The Gut Microbiome and Which Probiotic Supplements Are Worth Taking
Guest Writer| Oct 03,2021

Probiotics have become a popular way to treat health issues ranging from gut disorders to allergies and even mental health conditions. Probiotics are relatively new. The term ‘probiotic’ was first defined in 2001 and is now the third most common dietary supplement after vitamins and minerals with a $50 billion global market (1,2). Taking a step back from the buzz on these products, there is actually no Recommended Daily Allowance (RDA) for probiotics, a metric reserved for essential nutrients necessary for normal body function like iron or Vitamin D. Meaning probiotics are not essential, but we may think they are, persuaded by tempting health claims of products on supermarket shelves. To be clear, there are likely health benefits from some probiotic products, but we should exercise more scrutiny on which probiotics we trust to put in our body and spend our money on!

What is the microbiome? 

If we want to learn about probiotics, we should first understand the critical role bacteria and other microorganisms including fungi, archaea, and protozoa play in our health. Someone once told me we have 10 times the amount of these bugs living in and on our body compared to human cells. Oh how I underestimated the importance of microorganisms for our body! While this ratio has since been disproven (it is actually more like one-to-one), microorganisms aggregate to create microbiomes. Some functions of microbiomes include regulating our digestion, modulating immune response, and these bugs can even produce vitamins (3)! While the gut microbiome is home to the largest and most diverse collections of microorganisms, we also have microbiomes in our nose, mouth, lungs, stomach, sexual organs and skin. This post will focus on the gut microbiome since it has garnered the most public attention for health claims of probiotics in GI disorders. 

Where does the microbiome come from? 

As a fetus, we develop a mutualistic relationship (or friendship) with these microbes as suggested by their presence in the placenta and umbilical cord. By just three years of age, the bacterial composition of the gut microbiome resembles that of an adult. This is influenced by the type of birth delivery (vaginal or C-section) and breastfeeding, which has been shown to be more beneficial for enriching the microbiome compared to formula-fed babies. While it is important to establish a healthy microbiome early in life, our gut microbiome is not necessarily static from childhood. ging, long-term dietary changes, psychological and physical stress, prolonged high intensity exercise and illness are all factors that can influence the composition into adulthood (4).

What causes gut dysbiosis? 

Of all these influences, psychological stress may be one of the most pervasive factors causing gut microbiome imbalance or dysbiosis. The gut-brain axis, also known as the microbiota–gut–brain axis, acts as a line of communication from the brain to the gut and is why stress can impact GI function, appetite and weight control (6,7). Bi-directional communication means stress can impact the gut and gut dysfunction can cause stress. Intriguing new data suggests small molecules produced in the microbiome can mimic or act as neurotransmitters that may impact psychological status. Because of this bi-directional communication, we may even begin to identify CNS-related disorders in relation to GI disease as a result of gut dysbiosis (8).

Exhibit 3. Microbiota-Gut-Brain Axis

How does gut dysbiosis cause disease?

Over a decade of research has linked dysbiosis to chronic inflammatory disorders of the gut. Growth of dysfunctional or “bad” microbes among commensal or “friendly” ones can lead to inflammation and disease (8). Recently, specific bacterial species were linked to certain GI conditions, improving our understanding of the role of the microbiome in disease. A study in 2019 compared >2,000 fecal samples from Inflammatory Bowel Disorder (IBD) to non-IBD patients in Europe and discovered that the presence of specific bacterial strains were linked to disease (9). Similarly to how we define diseases like Cystic Fibrosis by genetic mutations, we can now do so for bacteria, opening up a completely new area of potential research and medicine!

What are probiotics and how do they work?

Probiotic species or health-promoting microorganisms naturally occur in some foods, but the overwhelming commercial success is attributed to products sold as nutritional supplements. Most probiotic supplements are available over-the-counter (OTC), and some by prescription. Each contains millions of microorganisms, predominantly bacteria, and are sold as oral capsules or powders. When ingested, these microbes become active once they reach the gut microbiome. Here, they are intended to help prevent survival of disease-causing bugs, reduce inflammation, and enhance the immune response, all of which improves overall intestinal health and may combat disease. Probiotics are transient and do not populate the gut, avoiding safety concerns associated with immediate and permanent changes to the microbiome composition. This means probiotics should be taken daily for best activity. Of note, probiotics differ from prebiotics, which serve as food for commensal microorganisms and synbiotics, which are a combination of prebiotics and probiotics (10).

Are probiotics effective? 

While probiotics are safe to use for most healthy people, consumers should exercise some skepticism when buying into purported health claims labeled on the product. 

Since the study of probiotics in disease is a relatively nascent field of science, there may not be enough controlled scientific studies to support every health claim on labels. Data supporting use of probiotic supplements are described below (10). A summary of vetted, scientific studies that describe probiotic efficacy based on specific strains in GI disorders are available here (11) and can help guide your supplement selection.

Table 1: Data Supports Activity of Probiotic Supplements in Some Diseases

Are probiotics approved by the FDA? 

No. Consumers should be aware that since most probiotics are sold as dietary supplements, they are not subjected to the same rigorous testing and approval by the FDA as therapeutic drugs. Therefore, manufacturers are largely responsible for the quality, safety and validity of health claims made on the label. Probiotic manufacturing is a complex process that requires extensive skill and expertise to ensure quality of the final product (12).  Since the research is still in its early innings, lack of FDA regulation, and complex manufacturing process, the bar for producing an effective probiotic product is high, meaning it is likely not all brands on the supermarket shelves are actually worth it. 

How do I choose a probiotic at the supermarket?

Look for the strain! Microbes in probiotics are defined in three levels: 1) genus, 2) species and 3) strain, listed in that order on the label. You need all three to define the probiotic(s) in the product, just like you need three pieces of information to complete an online order, your credit card number, expiration date, and 3-digit security code. Your probiotic is incomplete without these three levels. For the probiotic Lactobacillus acidophilus MN5, Lactobacillus is the genus, acidophilus is the species, and MN5 is the strain. Health benefits are dependent on specific bacterial strain, therefore consumers should seek products containing the exact strain(s) supported by high-quality scientific evidence of intended benefit. Lactobacillus, Bifidobacterium, and Saccharomyces are the most widely studied species in GI disorders (among a potential 3,000!), but some products may omit the strain on labels, making it difficult to associate probiotic activity with a particular health condition. Strain differences account for microbial tolerance to different environmental stressors (salt, antibiotics) and metabolic activity, which could directly impact product ability to deliver health benefits (12). Look for the strain on the label.

Dosage is also key. Doses vary by product and GI condition, so no general dosing recommendation can be made. But one piece of advice is consistent across brands: more is not necessarily better! Probiotic dose is measured in colony-forming units (CFU), which represents the number of live strains at expiration. However, current labeling regulations do not require manufacturers to always list CFU, they can just list the total weight of the microbes (i.e. milligrams), which includes live (useful) and dead (not useful) organisms. Always look for CFU numbers at the expiration or “sell-by” date as microbes can die during their shelf life. A product should also have an explicit sell-by date to indicate that its contents are living. Some brands, like Seed Health, use a new measurement called AFU or Active Fluorescent Units that measures probiotic cells one at a time, offering a more precise measurement of both alive and active cells (13). 

What about adding probiotic-rich foods into my diet?

These are just some criteria to consider when selecting a probiotic supplement. Overwhelmed? Consider incorporating fermented, probiotic-rich foods into the diet first, like yogurt, kimchi, sauerkraut or beverages like kombucha. While consumers may prioritize probiotic products for sufficient concentration of specific strains and the convenience of a daily oral pill, modifying diet alone may promote gut microbiome health. Just don’t be fooled by products like Danimals now marketed to contain probiotics! To that end, even consider eliminating processed, high sugar foods that alter the microbiome for the worse, creating a more inflammatory environment. Sleep and exercise are also overlooked, but are critical for gut health. 

Before You Go To The Supermarket…

Finding the right probiotic supplement might seem like a shot in the dark. Here is a checklist to consider when shopping for probiotics: 

  • Strain included on label

  • Data supporting clinical activity of strain 

  • Dose in CFU or AFU

  • A “sell-by” date

These criteria will help source the highest quality probiotic for your desired health benefits!

Written by Jordyn Fantuzzi: Jordyn Fantuzzi graduated with a Bachelor's in Biology from NYU in 2015. She began her career as a scientist at a biotech startup OncoMed Pharmaceuticals in the Bay Area, California before transitioning to biopharma equity research at Piper Sandler in New York City where she is currently employed. In January 2020, she began to pursue an R.D. and M.S. in Nutrition and Dietetics at Brooklyn College while maintaining a full-time job at Piper Sandler. One of Jordyn's goals as an R.D. is to simplify nutritional science into accessible information to improve people's understanding of food and health products. She is very excited to become a Nutritionist and thinks this industry is going to have an increasingly important role in medicine and public health. Jordyn can be reached at







  6. Track NS (1980). The gastrointestinal endocrine system. Can Med Assoc J 122, 287–292.








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