Fermentation: Great for your Micro-biome and Critical for Craft Chocolate

By Spencer Hyman  ·  23rd August 2020  ·  The Science of Chocolate

Many of the world’s greatest foods and drinks involve fermentation – think wine, coffee, beer, yogurt, bread, cheese and, of course, chocolate.  Life would be a lot less fun without the miracles that yeasts and bacteria perform in transforming grapes into wine, hops into beer and cocoa seeds into chocolate.

This week’s blog post aims to explain the importance of fermentation in 1) crafting great chocolate, 2) increasing cocoa farmer incomes and 3) catalysing the Craft Chocolate revolution (which involves a wide range of characters, including the United Nations Office on Drugs and Crime).

We are also pleased to announce a “Craft Chocolate Conversation” with Professor Tim Spector on the 24th September (see below and here for tickets and kits). Tim is Professor of Genetic Epidemiology at King’s College, a craft chocolate aficionado, and one of the driving forces behind one of the Covid-19 apps that actually works (get yours here).  He is also passionate about fermentation and its importance to our gut health.  Below, I’ve listed a few of the topics that we are going to discuss while we also taste some of his favourite Craft Chocolate bars.


Tim Spector trained in rheumatology and epidemiology before moving into genetic epidemiology in 1993 when he founded the UK Twins Registry of 12,000 twins.  And for the last twenty five years he has been researching the importance of the microbiome in explaining human health, well being and behaviour.  It’s not easy to summarise all his findings, but here are some of the topics we plan to discuss :

  • Why two identical twins can eat the same craft chocolate bar (or apple, glass of wine, etc.) but “react” completely differently (hint: it’s your micro-biome)
  • Why everyone is better off eating a greater variety of foods, especially fermented ones, (including Craft Chocolate)
  •  Why you should be extremely dubious about many of the “scientific claims”, “miracle cures”, “new diets”, “nutrition” etc.  surrounding today’s food.  This is the subject of Tim’s latest book – “Spoon Fed” – which is being released on the 27th August (and you can purchase the book, along with the bars we are going to taste with Tim, here).  And there are lots of overlaps with the worlds of mass produced, and Craft, Chocolate


Craft Chocolate is all about coaxing amazing flavours, textures and sensations out of a cocoa bean.  And to do this, you need great cocoa beans. And great cocoa beans are about great genetics and careful fermentation.  Even a “great bean” will be awful if it’s not properly fermented (they don’t just taste “mouldy”, they can also taste of rotten meat).

Quite how humans learnt about cocoa fermentation is lost to history.  But we can surmise that about 5-4000 BC some enterprising inhabitants of what is now modern day Peru and Ecuador realised that whilst the “seeds” of a fresh cocoa pod are incredibly bitter and astringent, if these seeds are left in a pile (or even in the open pod), after a few days they start to develop interesting nutty, fruity and (almost) chocolatey flavours. And then they started to cook, winnow and grind these cocoa beans into a paste which made a filling and nutritious drink.  And that was how we started to drink chocolate.

In the late 19th and early 20th century we started to eat chocolate, and we also realised that chocolate is a great vehicle for other flavours and as an ingredient (think candy bars, chocolate brownies, ice cream, etc.).  Creating mass-produced chocolate is all about achieving consistent taste along with the luscious mouthfeel of chocolate. 

Mass-produced chocolate achieves consistent flavour profiles largely through additives and flavourings.  Mass-produced chocolate is NOT about revelling in the amazing flavours that different bean varietals, different fermentations, different roast profiles and different conches can create (that’s what we do in Craft Chocolate).  Mass-produced chocolate doesn’t worry about the profiles of different beans and fermentations.  It’s more concerned about economies of scale –  beans are bought in “bulk”, fermented in huge batches and blended together with additives and flavourings

In contrast if you want great craft chocolate, you want to celebrate different beans and different fermentations.  This means that once a farmer opens a pod it needs to be fermented “properly”.  And proper fermentation is delicate, complex and requires scale.  It is a multi-stage process that involves yeasts, lactic-acid bacteria, acetic-acid bacteria, ethanols, aerobic spore forming bacteria and more.  All these stages interact, involve high temperatures and need to be managed over a period of 4-9 days and via “turning” or oxygenating beans in “vats” that contain 50-500kg (and up to 2,500kg) of cocoa beans.

Changing any of these conditions (i.e. time, bacteria, turns,  box size etc.) dramatically impact the flavour.  For example Mikkel Friis Holm’s “Double” and “Triple” Turn bars are made from the same beans, from the same harvest, they are roasted and conched in the same way, but one bar has beans that are “turned” twice, the other three times.  Similarly Mucho has two bars made from the same beans which have a radically different flavour as in one (the Lavado) most of the pulp is washed off before fermentation whereas in the other it is left on and a “classic” 5.5 day fermentation in wooden boxes carried out. (See below for details on both bars.)

A key component of the Craft Chocolate revolution is teaching farmers about fermentation and establishing fermentation co-operatives so they could achieve scale.  Most of the world’s cocoa farmers are small holder farmers with 2-5, and sometimes up to 10, hectares.  That means that individually they rarely have the “critical mass”, skills or even the “kit” to perform a proper fermentation.

For example the proliferation of Craft Chocolate bars from Tanzania is thanks to the pioneering work of Brian and Simran with Kokoa Kamili.  Efi and Max of Qantu (Canada) regularly travel down to Efi’s home county of Peru to help teach farmers more about fermentation.  Estella is similarly helping the farmers of Kablon Province in the Philipinnes.  Zoi Papalexandratou has worked with Luisa Abram and local farmers in the remote parts of the Amazon to improve their fermentation. 

This creates a win win for all.  We can now enjoy great craft chocolate bars from these beans, and local cocoa farmers can enjoy a higher income as their properly fermented beans now realise them far higher prices and incomes.  Please see below for these bars

Governments have also seen the benefits of encouraging farmers to grow, and ferment, premium cocoa as an alternative to cocaine. For example in Colombia the United Nations Office on Drugs and Crime (UNODC) has been working for a decade to get farmers to replace cocaine with cocoa, and teaching farmers about fermentation.  Similarly USAID has helped recreate cocoa farming to replace cocaine crops in San Martin, Peru (and that’s partly how Efi of Qantu learnt about fermentation).


In Craft Chocolate, fermentation is critical to create great tasting bars and also to help raise farmers’ incomes (whilst also replacing other less desirable crops).

And as we will discuss with Tim, eating fermented foods (including craft chocolate), is also critical for a healthy gut, microbiome and diet.

We really hope you can join us – and we’re sure that you will enjoy Tim’s great new book that debunks much of the nonsense around many food fads  (see here and below)