Can Probiotics Help to Improve Gut Health?

If you want to improve gut health, or even optimize your overall health, you’ve probably seen a thing or two about probiotics. An estimated 25% of people worldwide had used a probiotic supplement in 2021, according to one survey.¹ Probiotics are another hot topic in the health and wellness space, and for good reason. When probiotics are taken for specific, targeted reasons (as we will dive into later), they can have amazing benefits! In the functional medicine realm, the gut is commonly referred to as the “second brain,” because it has SO many important functions, including its impact on immune health, thyroid, hormones, and skin.

Studies Related to Probiotics and Improved Gut Health

If there is an imbalance in the gut, that can lead to a wide variety of symptoms. Some common gut imbalance examples are SIBO, leaky gut, IBS, IBD, and gut pathogen infections. Depending on the symptoms experienced, probiotics can be a useful treatment tool. One study among many found probiotics were beneficial in managing symptoms in those with IBS when compared to a placebo.²

Another prevalent gut imbalance is Small Intestinal Bacterial Overgrowth, or SIBO (you can read more about it in our blog here). In one meta-analysis, probiotics were a positive treatment method for SIBO by improving symptoms and lowering bacterial overgrowth.³ Also, several studies have shown promising impacts of certain probiotic strains on eliminating parasites, such as Blastocystis hominis.

When it comes to probiotics, there is lots of terminology used that may get confusing. Let’s break each of these terms down:

  • Probiotic – living microorganism with a positive impact on the host when present in sufficient quantities
  • Prebiotic – substance used as fuel for the beneficial bacteria to feed on
  • Symbiotic – a combination of prebiotics and probiotics
  • Post-biotic – the leftovers from probiotics that have a beneficial effect on the host
  • Microbiome – all microorganisms that live in a host environment

Now that we have covered the basics on probiotic-related terminology, let’s dive into how they are further classified.

Probiotic Classification

There are currently an estimated 100 trillion microorganisms in our world today, with more constantly being discovered! There are currently six main phyla (or families) of bacteria: Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, Actinobacteria, and Verrucomicrobia, which can further be classified into specific strains and species of bacteria. Each of these main families play a critical role in the body. The two most prevalent families of bacteria are Bacteroidetes and Firmicutes. When it comes to the amount and presence of bacteria in the gut microbiome, there are several factors at play:

Factors affecting gut microbiota

Image Source: Research Gate

With this in mind, it is important to determine the state of the microbiome before beginning probiotic supplementation. This is why gut microbiome testing is so important! Also, fun fact – nutrition accounts for over 50% of our microbiome, just another reminder that what we eat is critical! Now that we have covered how probiotics are classified, let’s discuss how they actually work in the body.

How Do Probiotics Work to Improve Gut Health or Achieve Other Health Goals?

As we have already discussed, probiotics have a lot of research-backed benefits. But how exactly do they work and how can they improve gut health?

Probiotics are meant to balance the gut’s microbiome. They can also fight against pathogens, help regulate the immune response, and strengthen the gut lining. Externally, probiotics have been shown to decrease GI and upper respiratory tract infections (URTI), improve mood, boost exercise recovery, and enhance gym performance. Who wouldn’t want that? Probiotics have also been shown to help reduce diarrhea and aid in skin health.

Although research is ever-evolving in probiotic usage, research is also limited, but expanding, into other proposed health benefits. Autoimmune conditions are becoming more common and increasingly diagnosed in the United States. Even though the scientific community has not proposed a strong, direct link between autoimmune conditions and probiotic use, current evidence suggests probiotics can help alleviate co-current symptoms experienced with autoimmune conditions, such as inflammation and impaired gut-barrier function.

In addition, a recent meta-analysis found promising evidence that probiotics can be used to help regulate hormone-related conditions, especially polycystic ovarian syndrome (PCOS). From the collection of studies analyzed, probiotics were shown to improve hormone levels and inflammation markers when compared to a placebo in those diagnosed with PCOS.

The 3 Most Common Types of Probiotics

There are currently three main types of probiotics studied in functional medicine relating to gut health: Saccharomyces boulardii, Lactobacillus and Bifidobacterium species, and soil-based probiotics.

Probiotic Type Benefits Example
Saccharomyces boulardii
  • Regulate bowel movements 
  • Lessen likelihood of diarrhea 
  • Lower inflammation
  • Support the gut-immune connection
  • Should NOT be used in those with a weak immune system 
Saccharomyces boulardii

from Klaire Labs

Lactobacillus and Bifidobacterium species
  • Decrease inflammation
  • Increase immune health
  • Can help rebalance gut microbiome 
  • Most studied species of probiotics 
  • Should NOT be used in those with a weak immune system 
  • Discuss supplement safety with your provider if you are elderly, pregnant, or breastfeeding 
UltraFlora Spectrum from Metagenics


Soil-based probiotic 

(aka “spore-forming bacteria”)

  • Minimize complications from antibiotics
  • May improve depression-related symptoms
  • May help alleviate allergies 
  • Alleviate diarrhea 
  • Limited research
  • Potential to become pathogenic in those with a weakened immune system
MegaSporeBiotic from Microbiome Labs



Saccharomyces boulardii is a specific, beneficial fungal strain. S. boulardii has specifically been shown to regulate bowel movements, including decreasing incidence of diarrhea. In addition, this yeast has been shown to help lower inflammation and support gut-related immune health. Although this bacteria does not colonize (or live inside) us human hosts, it does boast these beneficial impacts.

Lactobacillus and Bifidobacterium species are the most-studied probiotics, with hundreds of trials currently published. These species are also known as lactic-acid producing bacteria. They can help decrease inflammation and boost immune health. Similarly to S. boulardii, these bacteria do not colonize us as hosts, but do boast these beneficial impacts.

Beneficial bacteria in probiotics that can improve gut healthFinally, the soil-based probiotics consist of over 100 specific strains of bacteria. They also have gotten the nickname spore-forming bacteria. Although research is more limited compared to the other two categories, these probiotics can help alleviate diarrhea, decrease antibiotic-related side effects, improve symptoms of depression, and may even help alleviate allergies.


What Foods Contain Probiotics and Prebiotics?

In addition to probiotics taken from supplements, there are many prebiotic and probiotic rich foods that support a healthy lifestyle and can even help improve gut health.

Some examples of probiotic foods include fermented foods, like kefir, kimchi, natto, kombucha, yogurt, pickles, and sauerkraut, along with fermented vegetables. On the other hand, prebiotic foods most often contain more fiber, such as bananas, onions, asparagus, garlic, mushroom, and Jerusalem artichoke. These are all great to incorporate into your diet on a regular basis to continue to increase diversity of the gut microbiome.

Food sources for probiotics and prebiotics

Image Credit: Everyday Health

How to Choose the Best Probiotic Supplement to Improve Gut Health or Provide Other Benefits

When it comes to choosing a probiotic supplement, a multi-strain probiotic is a great option due to increasing the amount of species the host is exposed to. In addition, it is important to choose a high-quality, third-party tested probiotic supplement. That’s because low-quality supplements may further exacerbate symptoms or have a null effect on the host. If you don’t know where to start, comprehensive gut microbiome testing is a great first step, as probiotics can have a multitude of benefits.

At Rachel Scheer Nutrition, we offer comprehensive, functional lab testing that looks at not only your gut microbiome, but also hormones, heavy metals, thyroid, certain vitamins and minerals, and so much more. We believe in testing, and not guessing, to see not only the health of your gut microbiome, but also ways to optimize your health and wellness. Here’s to improving gut health with beneficial gut bacteria!


  2. McFarland LV, Dublin S. Meta-analysis of probiotics for the treatment of irritable bowel syndrome. World J Gastroenterol. 2008;14(17):2650-2661. doi:10.3748/wjg.14.2650
  3. Zhong C, Qu C, Wang B, Liang S, Zeng B. Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence. J Clin Gastroenterol. 2017;51(4):300-311. doi:10.1097/MCG.0000000000000814
  4. Dinleyici EC, Eren M, Dogan N, Reyhanioglu S, Yargic ZA, Vandenplas Y. Clinical efficacy of Saccharomyces boulardii or metronidazole in symptomatic children with Blastocystis hominis infection. Parasitol Res. 2011;108(3):541-545. doi:10.1007/s00436-010-2095-4
  5. ​​Jäger R, Mohr AE, Carpenter KC, et al. International Society of Sports Nutrition Position Stand: Probiotics. J Int Soc Sports Nutr. 2019;16(1):62. Published 2019 Dec 21. doi:10.1186/s12970-019-0329-0
  6. Stojanov S, Berlec A, Štrukelj B. The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease. Microorganisms. 2020;8(11):1715. Published 2020 Nov 1. doi:10.3390/microorganisms8111715
  8. Marttinen M, Ala-Jaakkola R, Laitila A, Lehtinen MJ. Gut Microbiota, Probiotics and Physical Performance in Athletes and Physically Active Individuals. Nutrients. 2020;12(10):2936. Published 2020 Sep 25. doi:10.3390/nu12102936
  9. Shamasbi SG, Ghanbari-Homayi S, Mirghafourvand M. The effect of probiotics, prebiotics, and synbiotics on hormonal and inflammatory indices in women with polycystic ovary syndrome: a systematic review and meta-analysis. Eur J Nutr. 2020;59(2):433-450. doi:10.1007/s00394-019-02033-1

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