongside antibiotics 3 4. 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 5.

In both research and my clinical experience, probiotics are excellent at addressing common gut ailments, such as irritable bowel syndrome (IBS) 6, inflammatory bowel disease (IBD) 7, and constipation 8 9. They’re also great for preventing the side effects of antibiotics, such as diarrhea, nausea, and Candida overgrowth 10.

Over the last decade, while working with hundreds of clients, one pattern became evidently clear. Probiotics were often treated as optional or secondary, when in practice they proved to be foundational. At the right dose and with the right blend, they consistently led to meaningful improvements in gut health in ways many other supplements did not.

That very insight is what ultimately led us to develop our own probiotic formulation, tailored to the dosage and strain combination proven to work best through years of clinical use and refinement. We call it Triple Therapy. If you’re curious, you can explore the research behind the formula here.

When we talk about probiotics, one of the most common sources of confusion is dose and duration. Many products are taken in amounts that are unlikely to meaningfully influence the gut, or are stopped before real change appears.

Below is the evidence-backed probiotic framework we typically start with in practice. It reflects the categories, dose ranges, and minimum timeframes we’ve found most consistently supportive for restoring balance.

best microbiome supplements

2. Herbal Antimicrobials

Our next microbiome recommendation is not a single supplement, but a category. And truthfully, it’s one that often gets overlooked or misunderstood.

When used thoughtfully, herbal antimicrobials can help address underlying gut infections and imbalances that keep the microbiome stuck in an unhappy state. Through clinical practice and research, they have been studied for their potential role in supporting people with:

They are also commonly used in SIBO protocols.

In a small clinical trial conducted by our team, herbal antimicrobials, used with or without biofilm-disrupting enzymes, eradicated SIBO in roughly 40% of clients. That’s close to the 50–60% eradication rate of antibiotics 31 32. When combined with probiotics, herbal antimicrobials may be almost as effective (86%) as antibiotics plus probiotics 2.

There is an important caveat: Herbal antimicrobials are potent and should be used with professional guidance, particularly for individuals with compromised immunity. “Natural” does not mean risk-free, and improper use can cause setbacks 33. 

That said, they tend to be gentler on the gut microbiome than antibiotics and do not appear to contribute to antibiotic resistance patterns, such as those seen with MRSA (a type of antibiotic- resistant staph) 34.

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

An elemental diet is technically more than a supplement. It’s a therapeutic meal replacement. And in the right context, it can be one of the most effective tools we have for resetting the gut and giving the microbiome a chance to rebalance.

Think of it as pressing pause.

Instead of asking your digestive system to break down whole foods, fiber, and complex proteins, an elemental diet delivers nutrition in its simplest, most absorbable form. That changes the gut environment in a few important ways.

Firstly, it gives the digestive tract a break 35 36. When digestion is less demanding, the gut lining can calm down, repair, and restore normal function.

Second, it may help reduce inflammation 35 37. By removing common dietary triggers and simplifying digestion, reduced inflammatory signaling in the gut often follows.

And third, it limits fuel for problematic microbes, including the bacterial overgrowth that is the hallmark of SIBO. An elemental diet is one way to starve out unwanted bacteria and help shift the microbial balance 38.

Ways to Use the Elemental Diet

There is more than one way to use an elemental diet, depending on your goals and how sensitive your gut is.

  • As a gut-supportive meal replacement, it can replace one or more meals per day.
  • As a short gut reset, it can be used for 1 to 4 days without clinical supervision.
  • As part of a protocol for suspected overgrowth, it can typically be used for 1 to 3 weeks with clinical guidance.

To learn more about how the elemental diet works and if it may be the right fit for you, check out our Elemental Diet article. 

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 39 40. Glutamine may reduce inflammation and leaky gut symptoms by supporting the integrity of the tight junctions that hold intestinal cells together 40 41 42 43. One study found that glutamine was better than a placebo for reducing leaky gut and improving IBS symptoms 41.

You’ll often see glutamine labeled as L-glutamine 44. L-glutamine is the molecular form found in foods and commonly used in supplements.

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

5. Zinc Carnosine

Zinc is an essential mineral in meat, eggs, shellfish, cheese, legumes, and tofu that enables enzyme activity and cell production, particularly in our gut lining and skin 45. 

Another nutrient in meat is L-carnosine, an antioxidant that may play a role in wound healing, immune function, diabetes, and vision 45.

The compound zinc carnosine is a combination 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 45. 

Randomized controlled trials (RCTs) have shown that zinc carnosine may improve stomach ulcers and leaky gut 46 47 48 49. Adding this nutrient may therefore improve the gut terrain to support a healthy microbiome. 

At the risk of sounding 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 proteins and immunoglobulin G (IgG) that exist naturally in the gut lining. IgG is an antibody that your body makes to help fight off infections. 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 (IBS-D) or mixed-type IBS 50 51. Similarly, other studies found that immunoglobulin therapy could be associated with reductions in IBS symptoms 52 53 54 55.

We typically use our immunoglobulin supplement, Intestinal Support Formula, at the clinic. Adding an immunoglobulin formula can support a healthy immune response in the gastrointestinal system 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 56. Human studies have found that curcumin can benefit people with IBS and IBD, and it has the potential to help eradicate H. pylori 57. In other clinical research, curcumin outperformed a placebo at reducing gut pain, diarrhea, constipation, and indigestion 58. An in vitro (test tube) study also suggests it has the potential to reduce leaky gut 59.

All of this highlights 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 often 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 foods, like oily fish) and supplemental vitamin D may regulate gut bacteria 60 61 62 63 64 65. However, the jury is still out on how and to what degree it can help 60 61 62 65. 

That said, a lack of vitamin D is often associated with gut disorders 66 67, so it stands to reason that improving your vitamin D status would potentially 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 68 69 70. 

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

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 71 72 73. 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 71. Five to 10 grams, or about one to two teaspoons, a day is the ideal range for most people. 

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

Prebiotics

Commonly used prebiotics 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 numerous 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 73 74 75 76 77 78.

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 aiming 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 considering taking the next steps in navigating your gut health and finding the best supplementation plan for your needs, the Ruscio Clinic is accepting new clients. We’d love to help you find what’s right for you.

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, natural health provider, 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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Written by Michael Ruscio

on January 16, 2026

Reviewed by Hannah Wright Hannah Wright

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