No. 09 The Complete Guide to Probiotics
The Complete Guide to Probiotics: What You Need to Know
Probiotics have become increasingly popular in recent years, but there's still a lot of confusion about what they are, how they work, and whether you should take them daily. Let's dive into everything you need to know about these beneficial bacteria.
What Are Probiotics?
Probiotics are live microorganisms—primarily bacteria and some yeasts—that provide health benefits when consumed in adequate amounts. These "good" bacteria are similar to the beneficial microorganisms naturally found in your gut. The word "probiotic" comes from the Greek words "pro" (promoting) and "biotic" (life).
How Do Probiotics Work?
Probiotics work through several mechanisms. They compete with harmful bacteria for nutrients and attachment sites in your intestines, essentially crowding out the bad guys through competitive exclusion. Many probiotics produce lactic acid, which lowers the pH in your gut, creating an environment where harmful bacteria struggle to survive. They help regulate your immune response, strengthening your body's natural defenses while maintaining the integrity of your intestinal lining, preventing harmful substances from entering your bloodstream. Some strains even produce vitamins like B12 and K and help break down certain nutrients for better absorption.
The Expert Perspective: Dr. Justin Sonnenburg
Dr. Justin Sonnenburg, a Stanford microbiologist and leading expert in gut microbiome research, offers a more nuanced view of probiotics. He emphasizes that most commercial probiotics are "transient"—they pass through the gut without establishing permanent residence. He often compares them to "tourists" rather than "residents" in our gut ecosystem. The strains in most supplements don't actually colonize the gut long-term and need to be taken continuously to maintain any benefits.
According to Dr. Sonnenburg, while commercial probiotics typically contain only a handful of strains, a healthy gut microbiome has hundreds of different species. This limited diversity can't adequately address the complexity of the gut ecosystem. His research, including a notable 2021 study published in Cell, showed that fermented foods like yogurt, kimchi, sauerkraut, and kefir may be more effective than fiber alone at increasing microbiome diversity. These foods contain more diverse bacterial strains, include beneficial metabolites produced during fermentation, and often come with additional nutritional benefits.
Dr. Sonnenburg is particularly passionate about the importance of dietary fiber, which he and his research partner (and wife) Erica Sonnenburg argue is more crucial than probiotic supplements. They advocate for feeding your existing gut bacteria with diverse fibers, which they call "microbiota-accessible carbohydrates" or MACs. As he puts it, "Most probiotics are like seeds thrown on pavement—they can't take root," emphasizing instead that we should "feed the gut bacteria you already have rather than trying to add new ones."
When Dr. Sonnenburg Does Recommend Probiotics
Despite his general skepticism about daily probiotic supplements, Dr. Sonnenburg does acknowledge specific situations where probiotics can be beneficial:
After Antibiotics
Dr. Sonnenburg recognizes that antibiotics can significantly disrupt the gut microbiome, sometimes causing lasting damage to bacterial diversity. In these cases, he suggests that probiotics may help prevent opportunistic infections and support recovery. He particularly notes that certain probiotic strains can help prevent antibiotic-associated diarrhea and C. difficile infections. However, he still emphasizes that rebuilding the microbiome after antibiotics requires more than just probiotics—it needs a diverse, fiber-rich diet to help resident bacteria recover.
During and After Travel
International travel can expose you to new pathogens and disrupt your normal gut bacteria. Dr. Sonnenburg has mentioned that taking probiotics while traveling, especially to areas with different food safety standards, may help prevent traveler's diarrhea and support gut health during dietary changes. He views this as a temporary, targeted use rather than ongoing supplementation.
Post-Illness Recovery
After gastrointestinal illnesses that cause significant disruption to the gut microbiome, probiotics might help restore balance more quickly. However, he still emphasizes that long-term recovery depends more on diet than supplements.
The key distinction in Dr. Sonnenburg's approach is that he sees probiotics as occasionally useful tools for specific situations rather than as daily supplements for general health. As he often states, "Context matters"—the effectiveness of probiotics depends heavily on the individual's circumstances and needs.
Good Probiotics vs. Bad Probiotics
When evaluating probiotics, quality matters significantly. Good probiotics contain clinically studied strains with proven benefits and have adequate CFU (Colony Forming Units) count—typically at least 1 billion. They include strain-specific information (like Lactobacillus acidophilus NCFM) rather than just genus and species. Quality products have proper storage instructions and expiration dates, are third-party tested for purity and potency, and are formulated to survive stomach acid to reach the intestines.
Well-researched strains include Lactobacillus acidophilus, Lactobacillus rhamnosus GG, Bifidobacterium lactis, Saccharomyces boulardii, and Lactobacillus plantarum. These have been studied extensively and show consistent benefits in clinical trials.
Red flags for poor quality probiotics include products with no strain identification, unrealistic CFU counts (hundreds of billions without evidence), no expiration date or storage instructions, proprietary blends without individual strain amounts, claims that seem too good to be true, and lack of third-party testing.
What Happens If You Take a Probiotic Every Day?
Taking probiotics daily can lead to various outcomes. Many people experience improved digestive health, including regular bowel movements, reduced bloating, and better nutrient absorption. Since about 70% of your immune system is in your gut, regular probiotic use may lead to enhanced immune function and fewer colds and infections. The gut-brain axis means improved gut health may support better mood and cognitive function, while certain strains help lower systemic inflammation and may improve skin conditions like eczema and acne.
The timeline of effects typically follows a pattern. In the first week or two, you might experience temporary bloating or gas as your gut microbiome adjusts. By weeks three and four, digestive symptoms often begin to improve. After two to three months, more consistent benefits become apparent, and with long-term use, many people report sustained improvements in overall health and well-being.
While most people tolerate daily probiotics well, some may experience initial digestive discomfort (usually temporary), bloating or gas, headaches (rare), or allergic reactions (very rare). People who should be cautious include those with compromised immune systems, serious underlying health conditions, central venous catheters, or those recovering from surgery.
Best Practices for Taking Probiotics
For optimal results, take probiotics on an empty stomach or with a light meal, maintain consistency by taking them at the same time each day, and follow storage instructions carefully. Support your probiotics with prebiotic foods—fiber-rich foods that feed good bacteria. Be patient and give them at least 4-6 weeks to show benefits.
The Bottom Line
As Dr. Sonnenburg's research suggests, while probiotics can be beneficial, they're not a magic solution. Quality matters significantly, and fermented foods offer advantages over supplements. The most important factor is supporting your overall gut health through a diverse, fiber-rich diet that feeds your existing microbiome.
Choose well-researched strains from reputable manufacturers, be patient as your body adjusts, and remember that probiotics work best as part of a comprehensive approach to gut health that includes plenty of dietary fiber and fermented foods. Always consult with your healthcare provider before starting any new supplement regimen, especially if you have underlying health conditions or are taking medications.
*Note: This information is for educational purposes only and should not replace professional medical advice.*
References
Research Papers and Studies
1. Sonnenburg, E. D., & Sonnenburg, J. L. (2019). The ancestral and industrialized gut microbiota and implications for human health. *Nature Reviews Microbiology*, 17(6), 383-390.
2. Wastyk, H. C., Fragiadakis, G. K., Perelman, D., Dahan, D., Merrill, B. D., Yu, F. B., ... & Sonnenburg, J. L. (2021). Gut-microbiota-targeted diets modulate human immune status. *Cell*, 184(16), 4137-4153.
3. Sonnenburg, J. L., & Sonnenburg, E. D. (2019). Vulnerability of the industrialized microbiota. *Science*, 366(6464), eaaw9255.
4. Deehan, E. C., Yang, C., Perez-Muñoz, M. E., Nguyen, N. K., Cheng, C. C., Triador, L., ... & Walter, J. (2020). Precision microbiome modulation with discrete dietary fiber structures directs short-chain fatty acid production. *Cell Host & Microbe*, 27(3), 389-404.
Books
1. Sonnenburg, J., & Sonnenburg, E. (2015). *The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health*. Penguin Press.
Scientific Reviews and Guidelines
1. Hill, C., Guarner, F., Reid, G., Gibson, G. R., Merenstein, D. J., Pot, B., ... & Sanders, M. E. (2014). The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. *Nature Reviews Gastroenterology & Hepatology*, 11(8), 506-514.
2. McFarland, L. V. (2014). Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review. *BMJ Open*, 4(8), e005047.
Relevant Research on Probiotics After Antibiotics/Travel
1. Goldenberg, J. Z., Yap, C., Lytvyn, L., Lo, C. K., Beardsley, J., Mertz, D., & Johnston, B. C. (2017). Probiotics for the prevention of Clostridium difficile‐associated diarrhea in adults and children. *Cochrane Database of Systematic Reviews*, (12).
2. McFarland, L. V. (2007). Meta-analysis of probiotics for the prevention of traveler's diarrhea. *Travel Medicine and Infectious Disease*, 5(2), 97-105.
Additional Resources
1. The Sonnenburg Lab at Stanford University: [https://sonnenburglab.stanford.edu/](https://sonnenburglab.stanford.edu/)
2. International Scientific Association for Probiotics and Prebiotics (ISAPP): [https://isappscience.org/](https://isappscience.org/)
3. NIH National Center for Complementary and Integrative Health - Probiotics: [https://www.nccih.nih.gov/health/probiotics-what-you-need-to-know](https://www.nccih.nih.gov/health/probiotics-what-you-need-to-know)