The gut microbiome is a colony of microorganisms or microbiota living in our Gastrointestinal (GI) tract. It consists of healthy bacteria and pathogenic bacteria. The healthy bacteria, called probiotics, are live microorganisms. They contribute to health by aiding digestion and absorption. They also make substances like vitamins, amino acids, and short-chain fatty acids. They break down toxic substances. Examples of probiotics that have been shown to have health benefits include Bifidobacterium and Lactobacillus. 

What disrupts the gut microbiome?

A healthy microbiome needs a balance between probiotics and pathogenic bacteria that can cause disease. In healthy individuals, it is normal to have a dynamic balance between the “good” bacteria and the “bad” bacteria. However, many factors can disrupt this balance. They can cause gut microbiome dysbiosis, an imbalance in gut bacteria. This indicates a disproportionate amount of “good” and “bad” bacteria. In this case, harmful bacteria compete and block the probiotic bacteria. They block them from helping to regulate the body.

An imbalance in the gut microbiome can be caused by: 

  • Antibiotic use 
  • C. Difficile infection and diarrhea
  • Emotional and/or physical stress
  • Diets low in fiber and high in refined carbohydrates
  • Food additives
  • Inflammatory bowel disease 
  • Irritable bowel syndrome 
  • Traveler’s diarrhea 

Dysbiosis can weaken the immune system. It also raises the risk of chronic diseases or infections. For example, an imbalance in the gut microbiome is associated with diabetes and obesity. It’s also linked to small intestinal bacterial overgrowth (SIBO), H. pylori and C. difficile overgrowth, constipation, irritable bowel syndrome (IBS), and colon cancer. 

Benefits of probiotics 

A healthy microbiome is crucial for promoting health and immunity. It makes key health-promoting substances. For example, probiotics help make vitamin K and vitamin B. They also make amino acids and short-chain fatty acids. These help health and aid weight loss. Probiotics in enough amounts support immune and gut health. They do this by improving the gut barrier, stopping “bad” bacteria from growing, and adding a protective layer to the gut lining. This layer helps a healthy immune system. 

Probiotics can be formulated to benefit specific conditions beyond the GI tract such as: 

  • Periodontal disease
  • Urinary tract infections (UTIs)
  • Bacterial vaginosis
  • Acne
  • Liver health 
  • Brain function

Where can you find probiotics in food? 

Probiotics can be found in fermented foods and drinks: 

  • Yogurt
  • Kefir
  • Cottage cheese
  • Kombucha
  • Fermented sauerkraut, kimchi
  • Pickles
  • Soy products (miso, tempeh)
  • Buttermilk

Prebiotics, often found in food,  fuel the probiotics.  They can help the gut by promoting the health of probiotics in the intestines. Diets higher in fiber and prebiotic sources may help aid in weight loss. 

Sources of prebiotics include foods high in soluble fiber:  

  • Asparagus  
  • Onions
  • Wheat 
  • Leeks
  • Garlic
  • Bananas
  • Rhubarb
  • Soy milk

Choosing a probiotic supplement and recommendations

Like all supplements, it is important to read the label. When searching for a probiotic supplement, you must look at strains. Also, look at the CFU at the end of shelf life, storage instructions, and quality assessment. 

When searching for strains in a probiotic supplement, it is important to know the purpose of that strain. For example, Lactobacillus probiotics help with chronic constipation and IBS symptoms. They also stop H. pylori from growing and prevent gut pathogens. But Bifidobacterium probiotics improve immunity. They also reduce low-grade inflammation. They help make vitamins in the gut. And they prevent harmful gut infections, like E. coli. 

The CFU or Colony-Forming Unit indicates the probiotic dose, which may vary depending on the targeted health benefits and strain. Human studies have shown that 50 million to 1 trillion CFUs provide potential health benefits. For health benefits, it is recommended to choose probiotic supplements with at least 1 billion CFUs per serving and more than 2 strains. The effectiveness of probiotics will depend on multiple factors. Storage instructions will depend on the manufacturer. It is best to follow the instructions on the package, as some probiotics require refrigeration, and some do not. 

Lastly, quality assurance can be validated through third-party testing. Dietary supplements are not FDA-regulated and do not need pre-market approval for the efficacy or safety of the product. So choosing supplements tested through an independent third party is best practice. For example, supplements with a USP label are third-party tested. The United States pharmacopoeia (USP) label is a third-party testing agency. It assesses the potency, purity, and stability of supplements. An example is two probiotic brands with USP labels. They include Trunature: Advanced Digestive Probiotic capsules. They also include Member’s Mark 10 Strain Probiotic Digestive Care Supplement capsules. 


Probiotics have many mechanisms that promote health. But, we still need more research to fully understand all the ways that probiotics work. However, probiotics can help beat harmful organisms. They are likely to prevent disease and maintain a balance in the gut microbiome. Overall, gut health can be promoted by consuming a well-balanced diet rich in prebiotic and probiotic sources. In the Bariatric Counseling center IOP program, our dietitians will help you learn what to look for. They will help you choose a probiotic that fits your needs. Contact us at 210-634-2200 to learn more about our program today!



Probiotics: What You Need To Know. National Center for Complementary and Integrative Health Website. https//www.nccih.nih.gov/health/probiotics-what-you-need-to-know.  Updated August 2019. Accessed February 27, 2024. 

Holscher H.D., Hutkins R., Sanders M.E. Evidenced-Based Use of Probiotics, Prebiotics and Fermented Foods for Digestive Health. Today’s Dietitian Website. https://www.todaysdietitian.com/marketing/issues/2021/supplement/isapp/Course.pdf. Updated 2021. 

Thursdby E., Juge N. 2017. Introduction to the human gut microbiota. Biochem Journal, 474(11), 1823-1836. https://doi.org/10.1042/BCJ20160510. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5433529/

Collins S.C. Probiotics: Improve Gut Health with Probiotic Supplements. Today’s Dietitian Website. https://www.todaysdietitian.com/newarchives/031115p14.shtml. Updated 2015. Accessed March 2, 2024.