Best Fermented Foods To Eat Daily For Your Microbiome - Lakeside Natural Medicine

Natural Health and Wellness for the Whole Family

Best Fermented Foods To Eat Daily For Your Microbiome

ByKatarina Meister, ND February 14, 2023

At our most recent Gut Reset Workshop, we discussed healing and restoring your microbiome. If you are new to this subject, you may find it interesting to know that as humans we are composed of 10 times as many bacterial cells than human cells. (*If you missed our Gut Reset Workshop, it’s not too late! Sign up for the recording here.) While some of us associate bacteria as “bad,” most bacteria are actually good for you and play an essential role in your health.

Typically when we talk about the microbiome, we are talking about microorganisms (including bacteria, fungi, archaea, and viruses) in your colon. Every part of your body can contain communities of microorganisms so it is important to differentiate this. Your colon predominantly consists of beneficial bacteria- some sources say as many as 100 trillion organisms! In today’s modern world, there can be occurrences of a microbiome imbalance (or dysbiosis). A microbiome dysbiosis is when the gut microbiota is compromised and therefore affects your overall health. Risk factors include food poisoning, stress (This study found stress hormones to increase risk for leaky gut)[i], low fiber diet, high sugar diet, and antibiotic use (especially broad-spectrum antibiotics). Read about more risk factors here & Read Modern Influences On Your Microbiome here.

To restore balance back to the microbiome we can supplement with fermented foods. Almost everyone can benefit from fermented foods. Fermented foods are made with microorganisms, and some fermented foods are considered probiotics with live microorganisms that help to restore and improve the microbial balance.[ii]  

The Benefits of Eating Probiotics (aka fermented foods)[iii]

  • Improves gastrointestinal health (helpful for symptoms of diarrhea, constipation, gas, bloating, IBS, IBD, etc) by crowding out bad microbes. Probiotics also help to heal the intestinal lining in leaky gut.
  • Improved mood (This RCT Trial found that depression severity significantly improved with the use of probiotics compared to placebo)[iv]
  • Reduces inflammation & supports your immune system
  • Increases bone mineral density[v]
  • Improved digestion of dairy products containing lactose[vi]
  • Supports vitamin synthesis. Probiotics make up to half of your daily vitamin K requirement and B Vitamin requirement (Biotin, Folate, B12).

Tips to purchasing fermented products

  1. Check the date & use them quickly! “Viability of Bifidobacterium strains in yogurt has been shown to decline after 4 weeks in refrigerated storage.”[vii]
  2. Proceed with caution with fermented foods if you are sensitive to histamine, as fermented foods are high in histamine and may exacerbate symptoms.
  3. Proceed with caution with fermented foods if you have SIBO (Small Intestinal Bacterial Overgrowth). Some people with SIBO can experience an exacerbation of their symptoms (gas, bloating, constipation, and diarrhea) if they eat fermented foods or take a probiotic BEFORE addressing the bacterial overgrowth. Fermented foods (and probiotics) can be helpful AFTER treatment.
  4. Make sure the label says “live and active cultures” as it ensures there are at least 100 million cultures per gram at the time of manufacture.
  5. Buy fermented foods in the frigerated section! Shelf-stable fermented foods may have altered levels of surviving live bacteria due to temperature fluctuations. Ex: olives, beer, chocolate, coffee, ginger beer, tamari soy sauce, and wine.
  6. Avoid heating your fermented foods to preserve the benefits. Heat may kill off the beneficial probiotic bacteria at temperatures >115 degrees F.
  7. Ensure foods were pasteurized prior to fermentation as pasteurization destroys bacteria.
  8. The difference between fermented Foods vs probiotic foods: Certain fermented foods are considered probiotics. Probiotic foods contain “live active cultures.” “Live active cultures” means there at least 100 million CFU/g. For example, cheese and yogurt are fermented foods, but only yogurt with “live and active cultures” can be a food with probiotics. Abbreviation “CFU” means colony-forming unit.
  9. Learn the difference between each strain of bacteria here.
Top Fermented FoodsBacterial Strains
*L = Lactobacillus
*B = Bifidobacterium
*S = Streptococcus
Stonyfield Organic Grass-fed Greek YogurtNot specified – contains live and active cultures
S. Thermophilus, L. Acidophilus, L. Bulgaricus, L. Paracasei, L. Rhamnosus, Bifidobacterium spp.
Kite Hill Greek Style Yogurt unsweetened / Plain Almond Milk Yogurt  Not specified – contains live and active cultures
S. Thermophilus, L. Bulgaricus, L. Acidophilus, Bifidobacterium spp.
So Delicious Dairy Free Coconutmilk unsweetened yogurtNot specified – contains live and active cultures
S. thermophilus, L. acidophilus, L. bulgaricus, L. casei, L. paracasei, L. plantarum, L. rhamnosus, Bifidobacterium spp.
The Coconut Cult (buy online)50 billion CFU per ounce.
S. thermophilus, L. acidophilus, L. brevis, L. casei, L. fermentum, L. gasseri, L. helveticus, L. lactis, L. salivarius, L. plantarum, L. reuteri, L. rhamnosus, B. breve, B. bifidum, B. infantis, B. longum
Cocoyo coconut yogurt by GT’s Living Foods100 billion CFU per 4 fl oz.
The dominant probiotics are Lactobacillus, Lactocuccus, and Leuconostoc strains.
Miso (Miso Master Organic)   *Make sure it is organic! Soy is a top GMO food.Various lactic acid bacteria (primarily Lactococci and Enterococci)
Tempeh (Lightlife Organic, Tofurky Organic)   *Make sure it is organic! Soy is a top GMO food.R oligosporus, R oryzae

*Derived from Koji mold – Aspergillus oryzae  
Sauerkraut[viii] (Bubbies, Wildbrine)L mesenteroides, L plantarum, P pentosaceus, L brevis, L plantarum, L brevis, L plantarum, L brevis
Wildbrine Salsa    L plantarum, L brevis 
*Wildbrine is a company that ferments foods with naturally occurring bacteria strains. Therefore, exact strains are unknown.
Pickeled Beets (Ozuké, Wildbrine)Lactic acid bacteria, specifically:
L brevis, L plantarum
Kimchi (Wildbrine, Ozuké, Seoul, King’s)L plantarum, L mesenteroides, L plantarum, L brevis, W koreensis

Other related blog posts:

Eat Fermented Foods For A Healthy Gut

Soy, is it good or bad?

Modern Influences On Your Microbiome

Recipes to try:

Sweet Potato Toast with Avocado and Sauerkraut

Spiced Forbidden Rice Bowl with Smoked Salmon and ‘Kraut

Super-Food Synergy: Optimal Food Pairings

[i] Freimer D, Yang TT, Ho TC, Tymofiyeva O, Leung C. The gut microbiota, HPA axis, and brain in adolescent-onset depression: Probiotics as a novel treatment. Brain, Behav Immun – Heal. 2022;26:100541. doi:

[ii] Kechagia M, Basoulis D, Konstantopoulou S, Dimitriadi D, Gyftopoulou K, Skarmoutsou N, Fakiri EM. Health benefits of probiotics: a review. ISRN Nutr. 2013 Jan 2;2013:481651. doi: 10.5402/2013/481651. PMID: 24959545; PMCID: PMC4045285.

[iii] Pandey, K.R., Naik, S.R. & Vakil, B.V. Probiotics, prebiotics and synbiotics- a review. J Food Sci Technol 52, 7577–7587 (2015).

[iv] Akkasheh G, Kashani-Poor Z, Tajabadi-Ebrahimi M, et al. Clinical and metabolic response to probiotic administration in patients with major depressive disorder: A randomized, double-blind, placebo-controlled trial. Nutrition. 2016;32(3):315-320.

[v] Scholz-Ahrens KE. Prebiotics, probiotics, synbiotics and foods with regard to bone metabolism. In Weaver CM, Daly RM, Bischoff-Ferrari HA, eds. Nutritional Influences on Bone Health: 9th International Symposium. Cham, Switzerland: Springer International Publishing; 2016:153-167.

[vi] Kechagia M, Basoulis D, Konstantopoulou S, Dimitriadi D, Gyftopoulou K, Skarmoutsou N, Fakiri EM. Health benefits of probiotics: a review. ISRN Nutr. 2013 Jan 2;2013:481651. doi: 10.5402/2013/481651. PMID: 24959545; PMCID: PMC4045285.

[vii] Ibrahim SA, Carr JP. Viability of bifidobacteria in commercial yogurt products in North Carolina during refrigerated storage. Internat J Dairy Technol. 2006;59(4):272-277.

[viii] Plengvidhya V, Breidt F Jr, Lu Z, Fleming HP. DNA fingerprinting of lactic acid bacteria in sauerkraut fermentations. Appl Environ Microbiol. 2007 Dec;73(23):7697-702. doi: 10.1128/AEM.01342-07. Epub 2007 Oct 5. PMID: 17921264; PMCID: PMC2168044.

Parker EC, Gossard CM, Dolan KE, Finley HJ, Burns CM, Gasta MG, Pizano JM, Williamson CB, Lipski EA. Probiotics and Disease: A Comprehensive Summary-Part 2, Commercially Produced Cultured and Fermented Foods Commonly Available in the United States. Integr Med (Encinitas). 2016 Dec;15(6):22-30. PMID: 28223894; PMCID: PMC5312833.

Editor’s Note: The information in this article is intended for your educational use only. Always seek the advice of your physician or other qualified health practitioners with any questions you may have regarding a medical condition and before undertaking any diet, supplement, fitness, or other health program.

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