What 100 Trillion Microorganisms Want You To Eat — Part Two: Probiotics
My last post was about prebiotics — foods that contain lots of indigestible fibres that the beneficial bacteria already living in our colon break down to produce butyrate, one of the most important and least talked-about nutrients in human health. If you missed the article you might want to read it before this one.
While prebiotics feed your existing gut bacteria, probiotics work slightly differently, by actively introducing additional beneficial strains that replenish and diversify your existing microbiome. And it’s this diversity, researchers are increasingly finding, that underpins not just a healthy digestive system, but also a strong immune response, stable mood, good skin, and a general sense of wellbeing that is hard to achieve any other way.
A little history
Fermented and cultured foods have been part of traditional human diets for thousands of years — not because our ancestors understood the science behind a balanced gut microbiome, but because these processes were one of the most reliable ways to preserve food before refrigeration existed. Every traditional culture developed its own versions: for example sauerkraut in Germany, kimchi in Korea, miso and tempeh in Asia, kefir in the Caucasus, and kvass in Eastern Europe. Even the Romans had a fermented fish sauce called garum, which they brought to England in the first century AD, and which is now widely considered to be a precursor to the original Worcestershire sauce.
What we now understand is that our gut microbiome evolved alongside these foods, and that their gradual disappearance from everyday meals over the past several decades is one of the more significant, and least discussed, changes in the modern diet. Bringing them back however doesn’t require a complete overhaul of the way you eat, just a slight change in focus.
First though, let’s clarify the difference between fermented and cultured foods.
Fermented foods rely on naturally occurring wild micro-organisms — bacteria and yeasts present in the environment or on the food itself — to drive the fermentation process. Sauerkraut, kimchi, and lacto-fermented vegetables all fall into this category, as none of these have been deliberately inoculated with a culture. (Note — some American fermenters do suggest adding a packaged culture, but in my experience, if you’re working with freshly picked, organic produce, this is unnecessary).
By contrast, cultured foods such as yoghurt, cheese, kefir, miso or tempeh are all made by introducing additional specific strains of bacteria or yeasts as a starter, which allows for greater consistency in both flavour and probiotic content. Both fermented and cultured foods are valuable, and ideally your diet would include a variety of each.
Listed below are some of the more easily available probiotic foods in New Zealand, and hopefully you’ll be surprised at the wide variety there is to choose from. One word of caution though: if you have a histamine intolerance, fermented and cultured foods can be problematic, as they are among the highest dietary sources of histamine. Introduce them slowly, pay attention to how your body responds, and seek guidance if you’re unsure.
Raw sauerkraut, kimchi and other lacto-fermented vegetables are among the most potent sources of Lactobacillus plantarum, a bacterium particularly helpful in maintaining the integrity of the gut lining. However, the key word here is raw, as pasteurised versions, and those made with vinegar rather than brine, have had their live cultures destroyed and offer none of the same benefits. Look for unpasteurised varieties in the refrigerated section of supermarkets and health food stores, rather than those on the shelf near the pickles. A spoonful or two alongside a meal is all it takes, and once you’ve acquired a taste for their salty acidity, they really become addictive. You can also make your own, as it’s surprisingly easy as long as you follow a few basic rules, and becoming increasingly popular.
Full-fat, unsweetened yoghurt and kefir are the most familiar probiotic foods for most people, and both contain beneficial bacterial strains including Lactobacillus acidophilus and Lactobacillus bulgaricus that help digestion. However if you’re buying them rather than making your own, choose those that contain live cultures, and always avoid low-fat versions as these are typically made with skimmed milk powder, an ultra-processed ingredient that undermines the very gut health you’re trying to support. These days I tend to eat more kefir than yoghurt, as it has significantly more beneficial bacteria as well as certain yeasts, and I make my own with locally sourced milk.
Unpasteurised miso, the Japanese fermented soybean paste, is also high in beneficial enzymes and probiotics, and adds a lovely depth of flavour to soups, main courses, dressings, and marinades. One important note though: high heat destroys its live cultures, so if you’re making miso soup, stir it into water that is warm but not boiling, and if you’re cooking with it, note that while the flavour remains, the probiotic benefits will be gone.
Tempeh is a traditional Asian food made by culturing whole soybeans to form a firm, cake-like block with a nice, nutty flavour. It can be chopped, sliced, or crumbled, and like miso, is an excellent source of both beneficial bacteria and enzymes that support digestion. It is also high in fibre and protein, making it a particularly useful food for anyone recovering from surgery. One of my favourite ways to use it — something I first tasted in London at Cranks Wholefoods in the 1970s — is to crumble it into small pieces, toss with a little traditionally fermented tamari, and bake in a moderate oven until crisp. This makes a delicious, savoury topping for vegetables or soups.
Note — with both miso and tempeh (plus naturally fermented soy sauce) always opt for traditionally made, organic varieties as based on the most recent data from 2025, 74% of the world’s soybeans are genetically modified. Non-organic soybean crops are also heavily sprayed with glyphosate, a known gut disruptor.
Naturally brewed kombucha made from a SCOBY, or a ‘symbiotic combination of bacteria and yeasts’, contains Saccharomyces boulardii, a probiotic yeast that again supports digestion and helps prevent the kind of gut imbalance that commonly follows antibiotic use. If you’re not making your own (again, a very easy process), choose raw kombucha and read the label carefully, as many commercial varieties are now made with sugar substitutes like erythritol, or are heavily processed in ways that eliminate the very cultures that make kombucha worth drinking.
Water kefir, which is made by culturing lightly sweetened water with ‘grains’ (another type of SCOBY), similar to those used in milk kefir. This produces a lightly fizzy, mildly sweet probiotic drink that supports gut health without containing any dairy — a useful option for those who are dairy-free.
Beet kvass is a traditionally fermented tonic from Eastern Europe, made from beetroot using the same method as lacto-fermented vegetables. It is available in some health food stores but again, is very easy to make at home.
High-quality aged cheeses such as certain cheddars, gouda, and Italian parmesan, which are produced by culturing milk using lactic acid bacteria. While these contain lower and more variable amounts of live bacteria than kefir or yoghurt, the aging process means that they still offer some probiotic benefits, especially if raw.
Other cultured dairy products include crème fraiche, cultured butter, homemade sour cream, clotted cream and labneh — the thick, tangy yoghurt cheese that is popular in Middle Eastern cuisine. Labneh in particular is worth exploring if you haven’t tried it, as it is delicious both as a spread or a dip, and is very easy to make at home from full-fat yoghurt.
Traditionally made sourdough bread, which relies on naturally occurring lactobacillus bacteria to break down proteins in the flour, making them easier to digest and increasing their nutritional availability. Not all sourdough is created equal though — many commercial sourdoughs, especially those from supermarkets, are made with added yeast and vinegar and offer none of the health benefits of traditionally made loaves. Look for bread made with a long, slow fermentation process, ideally from a good bakery or made at home.
As with prebiotics, variety is the guiding principle here. No single fermented food will transform your microbiome on its own — what matters is the cumulative effect of regularly including a range of probiotic foods in your diet, as each one introduces different bacterial strains, and it is this diversity of species that allows your microbiome to thrive.
If fermented foods are new to you, make changes gradually as your gut will take time to adapt. Try switching to a traditional sourdough loaf; buy some unpasteurised miso and enjoy a cup before lunch; find a friend willing to share some of their milk kefir grains and start making your own. All these strategies are incredibly easy to incorporate into even the busiest of schedules, and before long these foods will feel less like additions to your diet and more like things you really miss when you’re not having them!