Interesting genome sequencing of some yeasts

[Northern_Brewer]

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.

Well that was why I suggested doing it with what are hopefully clear-cut cases to see if it works or not, and then moving on to other strains. With biology you often just have to give it a go and see what comes out.

 

[sykesey]

Well that was why I suggested doing it with what are hopefully clear-cut cases to see if it works or not, and then moving on to other strains. With biology you often just have to give it a go and see what comes out.

So I just read the paper again and it does mention they used it to differentiate saaz vs frohberg via analysing where things landed to determine the ploidy. I'm going to get the 515 databank and try and align the sequences and merge to get a clearer picture than just taking the largest sequence read through the process, if that fails i'll just run it with the biggest sequence read.

"To test sppIDer’s ability to delineate hybrids, we used short-read data from two S. cerevisiae × S. eubayanus lager yeast lineages, Saaz (strain CBS1503) and Frohberg (strain W34/70). The known parentage of S. cerevisiae and S. eubayanus was statistically confirmed, and only these genomes produced positive residuals from χ2 tests of the mapped data (supplementary table S1, Supplementary Material online). By analyzing the distribution of coverage, we binned regions of the genomes with similar coverages, drawing boundaries based on local minima and maxima. These coverage bins roughly corresponded to the known relative ploidies and rearrangements (supplementary fig. S1c and d, Supplementary Material online) (supplementary fig. S1c, Supplementary Material online)."

here's the image , you can get it from the paper but this is the one in question. c) on the left shows the saaz, so same distribution thereabouts on the left hand violin plot and coverage map to show roughly same distribution of S.cer vs S.eub, d) on the right shows the frohberg, 2x as much S.eub vs S.cer material.

 

[sykesey]

Mixed success so far, I need to learn how to align + merge SRA's into a format that the process can use but I don't think its fully necessary. I'll probably just batch up a few analyses over the weekend and see what we get. The cloud server i'm running this on is reasonably powerful but has limited space and resources so I need to probably limit it to a few target strains of interest.

 

[Northern_Brewer]

Before we get too carried away with idea that WLP838 is an ale and Wyeast 1187 is a lager, we should perhaps also consider the idea that they've just got mixed up. It certainly happened in a couple of cases with the 1002 genomes from Strasbourg, it's tough managing this number of samples and mixups do happen. Remember this is provisional data at this stage.

 

[sykesey]

Indeed. Not worth getting too heavily invested in the results right now with provisional data.

I'm just glad there's more evidence that WLP800 is an ale yeast and I have another potential yeast to brew Kölsch with!

 

[Northern_Brewer]

Paper is out in Nature Ecology & Evolution :
https://www.nature.com/articles/s41559-019-0998-8

For those without access there's a press release here:
"By sequencing the genomes of more than 100 hybrid yeasts, the researchers discovered seven distinct combinations of yeast species, many of them tied to unique fermented beverages. Some yeasts were hybrids of as many as four species....Most hybrids had just two parent species, but some had three or even four parents. The current study doubled the number of known triple- and quadruple-hybrids. Some hybrids were preferentially found in cold-fermented wine and Belgian style beers, while others came from champagne and cider. Most were isolated from lager beers...Saaz and Frohberg, lost the (POF) genes in different ways. While Frohberg yeasts retain a broken version of a key gene, Saaz yeasts have lost both essential genes entirely....

The researchers found that all of the S. cerevisiae parents stemmed from three major, previously domesticated lineages responsible for brewing ale or wine. The hybrids developed when these domesticated strains met up with their wild cousins, all of which came from the Northern Hemisphere. While the domesticated yeasts were already adapted for successful fermentation — such as in their ability to completely digest common sugars — the wild partners offered their own contributions.

Most notably, the vast majority of the hybrids inherited their mitochondrial genome — a small snippet of DNA that drives energy generation in the cell — from their wild yeast parents, rather than from domesticated S. cerevisiae. Recent work out of the Hittinger lab has shown that the wild mitochondrial genomes permit yeasts to ferment at cold temperatures, like those favored for brewing lager...

One set of hybrids had no S. cerevisiae parent at all. These yeasts were combinations of the closely related species S. eubayanus and S. uvarum. They were isolated from the most diverse sources — strains were found in wine, cider, beer, fruit and the environment...

“We’ve learned more about how lager yeasts dispensed with undesirable aromas,” says Hittinger. “Now we’re starting to think more about the genetic basis of the flavors that you want present in a beer.”"

 

[Robert65]

Thank you for the new links, @Northern_Brewer. More stuff downloaded and queued up in hopes of adequate reading time!

 

[dmtaylor]

Hey cool, my son will be going to UW-Madison to be an engineer like his dad.

 

[sykesey]

Yay! the paper was released! Been waiting ages.

Still need a bit of time to dissect all the info, but in the supplementary data there's a lot of evidence that most commercial lager strains are Frohberg, even the Czech ones, corresponding to some of the analysis we did.

Hopefully I have time to look through it all later this week and work out what's of interest, and suregork can get an updated family tree out soon

 

[Northern_Brewer]

Just looking at some of their spreadsheets on the Nature site - I'm intrigued which of the Sheffield breweries (presumably either Wards or Stones, the former is suspected of having "interesting" yeast) has those eubayanus x uvarum and 4-way hybrids. I'm guessing the British stout that produced NCYC 1063/4 is most likely to be Courage RIS as there weren't many other notable ones at the time they were deposited (1958) other than perhaps Mackeson, although many UK breweries produced stout alongside their main brews and to be fair the NCYC themselves describe them as ale/stout production strains.

Vin7 is an interesting Stellenbosch wine strain that Scott Janish has been experimenting with as it is meant to be particularly good at releasing thiols. Is that a general property of kud hybrids, do Abbaye/WLP500/1214 do it too?

cerevisiae (50-60%) x eubayanus (40-50%) - Frohberg, all eubayanus mitochondria
WLP029 Kolsch, WLP051 California V, WLP515 Antwerp, WY1187 Ringwood(!!!),
SafLager-023,
WLP802 Budejovice, WLP810 San Francisco, WLP815 Belgian Lager, WLP820 Oktoberfest, WLP830 German Lager, WLP833 German Bock, WLP840 American, WLP862 Cry Havoc, WLP920 Old Bavarian, WLP940 Mexican,
WY2000 Budvar, WY2001 Urquell H-strain, WY2007 Pilsen, WY2035 American, WY2042 Danish (!), WY2112 Californian, 2xWY2124 Bohemian, 2xWY2206 Bavarian, WY2278 Czech, WY2308 Munich

DBVPG6283(yHCT111, Copenhagen beer !!), CBS1260(yHCT79 unknown beer), CBS1486(yHCT80 unknown beer), NA(yHCT145 Lager, New Glarus), NA(yHDD49 Lager, Middleton, WI), NRRL Y-48766(yHQL582 beechwood chip, Anheuser-Busch, St. Louis), CIBART79(yHCT133 Commercial beer)

Saaz : NRRL Y-12693(FM471, Copenhagen beer), CBS1538nt(yHCT83 unknown beer)

They have two 34/70 sequences that are Frohberg and one from Okuno et al that is a Saaz - presumably a mixup.

cerevisiae (45%) x eubayanus (45%) x uvarum (10%), uvarum mitochondria
WLP351, Muri
NRRL Y-48763(unknown lager 50%/1.3%/48.8%)

cerevisiae (67%-98.6%) x kudriavzevii, most kudriavzevii mitochondria
Anchor Oenology NT50 (98.6%, cerevisiae mitochondria), ABMauri EP2 (90%, cerevisiae mitochondria), YNN48(FM64, German wine 86%), Vin7 (67%), NA (Belgian beer brewed in New Glarus WI), LallemandAbbaye , WLP500 (x2), WY1214 (last four all 77-81%)

eubayanus x uvarum
NRRL Y-672(yHQL559 - Louisville KY distillery, 45% eubayanus)
NRRL Y-12624(FM473, South Manchuria Railway Company, China), DBVPG6282(yHCT110, London ON - Labatt????), NRRL Y-587(yHQL556, Schlitz beer), NRRL Y-648(yHQL558, unknown lager), NRRL Y-1566(yHQL566, Japan brewery)
NRRL Y-1901(yHQL567), NRRL Y-1906(yHQL569), NRRL Y-1910(yHQL581 all 3 from Sheffield UK beer)

cerevisiae x kudriavzevii x eubayanus x uvarum
NRRL Y-1531(yHQL563, UK ale), NRRL Y-1905(yHQL568 Sheffield UK beer)

cerevisiae
Muntons,
BelleSaison, LondonESB, Munich, Nottingham, Nottingham, Windsor,
S-33, SafaleK-97, SafaleS-04, SafaleS-05, T-58, US-05, WB-06,
WLP001, WLP002, WLP004, WLP007, WLP013, WLP023, WLP028, WLP090, WLP099, WLP300, WLP320, WLP380, WLP400, WLP510, WLP530B, WLP545, WLP550, WLP565, WLP566, WLP570, WLP644, WLP715, WLP775, WLP800, WLP838,
WY1007, WY1026, WY1028, WY1028, WY1098, WY1272, WY1318, WY1388, WY1728, WY1792, WY1968, WY2565, WY3068, WY3463, WY3522, WY3724, WY3787, WY3787, WY4766
CoteDesBlancs, EC1118, PasteurRed, YNN49(FM65, Bordeaux wine)
Turbo Super Yeast, Liquor Quik Whisky Pure - both distilling
AnchorBrewersYeast, NPC-HighfoamSuperbrew(both South African bakers yeasts)
NCYC1063(yHQL579 British stout), NCYC1064(yHQL577 British stout), NA(yHQL578 Irish stout),
NA(yHAB176 Pale Ale, Amana IA) - Millstream?
NA(yHAB174 Belgian Tripel Everett WA) - Scuttlebutt Tripel 7?
blueberryAle(yHKS338) - Tahquamenon Falls Brewery & Pub Blueberry Ale?
Belgian(yHCT146), Green(yHCT143), Weiss(yHCT147), White(yHCT144) - all New Glarus

 

[sykesey]

Solid work there NB. I see as well the Gallone paper has WLP860 in the mix, but not sure if the sequence data is available , maybe they've released other data to see if that's a Saaz type as them all being Frohberg is pretty unexpected...

I wonder if Vin7 is POF+ or POF- ? Maybe worth some experimentation for thiols, maybe a job for a lab made hybrid of Kudriavzevii & Cerevisiae, use something like WLP644 that's POF-, or an interesting strain like WY1318 / LAIII / Conan deriv. Or just add Rapidase, ß-lyase enzyme.

 

[dmtaylor]

Ooh.... Dan Carey might get pissed....

 

[sykesey]

Also really interesting to see so many S.eubayanus x S.uvarum hybrids being used commercially - Labatt & Schlitz?

Found the Okuno W34/70 read data as well - https://ddbj.nig.ac.jp/DRASearch/experiment?acc=DRX036594

I'll run that soon and see if it's saaz or frohberg

 

[Mer-man]

I was expecting that Saaz list to be longer!

 

[Robert65]

So now Urquell H is not only not cerevisiae, it's not even Saaz but Frohberg?

 

[sykesey]

So now Urquell H is not only not cerevisiae, it's not even Saaz but Frohberg?

WLP800 and the Wyeast equivalent seem to be different...

 

[dmtaylor]

WLP800 and the Wyeast equivalent seem to be different...

Indeed. And WLP838 is cerevisiae and NOT equivalent to 2308.

 

[Robert65]

WLP800 and the Wyeast equivalent seem to be different...

Then is either one actually Urquell? Provenance has been the constant bugbear of homebrew yeasts.

 

[sykesey]

eubayanus x uvarum
NRRL Y-672(yHQL559 - Louisville KY distillery, 45% eubayanus)
NRRL Y-12624(FM473, South Manchuria Railway Company, China), DBVPG6282(yHCT110, London ON - Labatt????), NRRL Y-587(yHQL556, Schlitz beer), NRRL Y-648(yHQL558, unknown lager), NRRL Y-1566(yHQL566, Japan brewery)
NRRL Y-1901(yHQL567), NRRL Y-1906(yHQL569), NRRL Y-1910(yHQL581 all 3 from Sheffield UK beer)

Did a bit of a search on NRRL and it lists the source of Y-1906 and co as "Wiles, Exch. Brewery, Sheffield, England". Could be the Tennant Brothers Exchange Brewery?

Anyway all this talk makes me wonder... can homebrewers actually get a Saaz strain??

 

[sykesey]

Then is either one actually Urquell? Provenance has been the constant bugbear of homebrew yeasts.

Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains. WLP800 looks like a kolsch yeast as its similar to wy2565 when run in a family tree. I've been trying to ferment a starter with it at 18C and it doesnt seem that great compared to actual kolsch yeasts, but it might be the starter. I'll sacrifice a kolsch wort to science and ferment it with wlp800 at warm temps when I have a chance.

WY2001 is probably closer to the mark, but I think people maybe assumed that the Czech strains were Saaz when it's also likely lots of these breweries were using mixed strains of saaz and frohberg lager yeasts, then EC Hansen isolated a single strain, which may have just been one of many. It doesn't seem likely that saaz yeasts could have transformed into frohberg yeasts. Then maybe over time the frohberg yeasts took over, after the Carlsberg single strain was isolated.

I think maybe the yeast suppliers might kick into gear and find an actual saaz strain, or just go culture from CBS1503 which is the reference strain. There may be one out there that hasn't been sequenced yet.

 

[Miraculix]

Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains. WLP800 looks like a kolsch yeast as its similar to wy2565 when run in a family tree. I've been trying to ferment a starter with it at 18C and it doesnt seem that great compared to actual kolsch yeasts, but it might be the starter. I'll sacrifice a kolsch wort to science and ferment it with wlp800 at warm temps when I have a chance.

No need to, did that already, makes a great warm lager!

 

[sykesey]

No need to, did that already, makes a great warm lager!

Cool. Worth a go next time i'm doing a kolsch then!

 

[Vale71]

Who knows, unless you managed to pull active yeast from Urquell, isolate the single pastorianus strain and run a comparison between that and the commercial strains.

Getting the yeast is not that hard as Urquell sells its beer unfiltered and unpasteurized in the Czech Republic mostly for events (but you get to sample it during the brewery tour too). The sequencing would be the hardest part though.

 

[Miraculix]

Cool. Worth a go next time i'm doing a kolsch then!

If I remember correctly, it was getting a tiny bit fruity above 22c, but just a very little bit and not in a bad way. I always had great results with the 800

Just one time I accidently infected it with an original kveik... First it tasted like a nice lager, after a few weeks in the bottle it turned into a nice kveik, so not much of a loss, but lesson learned regarding cleaning fermenters properly.

 

[Northern_Brewer]

Solid work there NB. I see as well the Gallone paper has WLP860 in the mix, but not sure if the sequence data is available , maybe they've released other data to see if that's a Saaz type as them all being Frohberg is pretty unexpected...

For those who don't know what sykesey is referring to, the Ghent/Leuven groups published their long-awaited paper on this stuff in the same edition of Nature E&E. They looked particularly closely at the loss of phenolic capability in lager yeasts, which requires losing POF-ness from both the cerevisiae and eubayanus genomes. Saaz yeasts have lost that bit of the cerevisiae genome altogether, but Frohbergs have the same 1bp insertion that disables ferulic acid decarboxylase (FDC1) in other Beer1 strains, suggesting that the cerevisiae that made the hybrid was already POF- before the hybridisation event. But the eubayanus genome lost the bit with the cluster in three different ways, so they now divide the Saaz group into two subgroups, which happen to each contain a different one of Hansen's original isolates at Carlsberg. :

Both groups have done their own version of Suregork's family tree in their Supplementary Information :
Langdon et al https://www.nature.com/articles/s41559-019-0998-8#Sec22
Gallone et al 2019 : https://www.nature.com/articles/s41559-019-0998-8#Sec22

The Saaz are really obvious on this, and no, there's no commercial homebrew yeast in the Saaz group on the Gallone paper, at least they've unblinded some of the White Lab yeasts (Chris White is listed as an author) :
WLP051, WLP515, WLP802, WLP810, WLP815, WLP820, WLP833, WLP835, WLP840, WLP845, WLP850, WLP855, WLP856, WLP860, WLP862, WLP920, WLP925, WLP940, WLP070 Kentucky Bourbon

So no WLP800 or WLP838 listed among the lager yeast....

I wonder if Vin7 is POF+ or POF- ? Maybe worth some experimentation for thiols, maybe a job for a lab made hybrid of Kudriavzevii & Cerevisiae, use something like WLP644 that's POF-, or an interesting strain like WY1318 / LAIII / Conan deriv. Or just add Rapidase, ß-lyase enzyme.

VIN7 is weakly POF+ and killer sensitive.

Did a bit of a search on NRRL and it lists the source of Y-1906 and co as "Wiles, Exch. Brewery, Sheffield, England". Could be the Tennant Brothers Exchange Brewery?

Hmm - I'm sure I've encountered that one before somewhere, now I think of it. It is indeed Tennants - AE Wiles worked in the lab there and published a couple of papers on contaminant yeasts after a lot of trouble in the summer of 1948. Y-1906 is his "S.carlsbergensis" T102 in this paper. I'm not sure if this is the same yeast he had designated "S. carlsbergensis Yorkshire Haze Strain I" in 1949 - the granddaddy of haze yeasts!!!!!

Getting the yeast is not that hard as Urquell sells its beer unfiltered and unpasteurized in the Czech Republic mostly for events (but you get to sample it during the brewery tour too). The sequencing would be the hardest part though.

Urquell used to be made with 5 strains fermented separately, after the fall of the Iron Curtain they went down to one, which some people have suggested is the cerevisiae. But that's not incompatible with a given homebrew coming from "Urquell" at some point and being different to 4 other Urquell yeasts.

 

[Vale71]

Urquell used to be made with 5 strains fermented separately, after the fall of the Iron Curtain they went down to one, which some people have suggested is the cerevisiae. But that's not incompatible with a given homebrew coming from "Urquell" at some point and being different to 4 other Urquell yeasts.

Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.

 

[Robert65]

Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.

Wyeast has been around. But the problem with all of the homebrew labs is provenance. Their strains have generally been acquired not directly from the original sources, but via a chain of homebrewers or other intermediaries at several removes from those sources . There has been plenty of opportunity for mix ups, misidentifications, misrepresentations, and so on.

 

[Northern_Brewer]

Where any yeast labs that sell to homebrewers active before the fall of the Iron Curtain at all? If not then I don't see how they could have smuggled any of the older strains out of the Eastern Block.

Most of the commercial homebrew strains were harvested and then passed around homebrewers for most of the 1990s before they ended up at commercial labs. The big change at Urquell happened in I think 1992 so there was plenty of time for people to get hold of the old beer.

Also don't forget that Urquell goes back a long time before the Iron Curtain went up, and given its history its yeast will probably have ended up in western yeast banks before the Soviets arrived.

 

[Andre3000]

Indeed. And WLP838 is cerevisiae and NOT equivalent to 2308.

Now I want to know if WLP833 is WY2487. I don't think these were compared.

 

[dmtaylor]

Now I want to know if WLP833 is WY2487. I don't think these were compared.

No they have not been tested as far as I know. At this point we have no means to support or refute, other than the ancient Kristen England list. I have not run any side-by-side tastings of these either --- if anyone ever does, please report your results!