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Decoding White Labs strains from Gallone et al. 2016 – Update

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Thanks to some amazing contributions and discussions in the comment section of my previous post on this article (special thanks to ‘qq’), we’ve now managed to identify (its at least a good estimation) the majority of the White Labs strains from the set of brewing strains in the Gallone et al. 2016 paper.

In addition to the genotype data, the Gallone et al. 2016 paper contains a huge amount of phenotypic data on these strains, and this information could be very useful for (home)brewers as well now that we know which strains are which (at least most of them). I’ve compiled the following spreadsheet (with the help of ‘qq’) containing all the identifications and useful phenotypic data (e.g. POF, flocculation, sugar use, various tolerances, and ester concentrations). See the ‘Notes’ sheet for more information. Press the icon in the lower right corner to open the spreadsheet in a new window (recommended). Please feel free to leave feedback or suggestions for improvement if you find something unclear or missing!

 

Updated family trees

I also put together the following dendrograms displaying the White Labs codes for those interested in how they look in the family tree (click to enlarge). As an added bonus, if anyone is wondering where the lager yeasts fit in on the tree, I’ve expanded it with the S. cerevisiae sub-genomes of two Frohberg strains (‘A15’ (VTT-A63015) and W34/70; names in purple) and two Saaz strains (CBS1503 and CBS1538; names in blue). We’ve sequenced A15 ourselves, while the other sequence reads were pulled from Okuno et al. 2016.

White_Labs_Gallone_Tree_Small_1_0

In addition, the following dendrograms are also available:

‘qq’ also put together the following dendrograms (Beer 1 and Beer 2 groups separately) from Figure 1 in the original study:

gallone1

gallone2

There are some really interesting observations that can be made, e.g.

  • WLP540, the ‘Rochefort’ strain, appears to be of British origin (POF- as well), and not related to other Trappist strains.
  • The group of ‘US’ strains appears to contain one English and one Belgian strain. The Belgian one could be WLP515.
  • WLP800 and WLP320 appear closely related, and their phenotypes seem very similar. Anyone want to try making a lager with WLP320 American Hefeweizen?
  • Not related to the White Labs strains at all, but two strains used for industrial lager production (Beer039 and Beer040) appear to be closely related to various Belgian Ale strains in the Beer2 group.
  • As can be seen, the lager yeasts branch off in the beginning of the ‘Beer 1’ clade together with the Hefeweizen strains. This is similar to the result obtained by Goncalves et al. 2016.

Phenotypic diversity

I’ve also recreated the heatmap from Figure 3 in the original publication, now with the White Labs codes in place of the strain codes. Strains (rows) that are grouped closely together are phenotypically similar. You can see a nice division between the ‘Beer 1’ strains and the rest of the strains. Click to enlarge.

White_Labs_Gallone_Heatmap_1_0

Furthermore, I performed Principal Component Analysis (PCA) on the phenotype dataset, and below you can find the scores and loadings plots for ‘PC1 vs PC2’ and ‘PC1 vs PC3’. These first three principal components explained about 40% of the variation in the dataset. In layman’s terms, you can interpret the plots in the following way:

  • Strains close to each other on the ‘scores’ plot (top) are phenotypically similar.
  • By looking at the corresponding location in the ‘loadings’ plot (bottom), you can find what phenotypic traits are strongly associated with those particular strains.
  • The larger the magnitude of the phenotypic trait (i.e. the further from the origin), the more it contributes to these principal components.
  • E.g. In the top of the ‘scores’ plot for ‘PC1 vs PC2’ we find ‘wine018’, ‘wine017’ and ‘WLP050’. Looking at the ‘loadings’ plot, we see that these strains are strongly associated with high production of ethyl, isoamyl, isobutyl and phenylethyl acetate, as well as isoamyl alcohol. The particular traits have a large effect on PC2.
  • Use these plots e.g. to find similar strains (if you want to substitute one yeast for another for example), or strains associated with particular traits.

PC1 vs PC2

White_Labs_Gallone_PCA_12_1_0

PC1 vs PC3

White_Labs_Gallone_PCA_13_1_0

Presence of STA1 in the strains

Following the recent news about a potential S. cerevisiae var. diastaticus contamination in White Labs yeast, I also did a BLAST search for STA1 (GenBank: X02649.1), the gene encoding for an extracellular glucoamylase, in each of the assemblies. Interestingly, there were full hits in multiple strains (partial matches in many strains as well). The strains are:

  • Beer002
  • Beer013
  • Beer059 (probably WLP026)
  • Beer085 (very likely WLP570)
  • Beer086 (probably WLP585)
  • Beer091 (probably a WLP strain)
  • Beer092 (probably a WLP strain)
  • Wine019 (probably a WLP strain)

I also assembled the reads from the WLP570 sample in the 1002 yeast genomes project, and STA1 was present in the resulting assembly as well. While these strains appear to contain STA1, it is unclear if any of them are diastatic (this needs to be tested). Interestingly, all the STA1 sequences contain a ‘T’ insertion at position 2406, close to stop codon (position 2427-2429). With the insertion, the amino acid sequence is extended by 39 amino acids (and these amino acids are homologous to the C-terminus of the SGA1-encoded intracellular glucoamylase). All this data is in the Excel spreadsheet as well!

Other information

In addition to these identifications, the comment section of the previous post contains a lot of interesting discussion on topics such as the history and spread of different strains, and whether interspecies hybrids have been included in the study. Please have a look! This information would definitely be worth a post of its own, but I’m sure someone else would be better at putting together such a post than me.

Hopefully White Labs will now be willing to unblind their own strains. It would make this data much more valuable, and I’m not really sure what they have to gain from keeping it secret.

Briefly, for those wondering how the tree was constructed: the Illumina reads from the lager strains were aligned to a concatenated reference genome of S. cerevisiae and S. eubayanus. FreeBayes was used to call variants. A consensus sequence for each strain was created using BCFtools and the FreeBayes VCFs. Only the S. cerevisiae sub-genome was retained for subsequent analysis. In addition, regions with coverage < 5 were excluded. kSNP3 was used for SNP detection and phylogenetic analysis on the set of assemblies from Gallone et al. 2016 and the four consensus sequences. The resulting SNP matrix was fed into IQ-TREE to produce a maximum likelihood tree with 1000 ultrafast bootstrap approximations. While the tree is very similar to the one in the Gallone et al. 2016 paper, there are some minor differences resulting from the different methodology (they e.g. only looked at SNPs located in the coding sequence of genes, while this approach looks at the whole genome).

My previous post contains information and discussion about how the White Labs strain identification was done.

DISCLAIMER: These are only guesses based on a range of evidence.

36 Comments

  1. Thank you very much for this!
    Very interesting and informative.

  2. There’s been some great discussion on your pages.
    Since you do some strain sequencing yourself, do you have any idea about the Saaz/Frohberg identity of any of the commercially available lager strains (apart from 34/70 being Frohburg and wlp800 being S. cerevisiae)?
    Thanks!

  3. Unfortunately we haven’t sequenced any commercial lager yeasts ourself (just from our own culture collection) and I’m not aware of any publicly available sequence data from others. My guess is that most are either Frohberg or S. cerevisiae. Saaz strains (with the exception of the Carlsberg strain) appear to be unable to use maltotriose, so their attenuations would lie in the 60-70% range in all-malt wort. Maybe the Wyeast version of the Urquell strain?

  4. Nice post thanks.

    With wlp540 it is noted that it has high O2 demands, I wonder if this originated from a british brewery which uses rousing through fan tails.

    Also, they used to say on this strain “An authentic Trappist style yeast. ” which is now removed, I don’t know if trappist is a trademarked name thus they can’t use it any more or if the origin made them change it. There are a few abbey breweries in the UK though.

    I can send you pretty much any of these yeasts if you want to test them btw.

  5. Hi Kristoffer,
    I came across your site just recently and it’s really great to learn that I was not the only one interested in the identity of the yeast strains sequenced in the Cell paper. I am really interested in yeast strains, specifically those strains used in beer brewing. I am a graduate student in chemistry working on developing a method for yeast strain identification using MALDI TOFMS, and I am looking at patterns of proteins/peptides secreted from the strains during their growth period. My research involves identifying the yeast strain used during the beer brewing using a cell free approach, where we match the peptides identified in the beer with a specific strain by a matching algorithm using an in-house created library of different strains. From my literature searches, it has been challenging to find a lot of information about protein and peptide analysis in regard to yeast strains. It seems like a lot of work is focused on genetics and metabolite identification. Your blog is very helpful and the information about the yeast strain predictions are of great interest to me to help understand the data I am now collecting. Thank you for sharing the information.

  6. Hi Elsa,
    Thank you for your comment! Nice to hear from a fellow graduate student. MALDI-TOF seems to be a promising approach to yeast identification, especially if it can be narrowed down to strain-level identification. You’ve probably seen this relatively recent study?
    http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181694

    Good luck with your research! Hope to read about your results once they are available.

  7. I’ve got a bit of a fascination with the Saaz/Frohberg identity of commercial dry yeasts in particular, just because so little seems to be known about them and there seems to be a bit of interest in which ones can be used at ale temperatures.

    And also it would be a secondary study to working out what is really in Nottingham – I’ve even got as far as ordering Diamond Lager from the Eurozone as for some reason Lallemand don’t sell it in the UK, and it’s the obvious candidate for the mysterious “lager” yeast in Nottingham. I can get myself some ITS primers, just need to find myself a lab with a PCR machine to borrow, and some Taq and HaeIII to scrounge… 🙂 In the meantime, I’m grabbing any out-of-date dry lager yeasts I come across when ordering other stuff, just so that I have them on hand when I get some lab access even if I’m not going to brew with them.

    I happen to have the official data on attenuations for most of the liquid strains available here in the UK (so not the smaller ones like ECY, and we are fairly restricted on what Omega/Giga strains we see). Here they are, sorted by the average of their attenuation range. It’s obvious that eg Giga are using different test conditions to the others, but it’s better than nothing. I’m not sure I see any particular pattern though…

    65 70 WLP810 – San Francisco Lager Yeast
    66 70 WLP862 – Cry Havoc Lager Yeast
    65 73 WLP820 – Oktoberfest/Marzen Lager Yeast
    67 71 2112 – California Lager
    66 73 WLP920 – Old Bavarian Lager Yeast
    68 72 WLP860 – Munich Helles Lager Yeast
    68 76 WLP838 – Southern German Lager Yeast
    70 74 2105-PC Rocky Mountain Lager
    70 74 2278 – Czech Pils
    70 74 2308 – Munich Lager
    70 74 2487-PC – Hella Bock Lager
    70 74 2782-PC – Staro Prague Lager
    70 76 2272-PC – North American Lager
    70 76 WLP833 – German Bock Lager Yeast
    70 76 WLP835 – German X Lager Yeast
    71 75 2000-PC – Budvar Lager
    71 75 2002-PC – Gambrinus Style Lager
    71 75 2007 – Pilsen Lager
    72 74 2352-PC – Munich Lager II
    70 78 WLP940 – Mexican Lager Yeast
    72 76 2001-PC – Pilsner Urquell H-Strain
    72 76 Omega Labs – OYL-114 Bayern Lager
    73 76 WLP4035 – Hessian Pils
    70 80 WLP885 – Zurich Lager Yeast
    72 78 WLP815 – Belgian Lager Yeast
    72 78 WLP850 – Copenhagen Lager Yeast
    73 77 2035-PC – American Lager
    73 77 2042-PC – Danish Lager
    73 77 2124 – Bohemian Lager
    73 77 2206 – Bavarian Lager
    73 77 2247 – European Lager
    73 77 2633 – Octoberfest Lager Blend
    74 78 GigaYeast – GY045 German Lager
    74 78 WLP4030 – Franconian Dark Lager
    74 79 WLP830 – German Lager Yeast
    75 79 GigaYeast – GY002 Czech Pilsner
    75 79 WLP845 – Fast Lager Yeast
    73 82 WLP925 – HP Lager Yeast
    75 80 WLP802 – Czech Budejovice Lager Yeast
    75 80 WLP840 – American Lager Yeast
    79 83 GigaYeast – GY005 Golden Gate Lager
    79 83 GigaYeast – GY030 American Lager

  8. TheTrappists seem to have been getting more aggressive in general about “casual” use of their name, and White Labs have purged their list of any mention of them, so the name of WLP500 is now “Monastery Ale” rather than “Trappist Ale”. Wyeast seem to allow themselves to describe beer as “Trappist-style” which is presumably a tougher nut for the IP lawyers to crack.

  9. Nice post. Makes sense, I see they have that trappist authentication stamp. I’ve seen brewers make “champagne-style” beers and be left untouched while another brewery makes a “definitely not champagne beer” to get around this.

  10. If you are on milkthefunk I can send you a message or if you prefer I can send you a message on HBT. I have all of whitelabs lager yeast minus wlp850/845 (off the top of my head), I can pick both those up this week though.

  11. Good idea about determining the Saaz/Frohberg identity of commercially available lager yeasts. We performed a similar study a couple of years back where we did this exact thing for all the lager yeasts in VTT’s Culture Collection. If you can get the strains to me, I’d be happy to check whether they are Saaz or Frohberg. ITS-PCR and HaeIII digestion is something we do very often at our lab, so we have all the primers and enzymes ready.

  12. In addition, it would be good to test if they are S. cerevisiae or S. pastorianus. The ITS-PCR and HaeIII digestion can’t differentiate between S. cerevisiae and Frohberg-type lager strains. For this there are other tricks, e.g. using primers specific to S. eubayanus genes found in lager yeast.

  13. Good news, soon it will be possible to both confirm a couple more White Labs strains, and expand the tree with more commercially available strains.

    The 1002 yeast genomes project is soon ready and they will publish the genome data of all their strains. The list is quite impressive and includes many brewing isolates:

    http://1002genomes.u-strasbg.fr/isolates/isolates/isolatestable.html

    Some strains are:
    DBVPG6694 – Artois Peterman beer
    DBVPG6695 – Orval Trappist beer
    Nottingham
    Safale S-33
    Safale S40
    Safale US-05
    Safbrew T-58
    Windsor British
    WLP090
    WLP099 (we already have this)
    WLP530
    WLP570 (this data is already available and I used it for IDing Beer085)

  14. I wonder if the irish beer strain is related to the one yeast labs have.

    Also look at what popped it’s head up!

    CBR NCYC_1187 Ale strain UK


    CBN NCYC_88 Ale strain UK

    Quite a lot of wine including several strains from an amphora.

    Thanks for the link to that, looking forward to the updates :).

  15. That’s very cool! Some of the wine ones in particular look really interesting. I also spotted NCYC88 (classic Burton strain, was the BRI benchmark for many years) and NCYC1187 “Hull/Ringwood”.

    Presumably they’ve plated out a “Nottingham ale starter” and picked a colony without being aware that it’s a multistrain?

    I assume Safale S40 is S-04!!!

    No idea what Win-8B from a UK brewery is. There’s also YJM271 and CBS1487 (unknown breweries), CBS1230 and DBVPG6693 (Belgian beer), CBS6503, CBS6505 and CBS7371 (UK breweries), CECT1462 (UK beer), CBS4507 (English brewer’s yeast), 1175 (“Spoiled beer”), CBS1171 (Oranjeboom), CBS7539 (Bulgarian beer), CBS1248 (brewer’s yeast), CBS1463 (unknown beer), CBS1782 (Japanese beer), CLIB227 (Dutch beer), CLIB272 (US beer), CLIB382 (Irish beer), CLQCA_10-386 (Ecuadorian beer),
    CBS2973 (“beer wort”), CBS382 (Brazilian beer), CBS422 (Ukrainian beer), CLIB650-5 (bili bili sorghum beer, Chad), CBS4454-6 (millet beer, South Africa), CH02-14 (millet beer, Ivory Coast),

  16. That’s very kind of you both, although I was happy to do it myself it obviously makes sense to do it in a lab that’s already geared up for it (for lurkers reading, enzymes and PCR ingredients come in small tubes which can do 1000+ reactions, it gets a bit expensive if you just want to do a couple but if you have the reagents already then the marginal cost is trivial).

    I have 9 lager yeast on my dry yeast list, of which I have about half, this will be an incentive to complete the set! I assume there’s no hurry, it’s not the best time of year to be posting living things to Finland?

    @Weehee – fraid I’m not on MTF, I had a look for you on HBT but couldn’t find you, Suregork has my email though. Thanks for the offer, I’m not so interested in lager strains but there’s a couple of Vault British ale strains that I’m getting bored of waiting for!! Not got a huge library myself but you’re welcome to anything I’ve got.

  17. “CBS7539 (Bulgarian beer), CBS422 (Ukrainian beer)”

    Oops, I meant to add – when these come out it’s probably worth checking them against BE002 and BE003 respectively, there can’t be too many Bulgarian and Ukrainian beers kicking round the yeast banks. I imagine there will be a couple more like that if you start looking closely, but those are ones that stick out!

  18. Hah, seems like White Labs have now updated the description of WLP570 on their web page to mention that it contains STA1:

    https://www.whitelabs.com/yeast-bank/wlp570-belgian-golden-ale-yeast

    They should test WLP026 and WLP585 next 🙂

  19. I think you should be getting a commission for this…

    Interesting that wlp585 will probably have it, if it’s part of the du pont multiculture it means they have diastaticus plus boulardii and who knows what else in there :).

    I wonder when the smaller companies will update. I heard dry belgian ale was diastaticus on MTF.

  20. Is this a new strain or an old one that they are making available again? I’m guessing it compares to wyeast’s. It says it fully attenuates but it has low flocculence so maybe it doesn’t ferment starches. Want me to order it?

    Looks online at the wyeast reviews there’s some ending 1.007 from 1.065-070

  21. Just throwing this out there – where does wlp041 come from? Seems to be a guess by Kristen.

    Isn’t wlp041 just the wyeast equivalent 1332? They have similar descriptions. If it is then it came from Hales via Gales, recently John Keeling said in an article about recreating George Gales Prize Old Ale that Gale’s yeast probably came from whitbred originally.^1 I see red hook have a collaboration with hales on ratebeer, but I found an article saying they originally got their yeast from a local university but the British yeast gave them banana and POF+ flavours :)!^2 It looks like they swapped yeast after that mishap.

    Also kind of cool to see burton and edinburgh yeast related if they are the historic strains. Considering their history together.

    1. http://protzonbeer.co.uk/features/2017/12/27/fuller-s-marble-revive-classic-old-ale
    2. http://mikesbrewreview.com/breif-history-of-redhook/ https://www.seattletimes.com/pacific-nw-magazine/cheers-to-beers/ The first banana tasting yeast they tried might be brewlabs devon 1 possibly O’Hanlon’s strain.

  22. Thanks, I’ve never heard about this strain so it could be a new one.

  23. I’m loving all the discussion about the history of these strains, as this is something I don’t know much about! Makes the family tree so much more valuable!

  24. I accidentally ran across this thread today discussing the origin of 1332! http://www.jimsbeerkit.co.uk/forum/viewtopic.php?f=12&t=71325&start=15

    It includes the whitbred and gales relationship rumour among other things. I guess with this new data you guys have brought to light we can settle it!

  25. In this small yeast trial, they seem to think wlp041 is a top cropper so that looks like another thing it has in common with wyeast 1332. It also includes a small tasting note from wlp515, another neutral review.

    http://www.jimsbeerkit.co.uk/forum/viewtopic.php?t=53146

  26. They said to search hbd and strathcona – http://www.beerandloafing.org/hbd/fetch.php?id=60210

    http://hbd.org/hbd/archive/5211.html

    More information there, wyeast is known to use numbers relating to the yeast bank so it’s a theory I’ve heard before. Likewise wlp076 might be named that because new albion was founded in 1976.

    Ooh, maclay’s was still around when those threads were made, that’d be a nice strain to isolate :).

  27. Looks like wlp026 used to be called burton ale, it has the flavour characteristics of wlp023 so they must have swapped numbers?

    http://web.archive.org/web/20160731093520/http://brewasaurus.com/index.cfm?action=ingredients&type=yeast

    https://www.homebrewtalk.com/forum/attachments/imageuploadedbyhome-brew1505869375-232280-jpg.414742/

    Another one noting how whitbred b allegedly morphed into gales… I can’t find HSB gales around here or I would send you a yeast sample
    https://www.homebrewtalk.com/forum/threads/yorkshire-square-on-a-home-level.635302/page-2#post-8095869

  28. Just a thought but whitelabs have provided some statistics on their strains for beers they have made. Combined with the attenuation you might be able to see if there’s a divide of diacetyl and acetaldehyde levels in conjunction for differentiation of frohberg/saaz strains.

  29. Looking at the aroma compounds might give some indication of Saaz (usually lower) or Frohberg, but I don’t think that would be very reliable. ITS-PCR will be the best way to proceed, and as I mentioned I’d be happy to do perform those in a couple of months!

  30. Interesting, as the strains that now are WLP023 and WLP026 (Beer059) are genetically very distant (Beer1 vs Beer2).

  31. Pingback: Phylogenetic tree of 1011+157 yeast genomes | Suregork Loves Beer

  32. If WLP800 is S. cerevisiae do we know if WY2001 also is S. cerevisiae? Quite possibly they are not the same strain?

  33. 2001 is meant to be derived from the Urquell H-strain, the one they still use. I suspect WLP800 is derived from one of the other 4 strains that they used to use until the early 1990s. Whether that means it shares the same origin as 2278 which is meant to be the D-strain, I don’t know.

    Sorry K, been a bit submerged with work, will get back to you on that stuff.

  34. No problems! I’ve been very busy myself. I’m still interested though to continue the project!

  35. Pingback: An updated brewing yeast family tree | Suregork Loves Beer

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