New & Noteworthy
Chocolate and Coffee Too?
April 20, 2016
A cornucopia of gifts from our friend, yeast. Wine image from Wikimedia Commons, coffee & chocolate from pixabay.com, bread from pexels.com.
Most of us know about yeast’s big part in making bread and booze. But those aren’t yeast’s only wonderful gifts. It also plays a big role in chocolate and coffee too. Is there anything this marvelous microorganism can’t do?
A new study by Ludlow and coworkers in Current Biology set out to look at the strains involved in cacao and coffee fermentation. Unlike the extensively studied wine strains, these have mostly been ignored up until now.
These researchers found that cacao, coffee and wine strains were very much different from one another. And they also found that unlike wine yeasts, which are pretty much the same most everywhere in the world, coffee and cacao strains are different depending on where they come from.
But the cacao and coffee strains did have one thing in common. Each had a lot in common with the other strains in its country and even on its continent.
So, for example, coffee strains from all over South America are very similar to each other but different from the coffee strains from Africa. And the opposite is true as well. African coffee strains are all pretty similar to each other but different from the South American strains. The same sort of thing is true for cacao strains as well.
You can think of coffee and cacao strains as the large, flightless birds of the yeast universe. Like a rhea, emu, or ostrich, they stay on their own continent. Wine yeasts are more like those chickens that are basically the same worldwide because humans have taken them along with them in their migrations.
The first step in their analysis was for Ludlow and coworkers was to get a hold of a bunch of different samples of cacao and coffee yeast strains from all over the world. They managed to get 78 cacao strains from 13 different countries and 67 coffee strains from 14 countries. The countries were from Central and South America, Africa, Indonesia and the Middle East.
The next step was to compare the genomes of these strains with each other and with the wine strains. They decided to use a technique called restriction site-associated DNA sequencing, or RAD-seq, that would give them an in depth look at around 3% of the yeast genome. As there was already a database with 35 wine strains that used the same method, Ludlow and coworkers only needed to generate data for their newly isolated strains.
These data revealed that coffee and cacao yeast strains were very different from one another. It also showed that the closer two coffee or cacao strains were to each other geographically, the closer they were together genetically. Using just these strains they could accurately predict the country of origin for a coffee yeast strain 79% of the time and 86% of the time for those associated with cacao.
The researchers next expanded the number of species they compared by using two additional databases. One included RAD-seq data from 262 strains from a wide variety of different places while the other contained another 57 strains.
This analysis generated 12 distinct groups of yeast, many of which had been identified before. Their new strains formed four new groups which they called South America Cacao, Africa Cacao, South America Coffee and Africa Coffee.
By comparing the four groups to the eight older ones, they were able to see that the new groups were not novel but instead were made up of mixtures of some of the other known groups. And who they shared alleles with depended on where the yeast strain was located. So, for example, the two South America groups shared alleles with the North American Oak group while the two African groups shared alleles with the Asian and European groups.
Make some room, Dog, good ol’ Saccharomyces cerevisiae is joining you as man’s best friend. Image from elsie on flickr.
It looks like that, unlike with wine where there are a limited set of best yeast strains that most people use, the yeast strains involved with making chocolate and coffee are continent and even country specific. This suggests that people either took their wine yeast with them when they moved or that cross contamination throughout the world resulted in homogenization of wine yeasts. Sort of like the chickens Pacific Islanders brought with them whenever they settled on a new island.
It is a very different story for cacao and coffee yeast strains. While there was cross contamination within countries and even continents, there was no worldwide contamination. The rhea stayed in South America and the ostrich in Africa.
Wherever these strains come from, they work hard to make our chocolate, coffee, bread, wine, and beer. What an amazing bounty! Make some room, Dog, good ol’ Saccharomyces cerevisiae is joining you as man’s best friend.
by Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
Categories: Research Spotlight
Tags: admixture , migration , population diversity