The Fresh Loaf

News & Information for Amateur Bakers and Artisan Bread Enthusiasts

Are you following the Sourdough project?

_vk's picture
_vk

Are you following the Sourdough project?

Hello friends. 

I've seen here a post about the the project. I even tried to send some of my starter, but missed the date.

I'm now receiving, via email updates from the project. I think you all gonna like it.

Anyone can sign for updates at their site.

http://robdunnlab.com/projects/sourdough/

here are the first two updates I received:

1-

Recently, we asked you to share your sourdough starters and stories and you did. You shared them not just from the United States, but also from around the world. More than five hundred starters poured into the first lab in their journey, Ben Wolfe's lab at Tufts, where they were tended to by graduate student Liz Landis, Kinsey Drake and Shravya Sakunala (the undergrads who did a lot of the processing).  At Tufts, the sourdough starters were curated. Liz opened them. She sniffed them. She unwrapped them. She fell in love with their diversity and she chose a handful, thirty or so, on which she would do more research. From those starters, Liz grew the bacteria and fungi that would grow. Liz will then study this subset of bacteria and fungi in much more detail. They will be her long-term quarry and she will report back about them, episodically, over the next three years.  The sourdough starters then traveled in Raleigh, where they were further curated by Erin McKenney, and then on to the University of Colorado. At Colorado Jessica Henley (in the lab of Noah Fierer) has set about identifying the bacteria and fungi present in each sourdough. The bacteria will be first. Jessica will then share those data with Erin who will carry out the next steps. When Erin gets the data from Jessica they will include the list of bacteria (initially) and fungi (later) identifiable from each starter. This list is likely to be longer than the list of microbes that Liz cultivated from the starters; we suspect (though don't know) that some of the microbes present in starters are not readily culturable. Maybe not. We'll know soon.  Once Erin has the data, a cascade of next steps will follow. Those next steps will take years. My suspicion is that in ten years we are still resolving new mysteries from the sourdough starters you have shared, maybe in twenty years. But the first step won't take so long. The first step is that working with Neil McCoy (a design specialist) and Lauren Nichols will make a map on which you can click on your own sourdough sample number and see, from that sourdough sample, which species were present in it. You will also be able to click on other peoples' (anonymized) sample numbers and see what is present in those starters as well.  Another next step that is already ongoing is that Erin will be working with her colleagues at the North Carolina Museum of Natural Sciences to begin to use the data from these sourdoughs to develop lesson plans that allow teachers around the world to study sourdough in their classes and, in doing so, to help contribute to new science. If you would like to help with the effort to get this science into the classroom, let us know. None of this work is possible without all of you and, as you can see, without the many many of us too.  That is all for now. More soon. I suspect you are anxious to know (soon) which bacteria were in your starter. I can promise we are more anxious and excited. We are like children who have fallen into a dark cave filled with paintings. We can't see much yet, but soon there will be light.  Best,

 

 

 

2-

Hey Everyone! We have good news. From the 568 sourdough samples our participants sent us we have completed the first (of many stages) of identification of the bacteria present in the sourdough. Most sourdough starters contain both bacteria and fungi. The fungi produce carbon dioxide, the bacteria the acid (usually, we actually think that some of the fungi in sourdoughs are producing acid too). We haven’t identified the fungi yet. Soon though.As for the bacteria, when we first looked at the results, we were in for several surprises. Though it took some steps to get there. The first thing we see is a file that contains the individual decoded DNA of the organisms present in the sourdough. Not the entirety of their DNA, but instead one gene that happens to be particularly good at telling us about the microbe. Think of that gene as the title of the microbe’s book. You can’t judge a book by its cover or title, but it is a good starting point for categorization. But there are too many individual decoded pieces of DNA for us to read  and organize on our own. We use computer algorithms (or rather, Angela… did) to sort the bacteria into something akin to species (what microbiologists call “OTUs,” or operational taxonomic units. Way to go microbiologists in making something marvelous, the names of life forms, boring. Just to make discussion a little easier I’ll refer to the OTUs as species from here on out but know that they are a little bit different from species). Once the computer algorithm lumps all of the different decoded sequences into their OTUs (akin to stacking books with the same name together), we get a sense both of how many kinds of microbes we found and in which samples we found them.
 
 Lauren Nichols
The answer? How many kinds of bacteria are in sourdough? Probably you want to know. But first let me give you some context.The Diverse World HypothesisOn the one hand, the study of microbes around the world has shown us that nearly every habitat that is studied is astonishingly diverse. In part this simply reflects the reality that one can pack so many individual microbes into what seems like a tight space. There are, for example, more individual bacteria in your colon than there are individual trees on Earth (one hundred times more!). As a result, a tiny sample of microbes can contain many resources, habitats, individuals and hence species. In tiny clump of soil one can find ten thousand species. In a sample of feces, thousands of species. In a swab of microbes from a belly button, hundreds of species. On the basis of these results, one might expect many, many, species in sourdough starters and also expect sourdough starters from different regions of the world to be very different. As one travels the world searching for sourdough starters, one encounters, we assumed, different bacteria in each and every place and so as one collects (we assumed) ever more species with ever more samples. One might never collect all of the sourdough microbes. The world is big, especially to a bacterium.The Simple Fermentation HypothesisBut we also had reason to believe the exact opposite.  The many hundreds of studies of sourdoughs have tended to culture just a small handful of bacteria and often a single (or no) fungus species. This is what is typically found in sourdoughs when one cultures (grows) the microbes from those sourdoughs on petri dishes as isolated single species all on their own. When we talked to our friends in the baking industry, this is what most expected. Each individual starter, they hypothesized, would tend to have a couple of bacteria species and most often a fungus. But sampling, they hypothesized, more sourdough starters would reveal different species because although each starter might have few species, collectively there might be many.What did we find? Wait one more second. Let me spell out the expectations a little more clearly in terms of the units that biologists like to use. We talk about alpha diversity (the number of species found in a sample) and gamma diversity (the number of species found when all of the samples are considered together). We talk about these measures of diversity when thinking about birds or fish and we can talk about them with sourdough. The diverse world hypothesissuggests that the alpha diversity present in any particular sourdough should be high and that the gamma diversity of all sourdoughs should also be high. And if one were to plot the diversity of sourdoughs against the number of samples it should continue to increase as more samples are taken. This is what soil samples look like. High alpha diversity, high and ever increasing gamma diversity. The simple fermentation hypothesis, on the other hand, predicts a low alpha diversity but agrees with the diverse world hypothesis in predicting a high gamma diversity (high and ever increasing).So what do we find already?So far, our results present the most interesting possible scenario. They don’t fit with either of our hypotheses. The alpha diversity of samples is high, which fits with the diverse world hypothesis. The average sourdough had tens (and often many tens) of species, dominated by species of Lactobacillus and their relatives. You can see this in the figure below. Some of these species we know a lot about. Among the most common species were Lactobacillus plantarumLactobacillus brevisLactobacillus paralimentariusand three other species of the Lactobacillaceae. Together these bacteria accounted for a large part of the microbial abundance we encountered. But, they were almost always accompanied by many other species, each of which we anticipate contributes something, be it conspicuous or subtle, to the abilities of the individual sourdough starter.But when we look across the starters, the results no longer match the diverse world hypothesis. I should note that the sourdough samples we considered came from all around the world. They were made using different ingredients, in regions with many different climates (from Alaska to Australia with many samples in between) While the alpha diversity of sourdoughs was high, the gamma diversity was lower than we expected. Far lower. Overall, we found around three hundred species of bacteria in the sourdoughs, which superficially seems like a lot. But it is almost a hundred times fewer species of bacteria than would be found in a thimble full of soil. It is fewer kinds of bacteria than live in some belly buttons. More to the point, some individual starters had nearly one hundred species of bacteria in them, which is to say nearly a third of what we have encountered in sampling the starters of the world. In other words, high alpha diversity, relatively low gamma diversity and very low beta diversity (a new term, beta diversity is a measure of how much the species present in one sample differ from those in the next. Finally, if we look at the curve below what we see is that as we add more and more samples that we may have actually reached what a kind of plateau (we call it an asymptote). Adding more samples does not seem to yield more kinds of sourdough bacteria.There are many caveats to what we have figured out so far. We expect to be building on the insights of this first analysis for a decade, or more. But we thought you would like to be in on the ground floor, to see and think about what we are seeing now even as we continue to explore.The biggest caveat is that we have so far only looked at bacteria, not fungi. The fungal data will be forthcoming (thank you Angela and Jessica!). What do we expect for the fungi? Now we have three hypotheses for the fungi, either the simple fermentation hypothesis and diverse world hypothesis might still hold for the fungi. Or the fungi might be like the bacteria, a pattern that doesn’t yet have a name (high alpha, low gamma). One thing we do know is that in our other studies, particularly those of homes, that while the bacteria in one site tend to be similar to those in another (and influenced more by human behaviors than by climate or geography), that the fungi show the opposite pattern. The fungi present in any particular house seem to be most influenced by climate, by soil type, and by region. Might the same be true for starters? We’ll know soon.In the meantime, keep sending us your ideas, notes, stories and photos about your sourdough starters and bread (even if we haven’t sampled your starter). We love them. We can’t always respond quickly to every email, but we always read them. And, if you did send in your starter (and if we were able to identity its microbes) we will soon be sharing with you, on a map, the list of the species of bacteria we found in the starter. Some starters were shy and wouldn’t share their secrets but most did. We would like to share those species lists with the name of your starter and its story (but without your name). If you would prefer to not have your starter’s story shared, please let us know.Warmly,Rob Dunn and The Sourdough Project teamPS: If you would like to join the Facebook Group for participants with more sourdough updates, join here: https://www.facebook.com/groups/SourdoughProject/

 

 

jimbtv's picture
jimbtv

High alpha... low gamma. Who-da thought!

 

leslieruf's picture
leslieruf

so yep, agree with jimbtv Who-da-thought!  I had to read the article several times but we will see what science tells us over time and keep on baking.  :)

Leslie

jimbtv's picture
jimbtv

Nice work, leslieruf! By the time I found out about the study they were no longer accepting samples.

This is actually a pretty fascinating study and a lot of effort has be put into it. Thus far the score is lacto - strong, others - present but not as strong. I think most of us kinda knew that already but I wasn't aware that up to 300+ "species" were swimming around in there too.

Now I guess the study is going to break down the yeast counts and I think that too will be interesting.

-vk, thanks for putting this on the forum!

 

Jim

leslieruf's picture
leslieruf

and I thought " why not". My starter obviously travelled across the Pacific and USA ok and was still alive when it arrived.  

I am looking forward to hearing what Rob Dunn lab tells us in the future.

Leslie

_vk's picture
_vk

This crazy baking business leading us to understand such terms as high alpha low gama.

I kind of got happy to know there is not so much of the wee beats around... Well, so far...

glad to share 

@leslieruf that is so cool that you got your starter into the project!! Have you checked if it is on the map?

:)

happy baking

leslieruf's picture
leslieruf

one of the 3 shown in NZ.  it is fascinating  and I wonder too what the next update will tell us.

Leslie

_vk's picture
_vk

Bay of Plenty. What a name! : )

 

3 in NZ

 

phaz's picture
phaz

and 4 in my small state of Vermont. 1 about 20 miles from me. Wish I had seen this sooner, would have loved to see the differences between 2 starters relatively close to each other. Oh well

leslieruf's picture
leslieruf

The greater bay was named Bay of Plenty by explorer James Cook, self explanatory judging by history.  And it is a relatively mild climate with no snow, no extremes of climate and most things grow very well here. In fact when we came here 20 years ago, we couldn't believe how much better things grew. 

Its a great place to live, we are only 15 minutes from our favourite surf beach too!

Leslie