What Are Probiotics? The Importance of Good Microbiome Health

Yogurt in glass jars

Probiotics (beneficial strains of bacteria) should make up the majority of your microbiome, the collection of live microorganisms that live in your digestive system (and on your skin). You’re born with some probiotics, but you can also obtain probiotics from foods, beverages, and probiotic supplements. 

In this article, we’ll cover why probiotics are important for your gut health, other systemic health benefits, types of probiotics (including food sources) and probiotic strains, as well as what to look for in terms of quality and efficacy.

What Are Probiotics and Why Are They Important?

What are probiotics: Good and  Bad Bacteria infographic

What are probiotics? Probiotics are beneficial strains of bacteria that live in and support the gut microbiome, a complex ecosystem of 300-500 bacterial species within your digestive tract. We know now from decades of research that the gut microbiome not only affects your digestion but also the functioning of your immune system, hormones, nervous system, and more [1].

Within the microbiome, there is a delicate balance between good and bad microbes; probiotics and pathogens. If this balance is skewed toward the pathogens (fungi, bad bacteria, or parasites) being the dominant force, we end up with gut dysbiosis. Dysbiosis can cause gut-related symptoms like diarrhea or constipation, but it can also cause many other health issues and conditions, including fatigue, poor mood, low energy, disrupted sleep, depressed immune function, autoimmunity, and more [1]. 

Fortunately, probiotics can tip the scales back in your favor and bring balance to your gut environment, helping to alleviate many of these symptoms and conditions.

Probiotics Are Essential in Modern Life

In pre-modern times, human beings had much more exposure to different species of bacteria: primarily through connection to rich soil where they foraged and grew their food, consumption of traditional fermented foods, contact with animals, natural childbirth, and breastfeeding. From birth, you were surrounded by a diverse range of microbial communities and interacted with them regularly.

Our environment today is much more sterile. Our exposure to microorganisms is limited by depleted soil and less consumption of whole and fermented foods. Antibiotic use, antibacterial soaps, hand sanitizer, and cleaners demolish the bacterial communities around and within us. Unhealthy diets and even a sedentary lifestyle and poor sleep only harm beneficial bacteria further [2, 3]. 

Due to these compounding factors, bacterial imbalances in our microbiomes have become the norm.

What are probiotics: hand in soil

How Probiotics Can Help You

This is where probiotic supplements come in. Probiotics can help increase the diversity and improve the balance of microorganisms in your gut [4, 5, 6] so that you feel the beneficial effects of a healthy microbiome. They can also modulate an overactive immune system [7, 8] and reduce inflammation both in the gut and throughout the body [4, 9]. Some probiotics are also antifungal, antibacterial, and antiparasitic, making the gut environment inhospitable to these bad bugs.

To understand how much your gut health impacts your overall health, it helps to take a closer look at nutrient absorption, immune function, and inflammation. 

Nutrient absorption: Inflammation from bad gut bacteria damages the gut lining, impairing your ability to absorb nutrients [10]. Even if you’re eating a healthy diet, you won’t be fully benefiting from it if you aren’t absorbing those nutrients. 

Immune system function: We know that about 70% of our immune system resides in the gut tissues [11]. This makes sense, knowing that the digestive tract is the first point of contact when we ingest substances from the outside world that have their own bacterial composition. Therefore, the immune system is highly sensitive to the state of our microbiome. If your gut bacteria are unbalanced, the immune system can become hypersensitized and over-reactive [12, 13].

Inflammation: When the immune response is overzealous, inflammation in the gut and throughout the rest of the body compounds. Chronic inflammation goes on to influence and contribute to conditions like cardiovascular disease [14, 15], inflammatory bowel disease, eczema, and rheumatoid arthritis [16].

Probiotic Foods

You can get probiotics through your diet. But you would have to consume a whole lot of probiotic foods to get close to the therapeutic benefits of probiotic supplements. For many people, this makes dietary probiotic supplements a better choice.

Still, it doesn’t hurt to add probiotic foods to your diet, as long as you tolerate them well. Here are some examples of probiotic foods and the dosages compared to an average probiotic supplement: 

  • Sauerkraut: contains Leuconostoc mesenteroides, Lactobacillus brevis, Pediococcus pentosaceus, and Lactobacillus plantarum strains at 3 billion CFU per cup (1/8 of a lacto-bifido blend probiotic)
  • Yogurt: contains Lactobacillus acidophilus, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. Bulgaricus at 2.5 billion CFU per cup (1/10 of a lacto-bifido blend probiotic)
  • Kefir: contains Lactobacillus brevis, Lactobacillus acidophilus, Lactobacillus casei, Lactococcus lactis, Saccharomyces cerevisiae at 2.5 billion CFU per cup (1/10 of a lacto-bifido blend probiotic)
  • Kimchi: contains Weissella koreensis, Lactobacillus sakei, Lactobacillus graminis, Weissella cibaria, Leuconostoc mesenteroides at 11.5 billion CFU per 1/2 cup (1/2 capsule of a lacto-bifido blend probiotic)
  • Lacto-fermented pickles: contains Lactobacillus casei, Lactobacillus rhamnosus, Lactobacillus plantarum, Lactobacillus brevis at 1.3 billion CFU per cup (1/20 of a lacto-bifido blend probiotic).

Additional probiotic foods include miso, tempeh, and kombucha. Everyone reacts a little differently to these fermented foods, so you may have to experiment with which ones work well with your gut microbiome. For those with histamine intolerance, fermented foods are not a great choice, as they’re naturally high in histamine.

What are probiotics: homemade Kombucha tea in glass bottles

What Are Prebiotics? 

Prebiotics are essentially the fuel source probiotics need to function. For example, to maintain a sourdough starter, a culture of probiotic bacteria, you have to add flour to it on a consistent basis, which the starter breaks down into sugar to sustain itself. A similar process occurs when you eat prebiotic foods that feed the bacteria in your gut. 

Prebiotics are mainly plant foods, such as apples, bananas, onions, garlic, asparagus, oats, carrots, and many others. Prebiotics are part of the reason getting a diverse range of fruits and vegetables in your diet is so important. However, prebiotic supplements are also available, sometimes combined with probiotics.  

But it’s important to note that prebiotics aren’t selective about which bacteria they feed. If you have an underlying dysbiosis, prebiotics may be feeding the bad microbes more than the good ones. 

For this reason, some people may need to actually restrict their intake of prebiotics until they can rebalance their gut. A diet such as low-FODMAP can help in this case and has been shown to be beneficial for IBS and IBD patients [17, 18, 19, 20, 21]. 


The term “synbiotics” describes dietary supplements that combine prebiotics and probiotics in one capsule. These work well for some people who don’t have preexisting digestive issues and simply want some extra support for their microbiome. But for others, they cause further symptoms due to an underlying dysbiosis already present in the gut.

What are probiotics: probiotic capsules

Probiotics Benefit Gut Health

Probiotics are most well known for helping with gut health conditions and symptoms. A large volume of research supports their effectiveness in this area. 

Probiotics Support These Gut-Related Conditions

There is significant scientific evidence to support the use of probiotic supplements for: 

  • Irritable bowel syndrome (IBS): Gas, bloating, diarrhea, constipation, abdominal pain [22, 23, 24, 25, 26, 27, 28]
  • Gut imbalances: SIBO, H. pylori, candida/fungus, pathogens, antibiotic associated diarrhea [29, 30, 31, 32, 33, 34, 35, 36, 37, 38]
  • Leaky gut: Gut damage and permeability [39, 40, 41, 42]
  • Infections: Vaginal infections, urinary tract infections, tooth decay [43, 44, 45, 46]
  • Inflammatory bowel diseases (IBD): Crohn’s disease and ulcerative colitis [47, 48, 49]
  • Mood: Depression and anxiety [50, 51, 52, 53, 54, 55, 56, 57]

There is more limited, but still promising, scientific evidence for how probiotics may help with: 

  • Autoimmune conditions: Type 1 diabetes, multiple sclerosis, rheumatoid arthritis [58, 59, 60]
  • Metabolic health: Blood sugar, cholesterol, blood pressure, weight loss [61, 62, 63, 64]
  • Allergies: Dairy intolerance, seasonal allergies [65, 66, 67, 68]
  • Hormonal health: Thyroid health, PCOS, endometriosis, bone density [69, 70]
  • Cognition: Cognitive function, brain fog [71, 72, 73, 74]
  • Sleep: Sleep quality and disruption [75, 76, 77, 78, 79].

Research Highlights for Probiotics and Gut Health

These are some of the highlights from the research we’ve found: 

  • Probiotics can be very helpful for irritable bowel syndrome (IBS) symptoms such as loose stools, bloating, gas, constipation, diarrhea, abdominal pain, and fatigue [22, 23, 24, 25, 26, 27].
  • They have been shown to be very helpful in treating SIBO, small intestinal bacterial overgrowth, both in clinical symptom presentation and testing results [29, 30, 31].
  • Probiotics help to heal and seal a leaky gut [39, 40, 41, 42].
  • Probiotics can help fight fungal, bacterial, and parasitic infections [32, 33, 34, 35].
  • Probiotics are an effective part of treatment for the inflammatory bowel diseases, Crohn’s disease [47] and ulcerative colitis [47, 48, 49].
  • In a systematic review of studies on gastroesophageal reflux disease and probiotics, 79% of studies found improvements in reflux, heartburn, indigestion, nausea, and other symptoms after probiotic therapy [80].
  • Another systematic review and meta-analysis found that probiotics increased stool frequency and gut transit time, improving constipation [28].
  • Probiotics help reduce instances of antibiotic-associated diarrhea [36, 37, 38].

How Probiotics Can Help With Non-Digestive Conditions

Probiotics don’t just benefit the digestive system. Research has found that probiotics can help treat non-digestive conditions as well. Probiotics:

  • Lower the instance of respiratory tract infections in children [81], and vaginal and urinary tract infections in women [43, 44, 45].
  • May help maintain oral health and decrease microbes that cause periodontal disease, cavities, and gingivitis [46].
  • Have shown significant benefits for depression [50, 51] and some benefit for anxiety [52, 53, 54, 55, 56, 57].
  • Can address stress-related symptoms in healthy adults [82, 83, 84, 85].
  • Improve sleep quality [75, 76, 77, 78, 79].
  • Can help with lactose intolerance [65] and gluten intolerance [86, 87].
  • Can improve seasonal allergy symptoms [66, 67] and may prevent allergies from developing in children [68].
  • Improve cognition for Alzheimer’s [71, 72], bipolar disorder [73], and fibromyalgia patients [88]. In IBS patients, probiotics have also helped with reducing brain fog [74].
  • Can help reduce hypothyroid fatigue and reduce the need for medication in hypothyroid patients [69].
  • Can help address skin conditions, like acne [89, 90] and dermatitis [91, 92].
  • May have benefits for babies, including reduction of respiratory infections, less colic and irritability, and less diarrhea [93].

Types of Probiotics 

3 Categories of Probiotics infographic

Probiotics come in a wide variety of combinations and dosage levels. But here’s a guide to the main types of probiotics: 

Lactobacillus & bifidobacterium species predominated blendsSaccharomyces Boulardii (a healthy fungus)Soil-Based Probiotics using various bacillus species 
These are the most well-researched, with over 500 trials assessing their validity. These live microorganisms are also known as lactic-acid producing probiotic bacteria. They typically do not colonize the host but do improve the health of the host.The second most researched probiotic, with over 100 studies. Saccharomyces boulardii (S. Boulardi for short) is not a normal part of human microbiota, meaning it does not colonize us but does improve the health of the host.The third most researched category of probiotics is soil-based probiotics. This group has roughly 14 clinical trials evaluating their effectiveness. This category is also known as spore-forming bacteria. This category of probiotic can colonize the host [94].

For a full-spectrum combination of probiotic support, I recommend purchasing a high-quality formula from each category and taking them all together for a few weeks. If you notice improvements in your symptoms, keep going. If not, you can discontinue the therapy. 

In my clinical experience, I’ve seen that people who take all three types of probiotics together see impressive results, while those only taking one type experience little to no improvement [26, 95, 96, 97].

Quality Assurance

Probiotic supplements do not undergo the same standardization process as medications do; research has shown that many probiotics don’t contain the species and CFU concentrations that they advertise, or they even contain detrimental microorganisms [98, 99, 100].

Look for these quality assurance markers when shopping for probiotic supplements: 

  • The number of colony-forming units (CFUs) should be in the billions and clearly stated on the packaging
  • A clearly stated list of bacterial species
  • Labeled free of common allergens and other substances you may wish to avoid (e.g. gluten-free, non-GMO, vegan)
  • Certified GMP (Good Manufacturing Practices)
  • A manufacture or expiration date
  • Probiotic species and potency verified by third-party lab analysis (independent lab testing)

Probiotics Are Safe

Hand forming a shape of a heart placed on top of the stomach

Consumers should be aware that probiotics (like all supplements) aren’t regulated by the FDA, but reputable manufacturers exist and good consumer vigilance like following the guidelines above can help you find a quality product.

Research shows that probiotics are safe even for babies, and that they have few side effects [101]. 

The National Institutes of Health Fact Sheet on Probiotics states, “Given the large quantities of probiotics consumed around the world, the numbers of opportunistic infections that result from currently marketed probiotics are negligible. For example, probiotics have been administered to thousands of newborn infants, including some who were premature, without a single case of sepsis” [101]. 

Probiotics Make Sense for Good Health

At this point, with all the successful research that has been done on probiotic therapy, it’s clear that probiotics help to support good overall health. We can (and should) always continue our research into its effects, but probiotics have proven useful in treating dozens of symptoms and conditions, from gut health to skin health to brain health. 

If you would like some additional guidance on beginning or adjusting your probiotic therapy, schedule an in-person or virtual consultation with one of our practitioners at the Ruscio Institute for Functional Medicine.


Functional Medicine Near You

Related Posts