Interesting genome sequencing of some yeasts

[sykesey]

So i've been finding more evidence that WLP800 is s.cerevisiae from some genome sequence reads, and in my travels I found this, the submission date is Feb/19 but the genome reads were uploaded at the end of August.

Here's the link to the study from Langdon et al which appears to have been run for a paper investigating the lineage of eubayanus hybrids, i.e. modern lager yeast

https://www.biorxiv.org/content/10.1101/709535v1.article-info

The data is in here:
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA522928

And more interesting is the table of data
https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP219635
(sort by sample name descending to see the WLP/WY strains)

I am not sure of the methodology used to determine the genotypes of the yeast, but if the organism taxonomy is to believed and these are the right strains analysed then some interesting findings...

WLP029 Kolsch could be Pastorianus not ale
WLP515 could be Pastorianus
WLP838 S.German Lager could be Cerevisiae
WY1187 Ringwood could be pastorianus
WLP800 probably confirmed further to be cerevisiae
WLP351 could be a cerevisiae x eubayanus x uvarum hybrid

I emailed the author last night as well as Mr Suregork so will see if anyone more qualified in genomics than I am has some insight...

Not sure if it changes much, I guess with WLP051 Cal V turning out to be Pastorianus and lots of "lager" breweries turning out to actually be using "ale" yeasts it's not surprising

 

[Vale71]

Be advised that the identifications are only unqualified guesswork. The original papers only identify the strains using anonimous numbers, so what the author of the taxonomy calls "WLP800" could very well be anything else.
IMHO short of doing your own sequencing to see if BE97 is really WLP800 instead of something else you're better off disregarding this before giving birth to some more homebrew myths.

 

[suregork]

Thanks sykesey for sharing! Very interesting stuff! The organism/hybrid designations are based on whole-genome sequence data and should be accurate. This is from one of the top yeast genomics labs in the world, so they know what they are doing.

Vale71, this is a completely separate study to the Gallone 2016 one. Here they've sequenced a large number of White Labs and Wyeast strains, and the strains are refered to with their original names. So no decoding or guesswork involved. WLP800 and WLP838 definitely seem to be ale yeasts, while WLP029, WLP051 and WLP515 are lager yeasts

 

[Vale71]

Vale71, this is a completely separate study to the Gallone 2016 one. Here they've sequenced a large number of White Labs and Wyeast strains, and the strains are refered to with their original names. So no decoding or guesswork involved. WLP800 and WLP838 definitely seem to be ale yeasts, while WLP029, WLP051 and WLP515 are lager yeasts

Sorry, I missed that.

The results are really surprising, to say the least.

 

[Northern_Brewer]

Be advised that the identifications are only unqualified guesswork. The original papers only identify the strains using anonimous numbers, so what the author of the taxonomy calls "WLP800" could very well be anything else.

You're referring to Suregork et al's original attempts to identify strains in the Gallone/White-Labs paper. For one thing - they were very clear about their confidence levels, some were confirmed by known sequences from other sources, some just fitted the pattern (US-UK-German etc just looked too much like WLP001/2/3 to be a coincidence when the US one was known to be 001), and they were clear that there were a few that just didn't fit. And White Labs confirmed many of them in updates to their own catalogue, only a few of the original guesses - all of them "we're doubtful" ones - were wrong. And then we've had other labs sequence genomes that haven't had a commercial interest in secrecy, so it's only been odd ones like WLP515 that we haven't been sure about.

It will be interesting to drill down to the detail - WL029 and Wyeast 1187 have previously been placed on the main ale family tree, it could be something like a small chunk of eubayanus DNA rather than a "full" lager hybrid. Kinda cute that WLP838 Southern German Lager is an ale yeast like WLP800, which would make sense in terms of the history, hopefully it will prove to be a kolsch yeast.

Also hopefully 1272 will prove to be a BRY-97 relative, and LondonESB close to Windsor as suggested by @isomerization 's PCRs.

Also notable that the "Chimay" group of Abbaye, WLP500 Monastery and 1214 Belgian Abbey are a kudriavzevii hybrid, which is usually found in wine yeasts. You can imagine monks buying some wine barrels and then either filling them with beer or using the lees for brewing.

 

[lump42]

How do any of these recent studies affect the practical aspects of these strains? Or is this all purely academic at this point?

 

[Vale71]

You're referring to Suregork et al's original attempts to identify strains in the Gallone/White-Labs paper.

Yeah, we cleared that up a couple of posts ago.
Seems that this new study has confirmed that at least two lager strains do not have any eubayanus DNA and therefore do not originate from the same hybridization event. This will certainly offer opportunities for further reasearch as clearly there must be more than one single point of origin for lager yeasts. I think will all agree that these yeasts do not exhibit typical ale behaviour (I wonder if they pass the melibiose test?) and there must be a reason for that.

 

[lump42]

Yeah, we cleared that up a couple of posts ago.
Seems that this new study has confirmed that at least two lager strains do not have any eubayanus DNA and therefore do not originate from the same hybridization event. This will certainly offer opportunities for further reasearch as clearly there must be more than one single point of origin for lager yeasts. I think will all agree that these yeasts do not exhibit typical ale behaviour (I wonder if they pass the melibiose test?) and there must be a reason for that.

I would expect them to consume melibiose. That was one the phenotypic tests to separate the species before genomics.

 

[Vale71]

Then why weren't they considered ale yeast if they passed the test?

 

[Vale71]

According to this what is thought to be WLP800 in the Gallone study does not metabolize melibiose. Curiouser and curiouser...

 

[lump42]

According to this what is thought to be WLP800 in the Gallone study does not metabolize melibiose. Curiouser and curiouser...

Now that I think about it more, it may have been maltitriose was distinguishing factors.

 

[Vale71]

No, it was indeed melibiose. Inability of any strain not to ferment maltotriose has never been proven.

 

[Northern_Brewer]

This will certainly offer opportunities for further reasearch as clearly there must be more than one single point of origin for lager yeasts. I think will all agree that these yeasts do not exhibit typical ale behaviour (I wonder if they pass the melibiose test?) and there must be a reason for that.

Depends what you mean by a "lager yeast". Talking about a point of origin implies you're talking about them in the genetic sense, and for geneticists a lager yeast used to be the informal name for S.pastorianus and now would be for any cerevisiae x eubayanus cross.

For a biochemist, it would be a brewing yeast that can produce alpha galactosidase and so can eat melibiose, a microbiologist would define it as one that can't grow at 37C. In commercial brewing, it's any yeast used to make beer that's sold as lager, and in homebrew it's any yeast isolated from a beer sold as lager, regardless of whether it was actually used to ferment it.

If the Gallone et al survey told us anything, it's that all kinds of yeast -even saison relatives - get used to make beer that is sold as lager. But it's not particularly helpful to say that all such yeasts are "lager yeast". And we know that when humans try to classify things into nice neat boxes, biology usually finds a way to make things messy.

For instance, if I told you without showing you pictures of a mammal weighing around 300lb that spends most of its life squatting on its haunches eating plants, then you'd probably think, based on its diet and behaviour, that it belonged to the primates, it was some kind of gorilla or something. But if I showed you a picture of a panda, you'd recognise it immediately as a bear. Even though they are members of the order Carnivora and are not designed for eating plants, there's still one of them that just eats bamboo.

There's a lot of pandas in the world of yeast.

They haven't heard of the rules and so instead of fitting into nice tight boxes, they bend the rules in various ways, the boundaries are much fuzzier than traditionally thought. So if Frohbergs like 34/70 are OK fermenting warm, or ale yeasts are happy at "lager" temperatures, then that's OK, biology is like that.

 

[dmtaylor]

Depends what you mean by a "lager yeast".

It may be time to outlaw now-meaningless terms such "lager" vs. "ale" vs. "bottom-fermenting" and "top-fermenting", and just refer to each strain by its commercial name only. That's best and easiest. Otherwise the only correct general terms now are species S. pastorianus and S. cerevisiae (as well as of course all those other pesky ones like S. eubayanus, Brettanomyces abcdefg, etc.).

I'm gonna go have a beer. It's all beer. I think I'll have some of the S. pastorianus kind tonight. Cheers all.

 

[Robert65]

I'm gonna go have a beer. It's all beer. I think I'll have some of the S. pastorianus kind tonight. Cheers all.

I think I'll have one that is bright, golden, and, when served rather cold, is crisp and bracingly refreshing, redolent of Saaz hops, underpinned by clean, sweet malt, and with only the faintest fruitiness and perhaps a hint of diacetyl. I won't even ask what yeast was used or other details of how it was produced (though you all can probably guess.) I've already described everything that affects my choice. Cheers!

 

[sykesey]

Hey everyone, sorry I was stuck in HBT post limbo for the past day as i had a new account and could only post 5 in 24 hours.

The owner of the data (Quinn Langdon) got back to me and the genome sequences aren't from the paper I linked but an upcoming paper about hybridisation of commonly used yeast strains. Not sure when it comes out for pre-release / peer-review, but soon. I quote

"Hybrids were identified using the whole genome data and a pipeline called sppIDer (https://www.ncbi.nlm.nih.gov/pubmed/30184140). The paper that goes with this data should be coming out soon and, indeed, there are some hidden surprises of some strains that are sold as one thing but are actually hybrids"

I was able to run some BLAST queries using a couple of Eubayanus primers (thanks to Suregork's papers with the details) against the genome reads and verify that WLP029 at least had some Eubayanus DNA. How much of the DNA they have is something I hope the paper goes into, as well as hopefully Suregork running an updated family tree with this new data.

The WLP838 / 800 connection for me is definitely interesting (maybe 838 is the missing link to where 800 came from originally via Groll's trip from Bavaria to Pilsen). I just did a split wort test between Kolsch yeasts (Lalbrew dry, WLP029, and GY021) so it might be worth running the same again with WLP838 and WLP800 and see how they go in that style. I'll probably write the initial experiment up when i get a chance to set up my blog again.

In terms of what this means, yeah it can be academic but there may be some practical applications. WLP838 and WLP800 may end up being just fine to use at ale/hybrid temps and market the resulting beer as Ale! Anything brewed with Ringwood you could potentially call a Lager (not the German sense unless you cold condition but because you're using a pastorianus strain)... Also with the genome data there's yet another chance to add to an updated family tree and maybe link back to some of the Gallone yeast identification.

But end of the day, if they make beer that tastes good and is in the right style, doesn't really matter that much

 

[Vale71]

For a biochemist, it would be a brewing yeast that can produce alpha galactosidase and so can eat melibiose...

I'll take that one, only the other way around as it's actually bottom-fermenting that can't eat melibiose.
What I mean is, there are obviously macroscopic differences between the two groups, however you define them. It would be certainly interesting, if only from an academic standpoint, to understand how those differences came about from a genetic standpoint.

 

[mediant]

For many years, the inability to metabolise galactose and melibiose (Gal− Mel−) was used to characterise the hybrid S. uvarum/S. eubayanus and to differentiate it from three other Saccharomyces species known at the time, S. cerevisiae, S. paradoxus and S. uvarum. Later, S. uvarum was merged with S. bayanus in spite of their phenotypic divergence (Vaughan-Martini and Kurtzman 1985).
[...]
Taken together, our results show that the absence of galactose and melibiose utilisation is a mutable character and is not informative for the characterisation of species of Saccharomyces. It should thus no longer be used in classifying yeasts to a given species.

 

[sykesey]

So I have managed to get the sppIDer program set up with the genome base data and ran some of the sequence reads through it, managed to get a couple of results, not that it means that much as they've already been classified. But for instance here's the plot of how much of the sequence reads maps to the various genome types - Scer = cerevisiae, Seub = eubayanus, Suva = Uvarum. This is for WLP838 - tells us it's mainly cerevisiae. I haven't managed to run the full thing yet but the graph it creates at the start gives a good idea of the classification.

I was reading more about WLP838 and everyone says its a bit weird, forms a krausen, works OK at higher temps, throws out a lot of sulfur at lower temps... would be really interested to see where it fits in the family tree

And here's WLP029... pink is eubayanus

 

[Northern_Brewer]

I'll take that one, only the other way around as it's actually bottom-fermenting that can't eat melibiose.

I think you might want to check that...

Oh, and bottom/top fermenting is another of those panda classifications. Although skimming open fermenters selected strongly for ale strains that float, the move to conicals selected for ale strains that sink, so a lot of ale strains look like bottom fermenters these days, it seems to be a pretty mutable characteristic that is strongly selected for depending on fermenter type.

What I mean is, there are obviously macroscopic differences between the two groups, however you define them. It would be certainly interesting, if only from an academic standpoint, to understand how those differences came about from a genetic standpoint.

My point is that just trying to define a group is fraught with problems, the boundaries are just too fuzzy. But things like melibiose metabolism are well understood - indeed that paper linked to by mediant goes into some detail.

The genomics of yeast get pretty complicated, as the selection pressure of a brewing environment has caused a lot of large-scale duplications in genomes, as well as them fairly freely swapping bits of genome with other species.

How do any of these recent studies affect the practical aspects of these strains? Or is this all purely academic at this point?

Number 1 - it's just really interesting, and can also illuminate some of the history of how yeast got swapped around etc.

Number 2 - you have to be a bit wary of relationships - nobody is more closely related to you than your parents, but one of them has very different lumps and bumps to you! But at the same time thee family trees can help see things that aren't immediately obvious - for instance T-58 looks like a POF+ version of S-33/Windsor, the small POF gene cassette produces a very obvious change in flavour, but otherwise they behave pretty similarly in terms of temperature, ester profile etc.

But yes, these insights have encouraged people to try a few things that they wouldn't have otherwise, particularly over on the warm-fermented lager thread where in the last 18 months WLP800 has become one of the favourites for such beers as a direct result of this kind of work. Also I've been doing a bit of work on relatives of T-58 for biotransformation.

Although I suspect a lot of the people who might otherwise have done such experiments are all too busy playing with kveik at the moment...

 

[Northern_Brewer]

So I have managed to get the sppIDer program set up with the genome base data and ran some of the sequence reads through it, managed to get a couple of results, not that it means that much as they've already been classified.

Good stuff. It does mean something, as there was a question mark whether the fact that eg WLP029 had been placed by White Labs on their main cerevisiae family tree meant that this new data was just picking up a small exchange of eubayanus DNA, but this looks like a full-blown hybrid. So a kolsch yeast is actually a lager yeast! I'd love to know what Gallone/White Labs sequenced though - are we looking at a mixed culture, did they just sequence the cerevisiae part of the genome, or what?

I guess exactly the same could be said of 1187 if you've got time to do it? WLP515 would also be interesting.

I've also always been curious about the Mixed group in Gallone, they've always been a bit vague about genome structure there and I've not seen any detail elsewhere. Does eg Windsor have any signs of foreign DNA?

The other useful thing you can presumably do with sppIDer would be to distinguish low-temperature Saaz lager strains from high temperature Frohberg strains. Something like WLP850 Copenhagen should be Saaz (2/3 eubayanus, 1/3 cerevisiae) and WLP830 German should be Frohberg (1:1 eubayanus:cerevisiae). If you can distinguish those then it would be interesting to see what the other lager strains show up as.

 

[Northern_Brewer]

the only correct general terms now are species S. pastorianus and S. cerevisiae

But what about S. carlsbergensis?

Personally I think there was a pretty good case for calling Saaz carlsbergensis and Frohberg pastorianus, but now that people like Suregork are making new cerevisiae/eubayanus hybrids, I suspect it's easier to just lump them all into pastorianus to stop our heads hurting.

 

[suregork]

I've downloaded all the data for all the WLP, Wyeast, Fermentis and Lallemand strains and have them running through my pipeline. Creating a list of Saaz and Frohberg lager strains is on my list of things to do (should be ready tomorrow). An updated family tree should be ready during the weekend maybe? I'm a bit hesitant to release too much of the results though, as apparently this data is from an unreleased paper. I don't want to step on their toes and steal their thunder

 

[Miraculix]

I've downloaded all the data for all the WLP, Wyeast, Fermentis and Lallemand strains and have them running through my pipeline. Creating a list of Saaz and Frohberg lager strains is on my list of things to do (should be ready tomorrow). An updated family tree should be ready during the weekend maybe? I'm a bit hesitant to release too much of the results though, as apparently this data is from an unreleased paper. I don't want to step on their toes and steal their thunder

Just asking them might be a good idea. Maybe they don't mind.

 

[Vale71]

I think you might want to check that...

Oh, and bottom/top fermenting is another of those panda classifications. Although skimming open fermenters selected strongly for ale strains that float, the move to conicals selected for ale strains that sink, so a lot of ale strains look like bottom fermenters these days, it seems to be a pretty mutable characteristic that is strongly selected for depending on fermenter type.

You're absolutely right, I've managed to confuse myself too..

I'm aware of the unsuitability of the bottom/top cropping definition in light of modern practices and that's why I was hesitant to use it.

 

[lump42]

Number 1 - it's just really interesting, and can also illuminate some of the history of how yeast got swapped around etc.

Number 2 - you have to be a bit wary of relationships - nobody is more closely related to you than your parents, but one of them has very different lumps and bumps to you! But at the same time thee family trees can help see things that aren't immediately obvious - for instance T-58 looks like a POF+ version of S-33/Windsor, the small POF gene cassette produces a very obvious change in flavour, but otherwise they behave pretty similarly in terms of temperature, ester profile etc.

But yes, these insights have encouraged people to try a few things that they wouldn't have otherwise, particularly over on the warm-fermented lager thread where in the last 18 months WLP800 has become one of the favourites for such beers as a direct result of this kind of work. Also I've been doing a bit of work on relatives of T-58 for biotransformation.

Although I suspect a lot of the people who might otherwise have done such experiments are all too busy playing with kveik at the moment...

Thanks, that clears up the reasoning.

 

[sykesey]

The other useful thing you can presumably do with sppIDer would be to distinguish low-temperature Saaz lager strains from high temperature Frohberg strains. Something like WLP850 Copenhagen should be Saaz (2/3 eubayanus, 1/3 cerevisiae) and WLP830 German should be Frohberg (1:1 eubayanus:cerevisiae). If you can distinguish those then it would be interesting to see what the other lager strains show up as.

I don't know how well it can pick that up, and I think with short sequence reads like this rather than full genome sequencing that might be hard. There's probably another way to do it, which I'm sure people smarter than me are all over My experience is some biochem in uni about 20 years ago and plenty of IT since then so setting up the tool is easy, but building the process chain and understanding the results to get further than that is something I need to spend more time with.

but when i get a chance i'll run 515 and 1187 through it, or just wait for the paper to come out and it should have something similar.

The lager/ale differences remind me of a German term, Obergäriges Lagerbier, or simply "top-fermenting lager beer" ... to a lot germans it probably made no real distinction between ale and lager it was all about the process and result

 

[sykesey]

I've downloaded all the data for all the WLP, Wyeast, Fermentis and Lallemand strains and have them running through my pipeline. Creating a list of Saaz and Frohberg lager strains is on my list of things to do (should be ready tomorrow). An updated family tree should be ready during the weekend maybe? I'm a bit hesitant to release too much of the results though, as apparently this data is from an unreleased paper. I don't want to step on their toes and steal their thunder

Yeah, good call. It's by chance I found them (oops) so there's something to be said for a little discretion on findings yet, and they'll need to have a chance to peer review. Hopefully it's soon though so we can get an updated family tree, which is going to be super interesting. So interesting in fact I want to learn how to set up my own pipeline to do my own freebayes+parsnp tree from the data to keep secret

 

[brewbama]

I've downloaded all the data for all the WLP, Wyeast, Fermentis and Lallemand strains and have them running through my pipeline. Creating a list of Saaz and Frohberg lager strains is on my list of things to do (should be ready tomorrow). An updated family tree should be ready during the weekend maybe? I'm a bit hesitant to release too much of the results though, as apparently this data is from an unreleased paper. I don't want to step on their toes and steal their thunder

This will be interesting to see when the time is right.

 

[Northern_Brewer]

I'm a bit hesitant to release too much of the results though, as apparently this data is from an unreleased paper. I don't want to step on their toes and steal their thunder

Of course, and talking to them is the way to handle it. I guess I'd see it as 5 levels

1) Correcting mistakes on the existing ale tree
2a) Adding new homebrew strains to the ale tree
2b) Adding ale strains that aren't readily available to homebrewers
3a) Simple Saaz/Frohberg typing of homebrew lager strains
3b) S/F typing of lager strains not readily available to homebrewers
4) Adding lager genomes to the cerevisiae family tree
5) More detailed analysis of genomic structure of hybrids

From our point of view, we're primarily interested in 1, 2a, 3a and to some extent 4. They seem to be primarily interested in 5, althought the other stuff all comes out of their work. So there seems to be room for some flexibility, at the very least 1 and hopefully 3 given that 3 should be doable by anyone with sppIDer once they release the sequences (and in theory 3a could be done by anyone via PCR after a trip to LHBS). I guess we see what they say.