Japanese Fermented Foods: Health Benefits of Miso, Soy Sauce, Natto and Tsukemono

Miso is produced by fermenting soybeans with koji mould (Aspergillus oryzae) and salt, sometimes with rice or barley added. Fermentation breaks down proteins into free amino acids (including glutamate — the source of miso's umami), produces B vitamins, and generates bioactive peptides with documented health effects. Research published in the Journal of Toxicologic Pathology found that regular miso consumption was associated with reduced incidence of radiation-induced cancers in mice — a finding attributed to miso's antioxidant compounds. A 2021 meta-analysis found that regular miso soup consumption was associated with significantly reduced risk of cardiovascular disease and gastric cancer in Japanese cohort studies. Miso also contains live probiotic cultures (Lactobacillus and Bifidobacterium species) when unpasteurised — which is why you should never boil miso, only dissolve it into hot liquid.

Natto is made by fermenting soybeans with Bacillus subtilis var. natto, producing a sticky, stringy, pungent food with an intense umami flavour. It is polarising outside Japan but is one of the most nutritionally dense fermented foods known. Natto is extraordinarily rich in vitamin K2 (specifically MK-7) — a nutrient critical for directing calcium into bones rather than arteries and associated with reduced cardiovascular disease and osteoporosis risk. A landmark 2004 study published in Thrombosis and Haemostasis found that natto contains nattokinase, an enzyme that dissolves blood clots. Natto also provides complete protein, iron, calcium, and beneficial Bacillus subtilis bacteria that survive stomach acid. Even a small daily serving (45 g — one packet) provides meaningful nutrition.

Traditional Japanese soy sauce (shoyu) is produced by fermenting a mixture of steamed soybeans and roasted wheat with koji mould and brine, then ageing for 12–24 months in cedar or stainless steel vats. This process produces over 300 flavour compounds and significant quantities of antioxidants called melanoidins (the compounds that give aged soy sauce its colour). Research from the British Journal of Nutrition found that naturally fermented soy sauce suppresses allergy responses and has anti-inflammatory properties attributable to its polyphenol content. The contrast with chemically produced 'soy sauce' (hydrolysed vegetable protein mixed with caramel colour and salt) is stark — the latter lacks all these beneficial compounds.

Tsukemono (漬物) are Japanese pickled vegetables — ranging from umeboshi (pickled plums) to shiozuke (salt-pickled cucumber) to nukazuke (vegetables fermented in rice bran paste). They are served as a side dish at virtually every Japanese meal, providing sourness, crunch and probiotic bacteria. Nukazuke, fermented in a nuka (rice bran) bed maintained at room temperature, produces lactic acid bacteria identical to those in yogurt and kefir. Umeboshi — small, intensely sour and salty preserved plums — have been studied for antibacterial properties against Helicobacter pylori and for their alkalising effect on blood pH. A typical Japanese meal that includes miso soup, tsukemono and rice provides meaningful probiotic and prebiotic benefits from naturally fermented sources.

The gut microbiome — the trillions of bacteria, fungi and viruses that colonise the human digestive tract — is now understood to influence immunity, mental health, metabolic function and disease risk. Fermented foods feed and diversify the microbiome through probiotic bacteria and prebiotic fibres. A 2021 study in Cell found that a diet high in fermented foods (including miso, natto, kimchi and yogurt) significantly increased microbiome diversity and reduced inflammatory markers in humans, outperforming a high-fibre diet for microbial diversity benefits. The traditional Japanese diet, with its daily miso soup, frequent natto, regular tsukemono and high fish intake, is a natural model for microbiome-supporting eating.