A while ago, I wrote a newsletter exploring the complexities of claims that eating fermented food has a measurable and long-lasting impact on overall health. My aim was to demonstrate how fiendishly difficult it is to directly interact with the gut microbiome, let alone take samples, measure, and speak with any degree of confidence. For that newsletter, I read research papers and entire books by gastroenterologists and bowel surgeons (links in the footnote), and sought the most cutting-edge opinions from multiple fields to try and build a larger picture of what was going on.

Why? Because I’m interested.

It would work in my favour to accept the same story that others do, that eating fermented foods is the next dietary holy grail. But I don’t take things at face value. And, unless my questioning can be satisfied, I won’t push a narrative even if it helps me sell more books.

Evidence lies at the heart of understanding. Please feel free to read the previous newsletter if you missed it. Contrary to the backlash, I thought it was quite balanced and explored some of the fascinating ways the microbes within us actually work (beyond ‘eat microbe = good’). Approaching any topic with inquisitive scepticism is healthier than only reading the opinions that reinforce your views.

But I knew I’d ruffle some feathers.

The newsletter they referred to can be read here.

In this newsletter, I thought I’d explore an alternative view. Admittedly, one guided by a hunch and a healthy dose of common sense. It’s easy to think of fermentation as a charming side quest humans discovered somewhere along the way. But what if it wasn’t a side quest at all? What if it made us human?

Today I want to tell you a story about how, long before we ever learned to bake bread or brew beer or even tame fire, fermentation could have been quietly remaking us from the inside out.

Drunken Monkeys

Let’s set the scene: we're in a humid prehistoric forest, two million years ago. Fruits fall to the ground. Within hours, yeasts from the air and on their skins get to work and begin feasting. The sugars break down into alcohols, acids, and gases. What some people call decomposition, others might describe as the fruit beginning to ferment naturally.

Most animals, when they encounter that boozy, sharp, slightly fizzy fruit, are put off (except for badgers, who stumble around drunk for hours). To them, alcohol is toxic in even small amounts. Their bodies can’t cope. They shuffle off or avoid it altogether, or risk leaving themselves vulnerable to mishap, competition, or predators.

But not us.
Well, not yet.

Somewhere deep in our primate lineage, around ten million years ago, one of our fruit-eating ancestors, known as CHLCA (Chimpanzee–human last common ancestor), picked up a tiny genetic tweak: a mutation in the ADH4 gene, which helps metabolise alcohol. This mutation allowed them to process ethanol forty times faster than their cousins. In other words, they could eat that fallen, fermenting fruit without being knocked sideways.

Imagine what that meant: a whole new food source, ripe for the taking. No competition. Less risk of food scarcity. And full of highly digestible sugars.

But when your great great great (etc) grandad eats this fruit, they aren't just ingesting calories, they’re also ingesting:

• Live microorganisms (yeasts like Saccharomyces, Candida converting sugars to ethanol and CO₂; lactic acid bacteria such as Lactobacillus, Leuconostoc producing organic acids; acetic acid bacteria turning ethanol into vinegar-like compounds; wild fungi and environmental bacteria)

• Microbial metabolites (alcohol, lactic acid, B vitamins, etc.)

• Structural elements like cell wall polysaccharides and bacterial DNA

Fermentation and Fire: Our First Invisible Technology

Fast forward to Homo erectus, about 1.8 million years ago, the first ancestor who started looking a lot like us. Around the same time we see evidence of fire use, we also find hints that humans were eating foods that required a little help to digest: tubers, grains, tough meats. Cooking on fire was a revelation. It unlocked calories, softened defences, and made more food available.

And so did fermentation.

Before we ever controlled fire fully, we almost certainly stumbled upon wild ferments:

• Fruits foaming lightly in the forest undergrowth

• Honey dripping and fizzing with spontaneous mead yeasts

• Fish buried in cool mud fermenting slowly into preserved protein

• Animal milk naturally souring into a digestible proto-yoghurt (later, following Homo sapien agriculture)

Fermentation pre-digests food. It breaks down complex, tough structures such as starches, fibres, even toxins, and it makes nutrients more bioavailable. In some cases, fermentation creates nutrients that weren’t there before, like certain B vitamins.

In a world where food was hard-earned and digestion was an expensive job, a little microbial help was game-changing. We tend to think of fire as the first big leap forward, but fermentation may have been an invisible twin technology, a quiet co-evolution that shaped our guts, our tastes, even our brains.

Ingested Microbes Can Influence the Gut, Even If They Don’t Colonise It

Modern research shows that some microbes in food could survive digestion, at least partially, leading to influences on the resident gut microbiome:

• Transient colonisation: Some foodborne microbes don’t stay long but still interact with gut microbes and immune cells. It’s important to note, there is evidence that when we stop eating fermented foods, our gut microbiome returns to a resting status quo, largely formed during the first six months to one year of life.

• Cross-feeding: Some incoming bacteria produce metabolites that feed beneficial gut residents, improving microbial diversity.

• Bioactive compounds in fermented food (short-chain fatty acids, bacteriocins) can suppress pathogens or modulate inflammation. (This last point is what we call postbiotics and is the part I think is most profound for health, but many get caught up on the idea that fermented foods need to be raw and alive to be beneficial.)

In the context of wild fermenting fruit, this means:

Early humans consuming these foods were regularly dosing themselves with seasonal environmental microbes, especially yeasts and lactic acid bacteria, which could have enriched their microbial diversity and resilience over time.

Primate Studies: Clues from Our Close Cousins

There are several studies suggesting a direct relationship between fruit consumption and gut microbiome structure. Wild chimpanzees eating fallen, fermenting fruit show high microbial diversity, including fermentation-associated bacteria (Hicks et al., ISME Journal, 2018). Frugivorous monkeys have gut microbiomes enriched in bacteria that metabolise plant polyphenols and pectins, especially when eating overripe or fermented fruit (Amato et al., Nature Ecology & Evolution, 2019).

Though these microbes don’t permanently colonise, they prime the immune system, aid digestion, and possibly influence gene expression in gut cells.

Mechanisms: How Did This Shape Evolution?

Selective pressure on gut microbial tolerance
Repeated exposure to fermentation microbes could have led to better cohabitation between host and microbial guests. Gut microbes that could metabolise lactic acid, ethanol, and plant polyphenols thrived.

Immune system training
Regular microbial ingestion could have led to better tolerance, less inflammation. Potential selection for humans with more adaptive, microbiome-friendly immune systems.

Nutrient absorption and detoxification
Microbial metabolites such as B vitamins and short-chain fatty acids enhanced nutrition. Alcohol dehydrogenase evolution helped process ethanol and potentially detoxify microbial byproducts.

Over time, natural selection smiled on the boozy fruit-eaters, and on us, their descendants.

It’s important to note that, in the same way we have largely lost our ability to survive on a raw, uncooked diet (a human won’t survive eating what a gorilla eats), these studies on our close evolutionary relatives are an indication of what might have shaped us, but are not to be taken as gospel for how such things might function in modern humans.

Fermented Foods as a Probiotic Bridge

In humans, early studies* show that regular consumption of fermented foods increases gut microbial diversity, though there is no evidence that microbes responsible for fermentation survive and are part of the increased diversity directly. Even short-term dietary interventions with fermented foods (like sauerkraut, kefir, and yoghurt) can improve immune markers and reduce inflammatory proteins like IL-6, thanks to the aforementioned postbiotics (bioactive compounds like short-chain fatty acids, bacteriocins), not necessarily the living, raw microbes found in fermented foods.

* If you’re into such things, it’s worth noting that none of these studies so far have been large enough to be considered reliable or repeatable at the time of writing this. This is why I am careful where I write the word ‘could’ and hope that you take note of this when reading this newsletter.

Critical Scrutiny: What We Can and Can’t Say

Supported by evidence:

• Fermenting fruit contains viable microbes that interact with gut ecology

• Eating such foods introduces new microbial strains, though not always those found in the food itself, and bioactive compounds

• ADH gene adaptation shows we metabolised fermented foods early

• Modern fermented foods improve microbial diversity and immunity for as long as they are being regularly consumed

Unproven or speculative:

• That foodborne microbes from fruit led to permanent colonisation

• That fermentation caused human microbiome evolution, rather than simply supporting it

• That tolerance of ethanol directly shaped our digestive tract (it likely helped access to calories, but not all gut changes are tied to it)

It's also important to stay honest about the gaps:

• Direct fossil or microbial evidence from early hominin guts is unavailable. We rely on indirect data: genetics, modern analogues (Hadza, chimps), and inferred diet

• We don’t know if any ingested microbes became permanent colonisers. It’s more likely they were transient but still impactful, even if we don’t know how

• Fermenting fruit is only one of many microbiome-shaping forces. Others include soil exposure, breastmilk, cohabitation with animals, consumption of dairy, and dietry shifts after agriculture

A Timeline: First Ferments and Ancient Kinships

Long before sourdough TikToks and supermarket kombucha, our ancestors were fermenting. Sometimes by design, sometimes by accident, but always guided by flavour, preservation, and transformation. Whilst the earliest examples likely predate the plough or even our taming of fire, the nature of fermented foods means these rudimentary frontrunners likely decomposed without a trace, leaving a gap in our records roughly 1.7 million years wide. However, once practices became more elaborate, involving clay and crocks, records began to show just how long we have been playing with pre-digested foods.

Alcoholic Ferments

Jiahu, China (~7000 BCE): The earliest known fermented beverage, a heady mix of rice, honey, and hawthorn in pottery jars. Sweet, sour, wild, and likely discovered when someone drank the puddle at the bottom of the fruit basket.

Georgia (~6000 BCE): The birth of winemaking. Grape skins, yeasts, clay vessels. A dance we still follow today.

Iran (~5000 BCE): Winemaking jars from Godin Tepe show this wasn’t just about pleasure. It was about preservation, ritual, and survival.

Egypt (~4000 BCE): Beer from barley and emmer wheat, brewed with wild yeasts and bacteria. A liquid bread, sometimes more nutritious than food.

Dairy Ferments

Central Asia and the Near East (~5000–6000 BCE): The age of pastoralism. Milk spoiled fast in warm climates, but yoghurt, kefir, and clabbered milk were safe, storied, sustaining.

Poland (~5500 BCE): Ceramic sieves, likely used for cheese. Imagine curds dripping in woven baskets over smoky fires. The first cheesemakers, perhaps children, licking the ladles.

Vegetable Ferments

East Asia (~3000 BCE): Fermented radish, proto-kimchi. Salt and time as preservation. Essential, especially for long winters and rice-scarce months.

Europe (~500 BCE): Sauerkraut’s early cousins. Cabbage buried in brine jars across Iron Age settlements.

Protein Ferments

Southeast Asia (~2000 BCE): Fish sauce. Ancestor of garum and nam pla. A powerful condiment born from salt, sun, and patience.

Ireland and Scotland (~2000 BCE): Bog butter, wrapped in bark, buried in peat. Possibly fermented, definitely mysterious, and seemingly regularly misplaced.

Did Fermentation Shape Human Digestion?

It might be easy to assume that, because fermented foods have seemingly been a part of our ancestry for so long, they have shaped our evolution in ways we might not fully understand. And here’s where it gets chewy and controversial. Fermented foods clearly helped us digest tough, raw, or perishable ingredients. But did they also change us, biologically?

Let’s start with the clearest case. Milk.

Northern Europeans and the Lactose Puzzle

Most mammals stop digesting lactose after weaning. This includes most humans. But somewhere in Northern Europe, around 5,000 to 7,000 years ago, a genetic mutation spread that allowed adults to keep producing lactase, the enzyme that breaks down lactose. I’ve seen the argument made that this is due to the region’s relationship with dairy farming and fermented milk products.

But here’s the twist. Fermenting milk into cheese, yoghurt, or kefir reduces its lactose content. In fact, fermented milk products are common in population where lactose intolerence is still high.

So why evolve the ability to drink milk raw?

The prevailing theories:

Calorie Access Hypothesis:
Fermented milk is good. Fresh milk is better if you can digest it; more sugar, hydration, and calcium. In harsh northern climates, that might have meant the difference between surviving winter and not.

Culture Over Genes:
In parts of Africa and Asia, people simply fermented their milk and never evolved the mutation. Culture provided the solution. No genetic changes were needed.

Co-evolution Hypothesis:
Fermentation came first. It bought time. Then, as dairying intensified, evolution followed, selecting for those who could digest it all.

In Conclusion:
The hypothesis goes like this: they were already fermenting milk, reducing the lactose load. This allowed them to begin tolerating dairy. Later, a mutation gave them the ability to digest it fully. So perhaps we could call this an evolutionary nudge? Fermentation made milk safer and less allergenic. That cultural buffer may have paved the way for natural selection to favour genes for full lactose digestion.

Whatever the case, fermented dairy wasn’t just a food. It was a bridge between culture and biology, milk and survival, gut and gene.

What Are We Getting Wrong Now?

Let’s be honest. In modern Western diets, we’ve mostly lost all our true fermented foods. And I can’t help but feel that this has led to a disconnection on both sides of the argument. On the one hand, you have the germaphobes, those who won’t even look at raw cheese and worship the all-important use-by date. On the other, those who think eating raw, living, “fermented” foods will heal every and any ailment. (I say “fermented” because sometimes their idea of fermenting food is to let it partly spoil without safety precautions.)

Neither of these extremes are helpful, reinforced by what’s widely available in most shops:

• Pasteurised cheese

• Vinegar-pickled (but not live) gherkins

• Sterilised, shelf-stable krauts

• A fridge full of preservatives, not probiotics

Meanwhile, we’re also:

• Consuming more sugar and emulsifiers (which disrupt gut flora)

• Eating less fibre (the food your microbes actually need)

• Facing record levels of autoimmune disease, gut disorders, and chronic inflammation

It’s a microbial mass extinction.

But Who’s Still Doing It Right?

Let’s look at cultures where fermentation still plays a starring role.

South Korea
Fermented vegetables (kimchi), fermented soy (doenjang, gochujang), and even fish sauces are part of everyday meals.

South Korea has:

• One of the highest intakes of live fermented food globally

• One of the lowest obesity rates in the developed world

• Strong longevity statistics (average lifespan ~83 years)*

* Although the widespread adoption of the negative sides of a Western diet may change this in years to come.

Japan

Natto, miso, soy sauce, pickled vegetables, and sake are routine.

The traditional Japanese diet is low in fat, rich in umami, and brimming with microbes.

Japan has one of the highest life expectancies in the world.

Rural Eastern Europe and the Caucasus
Raw fermented dairy (kefir), sour rye breads, (lacto) pickled vegetables, kvass.

Lower incidences of inflammatory bowel diseases. High centenarian populations in certain regions.

In Summary

Fermentation hasn’t just flavoured our food. It’s flavoured us. Whilst we might not have managed to provide conclusive evidence of more than a surface-level understanding of what has proven to be a deeply complex, shifting, and ancient relationship, it’s safe to say that microbes (including those we eat) have played a significant role in our lives. They shaped our digestion, opened up new food frontiers, and gave our immune systems something to practise with. It may not have rewritten our DNA overnight, but, as with most practices that last more than 1.7 million years, it certainly wrote footnotes in our biology.

We live in a microbial world. Microorganisms are the dominant lifeform on this planet. Plants co-evolved with microbes, first by piggybacking off them prior to evolving roots of their own, and later via the rhizosphere, a hub of living exchange around almost all plant roots today. And there’s no doubt in my mind that we, and all complex life on Earth, are similar. How it happens is still an incomplete picture, and not all fermented food is created equal. But the history points us in the right direction.

Now, in the sterile age of processed snacks and sugar-slicked yoghurts, we’re losing that connection. We’re feeding ourselves, but not feeding the microbes that feed us. A huge amount of evidence points towards a diet rich in fibre benefiting the microbial ecosystem within us, but if you want to include fermented foods too, here are some ways to do it:

• Add a spoonful of sauerkraut or kimchi to your dinner

• Let your miso soup simmer, not boil

• Seek out raw milk cheese

• Make kefir. Share a SCOBY. Taste your kimchi straight from the crock

• Add a spoonful of natural yoghurt (or two) to your breakfast

And above all, let your food take its time.

Fermentation isn’t just preservation. It’s participation. Let’s not lose the thread.

As always, thank you for joining me on another deep dive into the world of edible microbes. I’ve been meaning to write this newsletter, taking a different approach to the topic of the gut microbiome for a while now, as it’s important to tackle such things from multiple points of view, but I will admit I was spurred into action by the Amazon review. If you’d be so kind, feel free to help me report this reivew as off topic, which it is, as it says nothing about the book.

Thank you again for being here. Please feel free to share your thoughts and ideas down below. I’d love to hear from you, whether you agree or disagree. Let’s keep the conversation open and polite.

I hope you have a wonderful week,
Sam

Share

Footnotes/references:
Dudley, R. (2004). "Ethanol, Fruit Ripening, and the Historical Origins of Human Alcoholism in Primate Frugivory." Integrative and Comparative Biology.
Hicks et al. (2018). "Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania." Science.
Wastyk et al. (2021). "Gut-microbiota-targeted diets modulate human immune status." Cell.
Gerbault et al., 2011, Nature.
Itan et al., 2009, PLoS Computational Biology.
Parvez et al., 2006, Food Research International. Probiotic-rich traditional foods support metabolic and immune health.
Odamaki et al., 2016, Scientific Reports. Traditional Japanese diets support a unique and robust gut microbiome.
Ministry of Health Japan, 2023 (Diet and lifestyle are core to national health strategies).
Park et al., 2014, Journal of Medicinal Food. Kimchi consumption is associated with improved lipid profiles, gut health, and immune markers.