How to Use Fermented Vegetables to Repair a Damaged Microbiome

kimchiOne of the main recommendations of the microbiome restoration plan is to occasionally consume small quantities of a diversity of fermented vegetables. In the past, I’ve talked at length about the pros and cons of using various probiotic products, and I’ve looked into many of the biological mechanisms that are relevant with respects to how probiotics affect human health. I’ve also mentioned and talked a little about a study I recently conducted that was the first ever study to look into how the consumption of fermented vegetables, more specifically sauerkraut, affects gut health in patients with irritable bowel syndrome. What I haven’t done, at least not in a structured manner, is to break down the above recommendation and explain why it’s formulated the way it is. That’s something I thought I’d do today…

Breaking down the recommendation

There’s a reason why the above recommendation if formulated exactly as it is. It wasn’t created in a hurry. Its backbone consists of a structure of evolutionary and scientific concepts that took a long time to build. In order to make you understand what the premises that underlie the recommendation to occasionally consume small quantities of a diversity of fermented vegetables are, I thought I’d break the recommendation down into its constituent parts and talk a little about each one…

– Why ‘occasionally’ and ‘small quantities’?

Some people consume large quantities of fermented vegetables on a daily basis. As I’ve pointed out in many of my previous articles on probiotics and fermented foods (e.g., this one, this one), I think that’s unwise. Regular consumption of large quantities of fermented foods and/or other products containing probiotics is an evolutionarily novel behavior that may destabilize the gut microbiota.

Lactic acid bacteria, the type of bacteria that are most predominant in fermented foods such as sauerkraut, kimchi, and kefir, are no different form other bacteria in that they have evolved a capability to produce various compounds that help them keep up in the evolutionary arms race that takes place within the biotic community of the Earth. Many types of bacteria produce bacteriocins that are toxic to other microorganisms. They do so because it helps them outmaneuver competing organisms; hence, it aids their survival and reproduction.

It could be argued that the word probiotics, which means pro life, is a misnomer. Probiotic organisms are not harmless bugs that stay in the background and let all other bacteria do their thing in peace; rather, they are, like all other organisms on this planet, wired to fight for their survival.

If new organisms are introduced into an ecosystem, the ecosystem will obviously be affected in some way. The human gut microbiota is no different from other ecosystems in this regard. If you constantly pour great numbers of fermented food-associated bacteria into your gut, your microbiota may never get a chance to stabilize.

The quantities of bacteria that are present in fermented vegetables are relatively small compared to those that are present deep down in the human gut; however, in my experience, they are sufficient to cause problems in some people, particularly those who harbor a disturbed, degraded microbiota. Diverse, stable ecosystems are more resistant to invading organisms than degraded, disturbed once; hence, it goes without saying that people who harbor a resilient, diverse gut microbiota are more resistant to the potential adverse health effects that daily consumption of large quantities of fermented foods can have. That said, I strongly suspect that it’s unwise also for these individuals to consume a lot of fermented vegetables every day.

It’s important to remember that it’s only very recently – on an evolutionary time scale – that fermented foods such as kimchi, kefir, and sauerkraut became a part of the human diet. Many of our tree-dwelling primate ancestors are believed to have consumed some plant foods that had undergone natural fermentation processes (1); however, they obviously didn’t know how to or have the equipment to make large quantities of fermented foods via controlled fermentation. Neither did our Paleolithic ancestors. Most hunter-gatherers – both contemporary and ancient – consume primarily fresh food (2, 3, 4). They may occasionally eat some plants that have started to ferment as a result of being separated from their source of nutrients; however, they don’t consume a lot of fermented foods. It wasn’t until after the Agricultural Revolution that fermented foods such as wine, beer, and yoghurt were infused into the human diet.

What all of this is to say is that fermented foods did not make up a large part of the preagricultural diets that nourished our primal ancestors. This doesn’t mean that we – contemporary humans – shouldn’t consume any fermented foods; however, it does mean that we should think twice before we make fermented foods a large part of our diets, given that we are still – to a significant extent – hunter-gatherers from a genetic perspective.

The goal with consuming fermented vegetables in the context of microbiome restoration is not to get as many “probiotics” into the gut as possible, but rather to diversify the gut microbiome and build a resilient gut ecosystem that works well on its own. In other words, you could say that the goal is to not require a regular influx of immune-stimulating probiotics to maintain a healthy immune system and keep pathogens at bay.

It doesn’t take billions of microorganisms to make a difference. Just a s single microbe that is able to swim through the acidic bath of the stomach without drowning can set up shop deep in the gut, given that it finds an available niche, is adapted to live in the gut, and is not outcompeted by other organisms. In other words, you don’t have to take in 5 probiotic capsules every day or eat a big bowl of fermented vegetables to get some new bugs into your system. Actually, doing so may, as previously mentioned, do more harm than good.

With that said, there are some situations in which a high daily intake of fermented vegetables may be warranted. For example, some people who have an unhealthy gut (e.g., one in which problematic organisms such as Candida albicans have been allowed to grow uncontrollably) and are just starting out on their microbiome restoration journey may benefit from consuming moderate-large quantities of fermented vegetables every day for a small period of time (e.g., 1-2 weeks), in order to decrease the pathogen load of their gut and bring a lot of potentially beneficial bugs into their system.

A high intake of fermented vegetables may also help one recover from food poisoning, mild gastrointestinal disturbances, and the like. What is important to note though, is that these situations are temporary in nature, not chronic. Personally, I often eat some sauerkraut or other fermented vegetables during periods when I feel that my gut is not working optimally, as a way of trying to nudge it towards a healthier state.

– Why ‘diversity’?

It’s better to consume a variety of different fermented vegetables than just one or two types. You don’t have to be a genius to figure out why this is the case, all you need is a basic understanding of ecology. No two natural ecosystems that are present on this planet are completely identical. There’s pretty much always going to be some variation in the types and/or numbers of organisms that are present. The reason is that different environments support different biotic communities and that evolutionary processes cause inter-ecosystem genetic variation. The microbial ecosystems that are associated with fermented foods such as sauerkraut and kimchi are not exempt from these rules.

Let’s say that you go to the grocery store today and buy a couple of cabbage heads. You then head home, slice up the cabbage, squeeze out its juices, add some salt, and then compress everything into a fermentation crock that you leave to ferment in your kitchen cabinet. Then again tomorrow, you repeat exactly the same procedure.

After 2 weeks, you take out the first crock you made and eat some of the kraut, which is now nice and sour. The next day, you do the same thing with the second crock. You find that both products taste quite similar. This is not surprising, seeing as they are made from the same ingredients. The fact that their taste is quite similar doesn’t mean that the two product are identical with respects to their microbiota composition though. They undoubtedly contain many of the same types of bacteria, including Lactobacillus plantarum; however, there will undoubtedly be some inter-batch variation in microbiota composition. One of the products may contain more of certain types of bacteria than the other, perhaps harboring some strains that are not found in the other product.

These types of differences come to be because there’s always going to be some variation in the types of organisms that are present on the vegetables that are used for different ferments, as well as some variation in fermentation time, temperature, and so on. The more variation there is with respects to these factors, the more variation there is going to be with respects to the types of bacteria that are present in the ferments. Whereas the difference in microbiota composition between the two sauerkraut products above is going to be small; the difference between two fermented food products that contain different types of vegetables and/or have fermented for unequal times can be quite substantial.

The microbiota composition of fermented foods doesn’t just differ between different products; it also changes over time within each product. For example, if you had left the sauerkraut to ferment for another 7 days after you took it out and ate some on day 14, then its microbiota composition – and also its taste – would have changed, the reason being that different microbes are involved in different parts of the fermentation process and thrive under different conditions.

A diverse ecosystem is usually a more resilient and healthy ecosystem than one that is species-depleted. The microbial communities that reside on our bodies are no different from other biotic communities in this respect. A large body of evidence suggests that it’s better to harbor a diverse gut microbiota than a microbiota that is rid of diversity (5, 6, 7, 8).

It’s good to harbor a diverse gut microbiota as many different types of microbes are required to properly stimulate the human immune system and break down the wide diversity of fermentable compounds that are a part of the human diet. Moreover, a diverse gut microbiota tends to be more stable and resilient than a microbiota that lacks diversity, in the sense that it’s more resistant to being perturbed by pathogens, problematic foodstuffs, and pharmaceutical compounds. Diversity is not the only thing that is important with respects to microbiota health; however, it’s definitely something one should pay some attention to.

The purpose of eating a wide variety of fermented vegetables, as opposed to just one or a couple of types, is to maximize the diversity of organisms one is exposed to. It’s obviously more likely that you come in contact with many microorganisms that are both able to get through the harsh conditions in your stomach unscathed and survive and grow in your gut if you consume many different types of fermented vegetables, as opposed to just one type.

– Why ‘fermented vegetables’?

Why does the microbiome restoration plan say that one should consume fermented vegetables? Why not consume other types of fermented foods instead?

The reason why fermented vegetables are mentioned specifically in the microbiome restoration plan, whereas yoghurt and other types of fermented foods are not mentioned, is that fermented vegetables have some unique characteristics that make them particularly useful in the context of microbiome restoration. First of all, vegetables have been a part of the human diet for millions of years. Hence, we have co-evolved with vegetable-associated microorganisms for a very long time. By eating raw and fermented vegetables, you may expose yourself to some microbial old friends that have accompanied the human kind on its evolutionary journey (7). Dairy foods, on the other hand, are a new addition to the human diet.

Second, the microbiota of traditionally fermented vegetables differs markedly from that of fermented foods such as yoghurt. It’s typically more diverse than that of other fermented foods, particularly that of industrially produced, fermented dairy foods. It’s also less generic than the microbiota of yoghurt and other similar fermented foods: it changes markedly throughout the fermentation process and differs between different products.

Third, vegetables are very healthy; not just because they are a source of potentially beneficial bacteria, but also because they are high in fiber, vitamins, and minerals, have a low caloric density, and contain little or no salt, saturated fat, and sugar. As I’ve pointed out in some of my previous articles here on the site (e.g, this one), milk products are not so great with respects to their nutritional characteristics. Many of the problems with milk can be partly or wholly eliminated via fermentation; however, some remain pretty much regardless of what type of processing techniques that are used.

With all of that being said, there’s nothing wrong with consuming certain other types of fermented foods in addition to fermented vegetables. The reason fermented vegetables are at the center of the microbiome restoration plan is not that no other fermented foods contain bacteria that are beneficial in the context of microbiome restoration, but rather that fermented vegetables have some unique characteristics that make them particularly useful for repairing a damaged microbiota.

Other considerations

Homemade vs. store-bought

Homemade fermented vegetables are generally superior to store-bought varieties. The reason is simple: most of the fermented vegetable products that are sold in stores contain a more generic microbiota composition; there’s less variation between products than what is the case with homemade ferments. In particular masss-produced fermented vegetables made via the use of starter cultures are very bland with respects to their microbiota composition. Do not buy those products. Also, perhaps needless to say, stay away from products that have been pasteurized.

Homemade ferments have a somewhat different microbiota composition than industrially produced fermented foods and may harbor small numbers of some potentially benefical microorganisms that are not present in store-bought varieties, because the conditions (e.g., microbial environment, temperature, salt content) under which they are made are not strictly controlled.

The reason the microbiome restoration plan doesn’t specifically state that one should consume homemade fermented vegetables, as opposed to store-bought varieties, is that not all of the fermented vegetable products that are sold in stores are equally bad. Some stores carry fermented vegetables that are produced in a traditional manner and that are as good, or almost as good, as homemade ferments. If you manage to locate a store, farmer, or fermentista that sells high-quality fermented vegetables, then feel free to go ahead and buy and eat their products.

The use of starter cultures

As pointed out above, fermented vegetables that are made via the use of starter cultures are less varied with respects to their microbiota composition than products that are made via the use of bacteria that are naturally present on vegetables. It’s unwise to use starter cultures, particularly in the context of microbiome restoration. If you use starter cultures when you make fermented vegetables, you may inhibit the growth of certain types of organisms and make your ferments less varied with regards to the types of bacteria they contain. It’s better to do things the way nature intended. There’s no reason to mess things up by bringing unnecessary human inventions into the mix.

Salt content

From the perspective of maximizing microbial diversity, it’s unwise to use a lot of salt when making fermented vegetables. Salt hinders the growth of many types of bacteria, not just “bad” ones, but also some potentially “good” ones. A little salt goes a long way.

It is possible to make fermented vegetables with no or very little salt, but it’s not easy, seeing as salt is important for keeping molds and other nasty critters away. A while back, I talked to a friend of mine who runs fermentation workshops and sells fermented food products and recipe books about the possibility to making fermented vegetables with no or very little salt. She tried it out and actually managed to create a very good product. It tasted quite different from fermented vegetable products that are made with standard salt concentrations. It clearly had a different microbiota composition. I suspect that it may be possible to make fermented vegetables that are more therapeutic with respects to microbiome restoration than conventional ferments by tweaking around with variables such as salt content and fermentation time.

Fermentation time

As pointed out earlier, the microbiota of fermented vegetables evolves during the fermentation process. A lot of people who make fermented vegetables let their ferments stand undisturbed for a specific period of time (e.g., 2 weeks), before they bring them out onto the kitchen counter, eat a little, and then transfer all of the fermented vegetables to the fridge for storage. From the perspective of maximizing the number of potentially beneficial microorganisms one is exposed to, this is probably not the best strategy. It’s probably better to take out, eat, and store some of the fermented vegetables at several different time points. This way, one is exposed to the full spectrum of microbes that are present in vegetable ferments. This strategy is particularly great when fermentation crocks are used, as it’s easy to remove small quantities of fermented vegetables from fermentation crocks without messing with the fermentation process and/or ruining the ferment.

Obviously, after some time, one has to transfer the ferment to the fridge, or else it will go bad. The exact amount of time that you should let your ferments ferment before you transfer them to a cold environment for storage depends on several factors, including your taste preferences (the longer you let your ferments ferment, the more acidic they get), the temperature of the room you’re fermenting in, and the amount of salt you use.

Last words

Fermented vegetables are undoubtedly useful in the context of microbiome restoration. With that said, it’s important to point out that sauerkraut, kimchi, and the like do not contain the broad range of microorganisms that are required to repair a severely degraded gut microbiota. They primarily contain Lactobacillus spp., which make up a fairly small portion of the gut microbiota of a normal person. Also, many of the bacteria present in fermented foods are not conditioned to live in the human gut: they disappear from the gut or diminish in presence shortly after one stops consuming the foods in which they are found.

This is one of the reasons why the microbiome restoration plan lists several other microbiome restoration strategies besides the one I’ve talked about in this article. It’s also one of the reasons why I offer online health coaching (See this page for an overview of my online coaching services). There are no quick fixes for complex health problems. Moreover, no two people are identical or have identical needs. The tips I’ve shared in this article are obviously general in nature; they may not be equally useful for everyone.

Another thing I think it’s important to say is that not everyone “needs” to eat fermented vegetables. If your microbiota is in bad shape, you’d probably be wise to incorporate some fermented vegetables into your diet; however, if it’s in good shape, you may not attain that much benefit from eating sauerkraut, kimchi, and the like. You may get some new microbes into your gut; however, you’re probably not going to notice any dramatic health improvements.

There’s still some things we don’t know with respects to what constitutes the optimal approach to treating gut dysbiosis. With that said, there is a lot we do know. As long as we keep the evolutionary health model with us everywhere we go, we’re unlikely to get lost.

Picture: Creative commons picture by Marcus Buchwald. Some rights reserved.


  1. Thanks for a good article, Eirik. I like your perspective of “Less is More.” Many of the so-called health gurus push the idea that if a little is good, a lot more is better, whether it be with regard to fermentation, supplementation, or whatever. Possibly this is to increase the sales volume of whatever products most of them sell. The only thing you “sell” is the consumption of real food. There’s no conflict of interest, and I like that.

    • Less is indeed more, Shary, at least when it comes to fermented vegetables/probiotics. There’s little doubt in my mind that it can be very detrimental to health to take in a lot of “probiotics” (I’m liking that word less and less) on a daily basis. This is particularly true for people who harbor an imbalanced microbiota.

  2. Good point that one must use several strategies to repair s damaged microbiome. Not sure I agree with the recommendation to eat fermented foods occasionally, though spare servings might be wise if eating daily. See for reference to research that would seem to contradict your point that frequent consumption of fermented foods may not be healthy. Thanks for your site, And the work that goes into it!


  1. […] much better to focus on gradually building a healthy, diverse gut microbiota, for example by occasionally eating small quantities of fermented vegetables (which, in contrast to probiotic supplements and many industrially produced probiotic foods, […]

  2. […] One of the tips that are listed in the microbiome restoration plan is to eat fresh, raw plant foods derived from a trusted source. I think a lot of people underestimate the value of this tip. Most people understand that it’s important to eat healthy, fiber-rich foods and stay away from antibiotics. Most folks also understand that fermented vegetables can help them diversify their microbiome. […]

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