Apple wins privacy row, and microbes dictate chocolate taste

Chocophiles listen up! Because UK scientists say they’ve unlocked the secret to the tastiest chocolate. We make chocolate from cacao beans, which are the "seeds" inside cacao pods, which are themselves oblong shaped fruiting bodies, about the same size as an aubergine, that grow on the cacao trees cultivated, chiefly, in West Africa and South America. Previously the industry argued that different calibres and qualities of chocolate stemmed from different tree species or cultivars, and growing conditions. But, Nottingham University's David Gopaulchan argues, this isn't true. Much more significant, he's shown, is the effect of the microbes that colonise and ferment the beans when they are scraped out of their pods, surrounded by a mushy material called mucillage. He can recreate a range of different chocolates, indistinguishable to the refined palates of a panel of professional tasters, just by tweaking the microbes he adds to a batch of beans…

David - Cocoa beans are the raw material for producing chocolate. Depending on where the beans are grown, you can get different flavour profiles. For instance, beans from West Africa are usually very strong in chocolate flavours, while if you source beans from Latin America, they are usually filled with lots of fruity floral notes. It's pretty much like the wine industry. Depending on where it's produced, you could get different flavours. It's the same with the chocolate industry. The question we had was, why?

Chris - If you asked, and you used wine as an example, a wine grower that question, they would talk about terroir. They talk about things coming up from the soil, they talk about the environment the grapes are maturing and ripening in. So what do you think it is then with the cocoa and how have you sought to try and explore that?

David - We first went to Colombia. So depending on the locations, you can get different flavours. So we selected three farms in Colombia to study this phenomenon. We went to these farms to analyse the processing of cocoa. At these locations, the farmers would grow the trees, produce the fruit, harvest the beans and let it ferment. During this fermentation is where the magic happens. So we went about studying this using a range of methods, mainly the DNA sequencing of microbial communities that drive the fermentation process.

Chris - And just to be clear, because in a younger life I used to trade coffee and cocoa on the London Commodity Exchange, I'm one of the few people who's actually seen the raw material, the beans that you're referring to, because they're actually effectively the seeds that come out of the big pods that come off the cocoa-growing trees, aren't they? And those are the bits that we grind - the bean - up to get the raw material that becomes the cocoa solids in the chocolate bar. But around those is all this mushy stuff, and that is the material that you're saying then ferments. You've got various micro-organisms that get on that and ferment it when the beans are drying.

David - Yeah, essentially these beans are covered with a white sweet mucilage. And the farmers will leave the beans for maybe five to seven days. It's where we have micro-organisms that now infect the beans and drive the fermentation. And the fermentation, essentially, with these microbes,  they transform the beans from tasting like cardboard or just plant into something closer to what we would know as chocolate. So the microbes drive this chemical process.

Chris - How did you identify what microbes were doing what in this study then?

David - To do the study, we sequenced the total DNA from the fermentations. We used Oxford Nanopore DNA sequencing, and we analysed samples from day zero all the way to the end of the fermentation, about five to seven days afterwards. We were then able to identify which microbes were present and how much of them were present. And we did this across the three locations. Then we were able to compare the microbes and see which ones differed, by how much, and link this to actual chemical changes in the beans. This allowed us to link microbes to chemical profiles.

Chris - Obviously, the proof is in the eating. The way to test that would be to take what you think is the profile of microbes that goes with a profile of flavour, and apply those microbes to a different starting material and see if you can turn it into the other one. Did you do that?

David - Yeah, so to go about actually testing this hypothesis, we collected microbes, we isolated them, and then we inoculated beans. Then we monitored the changes in these beans, so we let these beans ferment in our lab. What we saw was quite remarkable. We saw similar chemical changes to the beans happening. So a lot of flavour precursor compounds. We were able to measure these volatiles. Ultimately, we had trained taste panels evaluate our lab-fermented beans and compare them to naturally fermented beans. Essentially what they found was, when it was re-fermented in the lab, it was very similar to what we saw in nature. And we were able to replicate this process.

Chris - This argues then that you could take beans from pretty much anywhere, even cheaper ones, and with the right magic from the right microbes, get something that tastes like really high-end chocolate. I can see that having both pros and cons though, because the industry purists are going to say that's removing some of the magic. On the other hand, the mass manufacturers are going to say, well, that's brilliant, we'll have a much higher-quality product and we can keep our cost base low.

David - I think at the very least, what we've shown in this study is that there is a lot of potential, and also it can be very disruptive to the industry. It's true, you can potentially take any variety, but having the right combination of microbes creates flavour profiles. For instance, if you want to produce a very high quality, with all these auxiliary notes in your beans, you just need the right combination of microbes to do this.

The question of when our ancestors first began to use tools is an important one: it steers our view of how our brains were developing and the relationships our ancestors had with the environment and various potential food sources. And what Emma Finestone, Associate Curator at the Cleveland Museum of Natural History, has found in Kenya suggests that tool use was very much embedded in our behaviour by as early as 3 million years; she's shown that early hominins weren't just picking up and using handy bits of stone laying nearby - they were venturing for tens of kilometres to find the right sorts of stones to bring home and turn into tools, arguing that they very much knew what they were doing…

Emma - One big question is how did tool use begin and how important was it to the earliest tool users and tool makers? When we think about humans today, we're really dependent on our tool technology to solve adaptive problems and to access different food items. It's part of our life that we are really tied to. Everyone on earth uses tools. And the question when we think of 3 million years ago, 2.6 million years ago, is how important was tool use to those early tool makers and how were they making and using tools and integrating it into their daily lives and their movements across the landscape?

Chris - And what have we got to go on so far? When you look at the fossils we have and the remains we have and the things we've found, what sort of picture emerges before you come along with this current piece of research?

Emma - The earliest period of tool use, we know relatively little about because there are only a handful of archaeological sites that are older than 2 million years ago. What we do know is that hominins, which is a word that includes anyone in our family tree, were making and using tools and accessing food items. But what we don't know is how big this investment was and how far they were ranging for food resources and for tool resources. Non-human primates are known to use stone tools and can accidentally produce flakes that look like the same ones we find in the archaeological assemblage unintentionally, but they do it through a very opportunistic process where they have a food item and then they have stones that are available locally and they're just breaking apart a food item to access that food. The big question is in the earliest archaeological record, when we're talking about older than 2 million years ago, were hominins accessing food items in a similar way to non-human primates - where they're just cracking open a nut or maybe cutting something with an available stone nearby - or were they doing something more? Were they foraging for stones across the landscape and bringing them to places to process food?

Chris - Is that the key then? Is that what you've built your story around? The fact that if you've got evidence that someone is going and getting particular bits of stone because they make good tools, that's evidence that this must have been common practice at the time at which those individuals were active.

Emma - It's evidence that they were investing in tool behaviour because travelling a distance of several kilometres or 10 kilometres or more to get a specific type of rock, that takes a long time out of your day and that shows that that's really integrated into your foraging strategy if you're travelling to get stones, which in and of themselves have no caloric value to tool makers or to humans and their ancestors. So travelling to get stones shows that this is a behaviour that they're investing in and it's part of their foraging strategy from the onset of tool technology. And it also shows that they've already incorporated stone tools into their landscape patterns in their mental maps, which is a step beyond what we see in non-human primates. So it's an indicator of having mental maps and cognition to incorporate stone resources into their foraging routine and also an indicator that these hominins are foraging for stones as part of their foraging strategy, not just as an opportunistic one-off way to access a food item that they couldn't otherwise access.

Chris - And you've got evidence that this was happening.

Emma - Yeah, so at the site Nyanga, it's in Western Kenya and we've been working there since 2014. We have a stone tool assemblage between 2.6 and 3 million years old that has been made using both local but also non-local stone materials. We did a landscape-scale study where we were looking at which different materials are available throughout the landscape and which sources the hominins were accessing. And what we found is that the hominins were accessing not just local sources of stone, but they were accessing sources of stone that were 10 to 13 kilometres away from the Nyanga site, bringing them to the site and then processing food there using the stones that they obtained from further distances.

Chris - And you're comfortable that those stones didn't arrive where the hominins were by accident, that you're saying they brought them there and in fact, the environment somehow didn't. You're comfortable that this is active recovery of those stone pieces?

Emma - Yes, and how we know that, we first do analysis of where stones are available on the landscape from ancient riverbeds and from transport through rivers from primary sources to outcrops and riverbeds, which is where hominins are accessing the stone. So we surveyed ancient riverbeds to check what stones are available in which places. And then we also did a type of analysis that looks at the geochemistry, which is the trace elements of things in the rock that can link them to the sources on the landscape to check which sources are most similar to the artefacts that we have in the assemblage. And all of those indicators suggest that these stones were not locally available and that hominins travelled to get these stones and sometimes transported them directly to the site and flaked them on location.

Chris - So what's the take-home then? If you had to sort of write the newspaper headline, how would you sell this to a classroom full of eager palaeoanthropologists of the future?

Emma - I would sell it as stone tool behaviour was integrated into the daily life patterns of hominins 2.6 million years ago. We are a technologically dependent species. We rely on tool technology to survive and to access food. And it's likely that that has been happening for millions of years. Travelling that distance to obtain stone resources and foraging for stones with the same effort that hominins were foraging for food resources shows that this reliance on tool technology to survive, adapt, and to access different foods is what started off 2.6 million years ago and has continued today into being a key component of what makes us human.