How fermented foods alter your microbiome

Written by: Kari Raman, PharmD, RPh
Published June 25, 2023

I am often asked by my patients about the effects of their diet on their health. One of the hottest topics in this realm is the consumption of fermented foods and their impact on the gut microbiome. There are a lot of articles in all kinds of magazines and on the internet talking about miracles that happen when people change their diet – but it’s sometimes hard to understand what’s real and what is just marketing. 

Well, great news for pharmacists like me who want to understand the latest science when talking to patients about the microbiome! A recent article in a microbiome focused medical journal investigated the gut microbiome changes in individuals who consume fermented foods versus those who do not. 

My article will provide a comprehensive overview of the authors’ conclusions, hopefully, help you understand the impact of fermented foods on your digestive health.

Quick background on fermentation

Historically, fermentation was a widely used method of preserving foods. Fermentation for foods is a biological process where microorganisms like yeast and bacteria convert carbohydrates, such as sugars and starch, into alcohol or acids. It was discovered that not only could it prolong the shelf life of food, but it also added new and pretty good flavors. Over time, it has been found that the microbial diversity involved in fermentation could have potential health benefits, particularly for the gut. Basically, the microorganisms used in the fermentation process (or maybe the actual foods they produce) can have health benefits on your digestive system. 

The American Gut Project – yup, that’s real

The study analyzed the gut microbiomes of 6,811 participants from the American Gut Project. Yes, there is a big study of American’s guts. And it involves analyzing not only what people eat, but a lot of poop. Participants were categorized as either “consumers” or “non-consumers” of fermented plants based on their reported intake frequency. So, basically, people who ate these kinds of foods or those who didn’t. Consumers included those who ate fermented plants daily, regularly (3-5 times/week), or occasionally (1-2 times/week). Nonconsumers ate fermented plants rarely (less than once/week) or never.

The demographics of the consumer group showed that they were typically younger, predominantly female, and had a more regular body mass index compared to nonconsumers. They also reported eating a broader variety of plants. The dietary patterns of both groups were analyzed, showing high-quality dietary habits and above-average socioeconomic status and education levels. But it seems like, in general, people who eat fermented foods are healthier. Not too surprising, yogurt is kind of considered a health food. And I sure do eat a lot of it. 

Upon analyzing the gut microbiome compositions, the researchers found significant differences between consumers and nonconsumers. This suggests that the frequency of fermented plant consumption has an impact on the gut microbiome. The researchers went a step further and identified specific microbial species associated with each group. They found that consumers, people who ate a lot of fermented foods, hosted a different set of microbes than nonconsumers. The most common items consumed included beer, kimchi, kombucha, pickled vegetables, sauerkraut, and yogurt.

The gut microbiota of fermented food consumers was enriched with strains of probiotics often found in fermented foods, including various strains of Lactobacillus. The researchers used a lot of analysis and some math to see that there is a correlation between the consumption of these items and the composition of the gut microbiome.

Interestingly, consumers were also associated with several other microbes unrelated to fermented foods. This suggests that the differences between consumers and nonconsumers might be influenced by factors such as the frequency of fermented plant consumption or different sequencing methods used.

Fermented foods made positive changes beyond the microbes

One of the most intriguing findings was that the gut microbiota of consumers was enriched with conjugated linoleic acid (CLA), a molecule that is thought to promote health. This is typically associated with people who eat a lot of plants (and it’s a good thing), but the interesting thing here was that they were able to see that CLA enrichment was potentially driven by specific types of gut bacteria associated with fermented food consumption.

The study concluded that the consumption of these items seems to subtly but persistently impact the gut microbiome, enriching it with potentially beneficial molecules like CLA. 


It’s important to remember that while these results are promising, the changes observed were subtle, and more research is needed to better understand the benefits of consuming yogurt and other items. Nevertheless, this study adds to the growing body of evidence suggesting that our dietary habits, particularly the consumption of fermented foods, can have a significant impact on our digestive health. And if you want to know how much probiotics are in yogurt, read my article.

As your friendly pharmacist, I would advise incorporating a variety of fermented items into your diet, provided there are no contraindications due to any specific health conditions. Always consult your healthcare provider before making any significant changes to your diet or lifestyle. So go get that yogurt parfait! 

While more research is needed, it’s clear that fermented foods can play a significant role in modulating the gut microbiome.

Some of my other articles on probiotics and health

In a previous article, I used my experience as a pharmacist to talk about how probiotics can help your digestive system if you are taking antibiotics. The piece underscores how the right probiotic supplements can support the healthy bacteria in your gut, even as antibiotics work to combat infection. It highlights strains like Lactobacillus and Bifidobacterium as particularly effective, given their proven compatibility with antibiotic treatment. Yet, because every person’s health profile is unique, I strongly encourage readers to consult with their doctors or with me for personalized guidance. You can gain deeper insight into this topic by exploring my article on antibiotics and probiotic tips.

I’ve also explored prebiotics, the non-digestible fibers that act as food for beneficial bacteria. Consumed primarily through plant-based foods, these prebiotics make their way to our large intestine, fostering a healthy microbiome. For a detailed examination of this topic, you can check out my full article on prebiotics here.

In a recent article exploring the world of gut microbiota, we discussed the crucial role these microorganisms play in maintaining our overall health. While factors like antibiotics, stress, and modern lifestyle choices can disrupt the delicate balance of our digestive system, it’s important to focus on nourishing it with the right foods. Plant-based foods rich in fiber are essential for a healthy microbiome, as they provide nourishment to the beneficial bacteria that reside there. For more detailed insights into maintaining a gut-friendly diet, refer to our latest article on “Top Foods for a Healthy Gut Microbiome.”

Pharmacist Kari Raman

I’m Kari Raman PharmD, RPh, and I am a licensed, practicing pharmacist. I hold a Doctorate in Pharmacy from The University of the Pacific, and I’ve served patients in retail, compounding and hospital pharmacies.

Probiotics are confusing!

One of the most common questions I get asked by patients is about probiotics. And the truth is, probiotics are not as well understood by the healthcare community as they should be.

So I’ve been reading a lot of probiotic clinical trials, and sharing what I’m learning here.

I hope Pharmacist Probiotics helps you find out if there is a type of probiotic that works for you!