Which Food Has More Good Bacteria for Optimal Gut Health?

January 14, 2026 •

4 min read

According to research published by Harvard Health, the global sales of probiotic supplements reached nearly $4 billion in 2016 and are projected to continue growing, yet many of the most potent sources of beneficial microbes can be found in common fermented foods. Navigating the world of probiotic-rich foods can be confusing, so it is important to know which food has more good bacteria to make the most impact on your gut health.

Quick Summary

This guide compares foods like kefir and natto to determine which offers the highest concentration and diversity of good bacteria, informing dietary choices for superior gut health.

Key Points

Kefir is a top contender: Milk kefir made with grains often contains a higher concentration and wider diversity of good bacteria and yeast strains than yogurt.
Natto is highly concentrated: This fermented soybean product, made with Bacillus subtilis, offers an extremely high bacterial count per gram and a resilient probiotic strain that survives digestion.
Kimchi and sauerkraut offer diverse benefits: These fermented vegetables provide lactic acid bacteria and additional nutrients, though their total CFU counts are typically lower than kefir or natto.
Check for 'live and active cultures': Always choose refrigerated and unpasteurized versions of fermented foods, as heat treatment can destroy beneficial microbes.
Aim for variety: For optimal gut health, incorporate a range of fermented foods and pair them with prebiotics (fibers found in garlic, onions, and legumes) to nourish the bacteria.
DIY can increase potency: Making your own fermented foods at home using quality starter cultures often results in a higher and more diverse bacterial content.

Understanding Good Bacteria in Fermented Foods

Fermented foods contain live microorganisms, or probiotics, which are known to improve digestive health and support the immune system. The fermentation process naturally cultivates these beneficial microbes by having bacteria and yeast feed on the food's sugars and starches. However, the amount and variety of good bacteria can differ dramatically depending on the food and how it is processed. Heat, for instance, can kill off these live cultures, so it is crucial to opt for products labeled "live and active cultures" or those found in the refrigerated section.

Key Players in the Probiotic World

Not all fermented foods are created equal when it comes to probiotic power. While yogurt is a common entry point, other, less familiar foods pack a much more significant microbial punch. The most common measurement for bacterial concentration is Colony Forming Units (CFU), although diversity of strains is also a critical factor for overall gut health.

Kefir: A fermented milk drink made with kefir grains, it is often cited as a more potent probiotic source than yogurt due to its wider variety of bacterial strains and beneficial yeasts. Some studies have found that homemade milk kefir can contain up to trillions of CFUs per serving, far surpassing commercial yogurts. Its fermentation process produces a diverse and robust microbial community.
Natto: This traditional Japanese fermented soybean dish is made using Bacillus subtilis var. natto bacteria. It has a distinctive smell and sticky texture but is a powerhouse of good bacteria. Studies suggest that natto can provide a billion or more CFUs per gram, making it highly concentrated. The Bacillus subtilis strain is particularly hardy and can survive the journey through the digestive tract.
Kimchi: A Korean staple of fermented cabbage and vegetables, kimchi is rich in Lactobacillus and provides a robust amount of probiotics. The probiotic count can vary with fermentation duration, but commercial products can contain hundreds of billions of CFUs per serving.
Sauerkraut: Made from fermented cabbage, raw, unpasteurized sauerkraut is a source of lactic acid bacteria. While it contains a respectable amount of probiotics, its CFU count is typically lower than that of kefir or natto.

Comparison of Top Probiotic Foods

To help visualize the difference, here is a comparison of some of the most potent probiotic foods. Note that CFU counts can vary significantly based on fermentation time, ingredients, and processing.


Fermented Food	Primary Bacteria/Yeast	Probiotic Potency (per serving)	Key Advantage	Processing Factor	Serving Suggestion
Milk Kefir	Lactobacillus, Lactococcus, Bifidobacterium, Yeast	Hundreds of billions to trillions of CFUs	Highest diversity and concentration	Unpasteurized, made with live grains	Drink plain, in smoothies, or as a dressing base
Natto	Bacillus subtilis	Billions of CFUs per gram	Extremely concentrated and shelf-stable	Made from fermented soybeans	Traditionally eaten with rice; mix with mustard or soy sauce
Kimchi	Lactobacillus kimchii	Billions to hundreds of billions of CFUs	Anti-inflammatory properties	Unpasteurized; found in refrigerated section	As a side dish, topping for tacos, or scrambled eggs
Yogurt (Live Culture)	Lactobacillus bulgaricus, Streptococcus thermophilus	Millions to hundreds of billions of CFUs	Widely available and palatable	Look for "live and active cultures" label	Breakfast bowl, snack, or ingredient in sauces
Sauerkraut (Raw)	Lactic Acid Bacteria	Billions of CFUs	High in vitamins C and K	Unpasteurized and refrigerated	Side dish for meats, topping for salads or toasts

Maximize Your Good Bacteria Intake

Beyond simply consuming these foods, optimizing your good bacteria requires a holistic approach. The key to a thriving gut microbiome is diversity and consistency.

Eat a Variety: Incorporate a range of fermented foods to introduce different bacterial strains and yeasts. For example, alternate between kefir, kimchi, and yogurt to ensure a broad spectrum of microbes.
Combine with Prebiotics: Probiotics thrive on food called prebiotics, which are non-digestible fibers. Pairing probiotic foods with prebiotic-rich items like bananas, garlic, onions, and legumes helps sustain the good bacteria already in your gut and the new ones you introduce.
Choose Unpasteurized: High heat processing, or pasteurization, kills live bacteria. Always check labels for phrases like "live and active cultures," or buy refrigerated, unpasteurized versions of foods like sauerkraut and pickles.
Consider Homemade: Making your own kefir, kimchi, or sauerkraut can often result in higher bacterial counts and greater strain diversity than many commercial products. Just be sure to follow safe fermentation practices.
Start Slowly: If you are new to probiotic foods, introduce them gradually to avoid digestive upset like bloating or gas.

The Winner: Which Food has More Good Bacteria?

While yogurt is the most well-known source, foods like kefir, natto, and kimchi generally offer a greater concentration and diversity of beneficial microbes. Homemade kefir from grains is potentially the most potent in terms of sheer numbers, but natto offers an extremely concentrated and unique probiotic strain. For a more balanced, all-around approach, a diverse diet that incorporates a variety of fermented foods is the best strategy.

Conclusion

When seeking to enrich your diet with beneficial bacteria, the choice extends far beyond simple yogurt. Kefir, natto, and kimchi are exceptionally potent sources, offering diverse and concentrated microbial populations that can significantly benefit gut health. To maximize the effect, prioritize variety, choose unpasteurized options, and pair them with prebiotic-rich foods. This dietary strategy supports a thriving gut microbiome and contributes to overall wellness. The ultimate powerhouse is not a single food, but a diverse and consistent intake of multiple fermented options.

Harvard Health Publishing

Frequently Asked Questions

Yes, pasteurization uses high heat to kill bacteria and can destroy the beneficial live cultures in fermented foods like sauerkraut, yogurt, and kefir. For probiotic benefits, choose products explicitly labeled "live and active cultures" or those found refrigerated and unpasteurized.

Probiotics are the beneficial live microorganisms found in fermented foods, while prebiotics are non-digestible fiber compounds that act as food for the good bacteria in your gut. A balanced diet should include both to ensure a healthy gut microbiome.

Kefir is generally considered a more potent source of probiotics than most yogurts. It is made with kefir grains that contain a wider variety of bacterial strains and yeasts, often resulting in a higher CFU count.

Not all fermented foods contain live cultures when consumed. For example, foods like sourdough bread and most commercially pickled vegetables are often heat-processed, which eliminates the live bacteria. Look for refrigerated, unpasteurized products for probiotic benefits.

The best way to increase the diversity of good bacteria is by eating a wide variety of fermented foods and prebiotic-rich plants. Different foods introduce different strains of bacteria, leading to a more robust and resilient microbiome.

Yes, you can make fermented foods like kefir, sauerkraut, and kimchi at home using specific starter cultures or naturally present bacteria. Homemade versions often have higher probiotic counts and are free of preservatives.

While generally safe, consuming large amounts of fermented foods can sometimes cause digestive discomfort like bloating or gas, especially if you are not used to them. It's best to introduce them gradually into your diet.