With the upsurge in probiotic foods and drinks in the food marketplace, this paper explores some of the science behind fermentation and the scientific evidence supporting claims that nurturing our gut health and specifically our gut microbiome (friendly bacteria) can be important for our physical, mental and emotional wellbeing.


As people who practice the “Macrobiotic way” we are aware of the importance of fermented foods and how they can improve our gut health and also our overall health and well-being. In the past few years in the UK, there has been a surge of interest in so called “probiotic” foods, with the introduction of probiotic drinks, some with plenty of added sugar and some smaller brand names with a purer pedigree, as well as living fermented vegetables. Recent research relating to our friendly gut bacteria has resulted in a rash of recent popular book publications on the subject such as The Good Gut by Justin and Erica Sonnenburg and the Clever Guts Diet by Dr Michael Mosley. Here I look at some of the recent scientific evidence on which this upsurge has been based.

Fermentation in a Nutshell

During the fermenting process, starches, sugars and sometime proteins in vegetables, beans, grains, milk products or even meat are converted into more digestible form through the work of micro-organisms. These natural fermenters are usually bacteria or fungi and may be introduced specifically or we may rely on what is naturally present on the vegetable or in the air (wild fermentation).

Here, I’ll be focussing on lacto-fermentation, where starches and sugars in the vegetable, fruit, grain or milk are converted into lactic acid by many species of lactic-acid-producing bacteria (Lactobacilli). Lactobacilli are ubiquitous in our environment, found all around us on every surface, but more especially on the leaves and roots of plants. The presence of these “good” bacteria makes the vegetables more easily digestible, the vitamin content (notably certain B vitamins and sometimes vitamin K2) increases and they augment our healthy intestinal flora. The good bugs also produce helpful enzymes and have an antibiotic effect, inhibiting the growth of other “bad” bacteria.

Traditions that truly Nourish

Fermented foods can be found in just about every traditional culture the world over: traditional breads such as sourdough; idlis and dosas from India; maize was pounded and then fermented before being consumed in many cultures throughout the world. Other examples include salamis and hams, yoghurt, kefir, cheese, even wine is fermented, as are all forms of alcohol.

Throughout Europe there are many well-established traditions of making sauerkraut and other vegetable-based brine pickles. Further east, in the Ukraine for example, a drink known as beetroot kvass derived from beetroot fermented in brine with a whey or vinegar “starter” is well-regarded as a health tonic. Kvass, a lacto-fermented beverage made from stale rye bread, has been enjoyed throughout Russia for hundreds, even thousands, of years. In Korea, kimchi, a ferment of Chinese cabbage and other vegetables, spiced up with garlic, ginger and chilli, is a national obsession, while tempeh hails from Indonesia. There is kombucha: this and other fermented teas are consumed variously through Japan, Poland, Bulgaria, Germany, Manchuria and Indonesia and many are considered beneficial to health. (ref. 1)

In Japanese culture there are many fermented foods and we all appreciate the benefits of miso soup, pressed vegetables, natto, tamari, umeboshi plums. The Japanese enjoy plenty of other fermented products, many less well known to us in the West.

Although I have been following a generally “macrobiotic” lifestyle for the past 15-20 years, I only became particularly interested in fermenting foods for myself when I to made my own “umeboshi plums”.  At that time, my research on the internet for how to make umeboshi plums came up with nothing clearer than a few youtube clips in Japanese. So, my plums became a bit of a culinary adventure. However, 18 months later the result was fabulous fermented plums which passed for “umeboshi” (right).

Soon after I discovered the book Wild Fermentation by Sandor Katz. By “wild” Katz is referring to the fact that the bacteria in the product come either from another “wild” ferment, from the surfaces of the vegetables themselves and/or from the air around us, rather than being introduced into the product in a controlled or specific way. In a 2012 youtube interview with Dr Mercola, Katz acknowledges the influence that his then macrobiotic lifestyle had on sparking his interest in fermentation of foods. (ref. 2)

Generally speaking, many of these fermented foods “self-regulate” (my term). By this I mean that the bacteria present multiply in the favourable conditions, such as the correct salinity (percentage of salt to water can be critical, although I have witnessed that Katz can be quite off-hand about it!), anaerobic conditions (no air), acidity and temperature. These conditions allow the “beneficial” bacteria to multiply, whilst inhibiting the “baddies”.

What’s Going On in that Fermentation Jar

It is also now well known that the species of bacteria found in sauerkraut, for example, change over the fermentation period. For cabbage-based ferments, Lactobacilli bacteria are introduced naturally, as these air-borne bacteria grow on fresh cabbage leaves. Yeasts also are present on the leaves and if allowed to dominate (for example if the fermentation temperature is too high) may result in a soft sauerkraut of poor flavour.

The fermentation process has three phases: in the first phase, anaerobic bacteria such as Klebsiella and Enterobacter lead the fermentation, and begin producing an acidic environment that later bacteria prefer. The second phase starts as the acid levels become too high for many of the early bacteria, and Leuconostoc mesenteroides and other Leuconostoc spp. dominate. In the third phase, various Lactobacillus species, including L. brevis and L. plantarum, ferment any remaining sugars, further lowering the pH.

A 2004 study found an unexpectedly large diversity of lactic acid bacteria in sauerkraut, and also that previous studies had oversimplified this diversity. Weissella was found to be a major organism in the initial, heterofermentative stage, up to day 7. It was also found that Lactobacillus brevis and Pediococcus pentosaceus had smaller population numbers in the first 14 days than previous studies had reported. (ref. 3) 

The end result is a vegetable ferment that many consider to be a tasty food that also contains a wealth of bacteria that are beneficial to our gut. In one test conducted by a Channel 4 TV programme (ref. 4) 30g of unpasteurised sauerkraut was found to contain the same number of beneficial bacteria as about 50 probiotic capsules. And a 2016 study in the journal Functional Foods in Health and Disease concluded that a two tbsp serving (30ml) of sauerkraut contains the recommended daily number of CFU (colony forming units) of Lactobacillus. Based on these findings, sauerkraut can be considered a “probiotic superfood”. (ref. 5)

Although it would seem that a fermentation period of 7 to 14 days would be best for, say, sauerkraut, variation in temperature can alter the speed of the process and even the bacteria that develop. Traditionally, sauerkraut would have been considered a good way of preserving cabbage for consumption during the lean winter and spring months. As such, it would probably have been fermented in a large crock in a cool cellar, where it would have remained until eaten.  This is in contrast to our warm kitchens, where many make their own sauerkraut. Commercially, it has been long established that the best temperature to ferment cabbage is between 13 and 18 deg C (ref. 6) as too high a temperature can result in overly soft sauerkraut that doesn’t have a good colour. We have a saying in the UK fermenting community: if there’s pink innit, bin it! This refers to a pinkish tinge that can result from the growth of unfriendly bacteria that are best not eaten.

The Benefits of Fermented Foods for our Physical Health

1. Pre-digestion – make the food more easily digestible. Soya beans are the classic example.

2. Detoxification – There are many anti-nutrients in foods (for example phytates) that prevent us from digesting and absorbing them properly. This is why nuts, beans and grains are not easily digestible unless they have been pre-soaked and/or fermented.

3. Nutrient enhancement – Different ferments enhance different nutrients.

The process of converting cabbage to sauerkraut helps preserve the vitamin C content, whilst some B vitamins and vitamin K2 are enhanced. They and other cruciferae produce iso-thiocyanates which are anti-carcinogenic and these are present in sauerkraut. (ref. 7)

Natto (fermented soya beans) contains natto-kinase, an enzyme that regulates blood clots and reduces ulcer formation in the elderly; it is also thought to break down fibrin in blood vessels.  Natto is rich in vitamin K2, the substance that makes the vitamin A- and vitamin D-dependent proteins come to life. While vitamins A and D act as signalling molecules, telling cells to make certain proteins, vitamin K2 activates these proteins, allowing them to bind calcium. In some cases these proteins directly coordinate the movement or organization of calcium themselves; in other cases the calcium acts as a glue to hold the protein in a certain shape. These proteins are only functional once they have been activated by vitamin K. (ref. 8)

4. Enhance the good bacteria in our gut microbiome. These good bugs– lactobacilli and others — can be an effective probiotic, that is, they add to the beneficial bacteria and other micro-organisms in our gut (microbiome). Foods containing beneficial bacteria are now known as “functional” foods.

It is well established that bacteria can survive the transit through the highly acid environment of the stomach. In 2006 a paper published in the Journal of Gastroenterology concluded that “immune responses can be modulated by probiotic bacteria” and that the bacteria stimulate antibodies and activate macrophages, lymphocytes and nerve cells (ref. 9). But let’s not get too excited, as the following year a summary of scientific studies concluded that “ingested strains do not become established members of the normal microbiota” (ref.10). Who do we believe?

Providing it has not been heated, lacto-fermented beetroot juice (kvass) contains anti-oxidant beta-cyanins and also live Lactobacillus bacteria and may be considered a functional food. Researchers say the “activity of these live bacteria modulate the composition and metabolic activity of intestinal microbiota”. (ref. 10)

The bacteria and fungi in our microbiome outnumber the cells in our body. Research is now establishing that our microbiome plays an important role in the function of our immune system, autoimmunity (ref. 11), inflammatory diseases and diseases of the central nervous system, including Alzheimer’s and Parkinson’s. Conversely, it has recently been shown that the presence of certain undesirable bacteria in the human microbiome stimulate symptoms of multiple sclerosis in mice (ref 12). There is also evidence emerging to suggest that gut microbiota may improve the activity of anticancer agents. (ref. 13)

Yet in 2010 the US yoghurt giant Dannon, known as Danone in Europe, was found to have made false and misleading claims about its probiotic yoghurt line when it suggested in promotional advertising that its line “reduces the likelihood of getting a cold or flu” and is “scientifically proven to help with slow intestinal transit”.  Dannon had to pay out to the tune of $21 million to the US states. (ref. 14)

So, it may come as no surprise to learn that in 2012 a new initiative– Gut Microbiota and Health, whose “mission is to share knowledge and promote debate regarding gut microbiota”— launched by the European Society of Neurogastroenterology and Motility is “supported” by Danone. (ref. 15)

The Gut Microbiome, the Brain and Mental Wellbeing

As long ago as 1807 the French psychiatrist Phillipe Pinel said: “The primary seat of insanity generally is in the region of the stomach and intestines.” Pinel is known as the father of modern psychiatry and came to this quote after working with mental patients for many years.

His words are finally beginning to be researched and understood. To me, this new area of Gut Science is really exciting.

Evidence has emerged that our gut bacteria communicate with our brains via the vagus nerve, which is known as our gut–brain axis.  This may perhaps be why researchers have found that 90% of the feel-good hormone serotonin is found in our gut rather than in our brain. And, although serotonin may be primarily found in our gut, its influence is exerted directly on our brain.

Six years ago, an American scientist Javier and his co-workers created some interesting experiments and were able to see a difference in the stress-response behaviour of rats that had been given a Lactobacillus-rich diet and those that hadn’t. They also demonstrated that there is bidirectional communication along the vagus nerve (gut–brain axis) and concluded that certain organisms may prove to be useful therapeutic adjuncts in stress-related disorders such as anxiety and depression. (ref. 16).

In a review called: Gut Microbes and the Brain: Paradigm Shift in Neuroscience, Mayer and co-authors point to a growing body of pre-clinical evidence that there is substantial signalling between gut and brain, brain and gut and that changes to the gut microbiome may play a role in diseases/disorders “including autism spectrum disorder, anxiety, depression and chronic pain”. (ref. 17). There is also mounting evidence that our weight, obesity and cravings for certain foods are in fact driven primarily by our microbes. This month, a newly published study involving healthy women supports “the concept of brain-gut-microbiota interactions in healthy humans”. (ref. 18)

So should we be encouraged or disturbed by recent news of “Pioneering research into benefits of nerve stimulation for some conditions” (ref 19)? This article is an interesting review of extraordinary research published in 2016 involving inserting a pacemaker-like device that effectively short-circuits the vagus nerve. Clinical trials have already shown some success in alleviating the pain of rheumatoid arthritis using this device and it is being used to tackle treatment-resistant epilepsy and depression.


The importance of our gut microbiome for our physical and mental wellbeing is vast. So, nurturing our symbiotic partners, our microbiome, is vital for our wellbeing.  Yet the modern world, so full of antibiotics which our gut bacteria take approximately 2 years to recover from, pesticides and herbicides whose effect on our gut bacteria may not have been considered, is a total minefield for the health of our microbiomes.

As scientists are realising the value of beneficial bacteria to our health, it has been proclaimed that probiotics may “prove to be one of our most effective tools against the new and emerging pathogens that continue to defy modern medicine in the 21st century” (ref. 20).

A new race for scientists is now on: a race to determine exactly which micro-organisms do what in the gut; a race to develop new therapeutics that can selectively target and promote or eliminate these micro-organisms. Dr Lindsay Hall of the Institute of Food Research in the UK, believes that the bacteria and other microbes in our microbiome that relate to specific infections, diseases and health conditions will be specifically identified in the next 3 to 5 years. (ref. 21)

Is there any way in which we can influence and shape what may be to come in this field?

I would like to clarify current patenting law as it relates to micro-organisms:

Native microorganisms in their natural form cannot be patented. However, microbes like yeasts, bacteria, protozoa, unicellular algae, fungi, actinomycetes and viruses can be patented if they have been genetically modified. The process and the product obtained can also be patented. (ref. 22)

Let’s not lose our perspective, let’s return to our naturally fermented foods. No single food, and that includes fermented food, is a cure-all. There are a number of considerations that should be taken into account before suggesting everyone reaches for the sauerkraut jar. Part of Macrobiotic philosophy is to take a “big view”, where we consider how our whole lifestyle affects our body and mind; how our diet, the quality and origins of our food affects us. So miso soup, which may be considered a perfect probiotic food — when made with live miso that is not over-heated – which is also rich in prebiotic raw spring onions, is part of a meal that is balanced energetically and nutritionally with other health-giving foods.

We have to take care not to have too much of a good thing. In Korea, for example, oesophageal, throat and stomach cancers are common; could this be related to over-consumption of their favourite: kimchi?

Too much acidic food (fermented vegetables contain lactic acid) can damage tooth enamel. Fermented foods are also often salty, although vegetables can be fermented successfully with low levels of salt or salt-free.

We have to remember that we’re all different. Everyone has their own unique microbiome. It is known that our microbiome is influenced by many factors, including ethnicity (our genes), a number of factors at and after birth (vaginal birth, breast feeding, vaccinations), the environment we grow up and live in, including the foods we eat, antibiotics that we take.

It is clear that foods which help one individual may not work for another, depending on their microbiome and their health status. For example, some are unable to tolerate the high histamine found in some fermented foods, such as sauerkraut. For many who have not enjoyed live foods before, it is advisable that they introduce these new foods gradually, starting with small amounts. For others, their gut may require a cleansing programme incorporating other healthful foods before they are able to tolerate or benefit from fermented foods.


Our body works as a well-coordinated whole within which there are myriad biochemical and neurological interactions going on all day, every day. The workings of the body are truly astounding. Our microbiome is just one part of that fabulous functioning system and we still have much to learn about how it interacts with the rest of our body and the role it plays in our health and wellbeing. As health professionals we need to keep abreast of the scientific developments in this area. And perhaps we should also be paying fresh attention to those “gut feelings” we have about people, places and situations.

Suggested Reading

Sandor E Katz Wild Fermentation (2003). Excellent recipe resource

Sandor E Katz The Art of Fermentation (2012). Fabulous history, background and more recipes



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