Brewing yeast family tree (Oct 2019 update)

Two new fantastic paper on interspecies Saccharomyces hybrids were recently published in Nature Ecology and Evolution. One from the Hittinger lab and collaborators, and the other from the Verstrepen lab and collaborators. A bunch of new commercially available brewing yeast strains were sequenced during the projects, and this meant there was yet again more data available to add to the brewing yeast tree (latest version now always available from the link The tree has been updated mainly with lager yeasts and a number of Wyeast strains. I’ve left out the S. kudriavzevii hybrids for now (e.g. WY1214, WLP500 and Abbaye, but these group in the Beer 2 clade). Anyways, enjoy (click for PDF):

I’ve left out a couple of strains, because they didn’t seem to make much sense (possible mixups or mislabelling?).

WLP530 and WLP775 grouped closely together off in a long branch in the wine clade, so I left these out. But it might be that they belong there?

WLP566 grouped in the Beer 1 clade, and had homozygous nonsense mutations in both PAD1 and FDC1 (meaning it should be POF-), despite being a POF+ saison strain. I left in WLP566 from the Gallone et al. 2016 paper instead.

WY1187 was sequenced in three runs, one was pure S. cerevisiae the other two were lager strains. So I don’t know if there has been a mix up or if this is a blend? I left in the S. cerevisiae run.

As revealed in both papers, WLP029, WLP051, and WLP515 are lager yeasts. WLP838 seems to be a S. cerevisiae strain.

It’s interesting to see that there are no Saaz strains among the commercially available lager yeast, they all are Frohberg.

The infamous WLP644 strain was also sequenced, and it can be found in the Beer 2 clade, close to the ‘Duvel’ strains.

For old versions, with a lot of good discussion about the strains, see here: Nov 2018, Apr 2018, and Dec 2017.

Thanks for having a look and feel free to leave a comment 🙂

23 thoughts on “Brewing yeast family tree (Oct 2019 update)

  1. qq

    Great stuff.

    If I was guessing what English cider yeasts were, I’d expect them at a first guess to be a slightly distant member of the Beer2/wine group, so it’s plausible that WLP775 English Cider is right – and if that’s right then Westmalle using a cider yeast is no less weird than anything else that happens in Belgium….

    I think we have to assume 1187 is a mixup, in the absence of other information – I guess if you got your hands on some you could at least do the “lager PCR” on a few colonies?

  2. qq

    Also interesting to see some of the links in the English strains shuffling around – S-04 and 1098 are now quite close which makes a bit more sense, and the fact that WLP838 is close to a 1187 sequence reinforces the idea that WLP838 and 1187 got mixed up by the Hittinger lab.

    Next time, you could throw in WLP070 Kentucky which is a lager strain in the Leuven sequences?

  3. suregork Post author

    There was a bit of shuffling around yes, as there were some strains from the Fay et al. paper that were sequenced at a very low coverage, so the SNP calling wasn’t very reliable. I’ll add in WLP070 next time (and possible other missing WLP lager strains from the KULeuven paper)!

  4. tbln

    Thanks a lot Kristoffer!

    Overall I like Kristen Englands MrMalty yeast comparison chart, but a couple of strain obviously don’t match up anymore:

    WY 1098 British ale & WLP007 Dry English Ale
    WY 1728 Scottish Ale & WLP028 Edinburgh Ale
    WY 1028 London Ale & WLP013 London Ale

    WY 2206 Bavarian lager & WLP820 Oktoberfest/Marzen Lager
    WY 2007 Pilsen Lager & WLP840 American Pilsner Lager
    WY 2124 Bohemian lager & WLP830 German Lager // W3470

    Also WY 3787 Trappist High Gravity & WLP530 Abbey Ale were considered of the same brewery namely Westmalle, right? So definitely not the same yeast strain?

  5. suregork Post author

    Yes, I already promised Lars and Richard that they would be back in for the next version 🙂

  6. hubhub

    I tried finding a Saaz yeast strain for a historic beer project. Let s just say it as general as possible: commercial yeast banks know about it, but don t like to talk about it. Seriously considering just ordering NCYC396 whenever I ve got more time for it.

  7. Johnny H

    Hi Kristoffer

    I’m Tilo, a homebrewer from Germany.

    Thanks a lot for your amazing work!

    I have a few questions regarding lager yeasts, in particular the difference between Saaz and Frohberg strains:

    1) Are you aware of any breweries that still use Saaz strains for making lagers, or have they basically vanished into the archives?

    2) 19th century lagers often seem to have exhibited much lower apparent attenuation figures (Ron Pattinson has collated und published a lot of old German brewery records), sometimes as low as 46% and often in the range of the lower 60%s. Could this be an indication of a much wider use of Saaz strains, as the latter seem to have issues with utilising maltotriose?

    3) The history of the yeast(s) used at Pilsen is somewhat shrouded in mystery, and there are contradictory articles regarding the use of several different strains in parallel. Also, your work shows up a lot of contradictions regarding strains being sold as “Pilsen” strains. However, even today, published attenuation figures of Pilsner Urquell still seem relatively low (ca. 72%). Probably on its own a low AA figure is not enough to judge, but could this still be an indication that they still use (a) Saaz strain(s), or is this mostly unlikely?

    Best regards

  8. suregork Post author

    Hi Tilo,
    Thanks for your great comment! I will need to do a bit of research before being able to properly answer your question. But, yes, commercial use of Saaz strains appears to be rare in brewing industry, probably because the Frohberg strains are so much more efficient at wort fermentation. I don’t know if you have seen this already, but in the meanwhile, you can have a look at the text in the end of this document for some history of lager yeast:

  9. suregork Post author

    Oh, and one more thing before I forget 🙂 Latest research seems to indicate that many Saaz strains do in fact use maltotriose.
    Here is a report of one Saaz strain using maltotriose:
    And many of the Saaz strains that were tested here used maltotriose:
    So the initial reports that Frohberg strains use maltotriose, but Saaz strains do not were incorrect (from insufficient sample size).

  10. Johnny H

    Hi Kristoffer

    Many thanks for sharing these interesting links. I’ll definitely need some time to process all this information and try fitting it into a bigger picture!

    To start with I conclude:

    With the reported ability of a number of Saaz strains to be able to utilise maltotriose, the picture regarding 19th century lagers and lager yeasts doesn’t become much clearer, unfortunately. In particular, as Hansen’s “Unterhefe 1” (CBS1513) seems to belong into that group. Could it be significant that this strain, its ability to process maltotriose, and its subsequent distribution all over the lager-producing countries was probably quite important for the narrowing down of the lager strain variability and perhaps even for a change of drinking habits?

    After an initial reading of your links and about the history of the lager strain development “post-Hansen” I also find it more difficult to imagine that they still use a Saaz strain at Pilsen. Perhaps there is another explanation for their low AA% figure.

    For the record, here are a number of the aforementioned old brewery records that Ron Pattinson has put together:
    Munich Winterbier: AA 49-68%, average value 61%
    Munich Export 1879-1899: AA 53-74%, average value 64%
    Munich Helles 1902: AA 66-76%, average value 72%, a bit higher already!
    Salvator-type Bock beers pre-1900: AA 45-66%, average value 57%
    A single dark Bavarian lagerbier (from 1865 or before): 46%.

  11. qq

    You’ve got to be a bit careful with reading too much into historical attenuation figures. For one thing they tend to not reflect final attenuation, typically the FG was recorded at racking but a bit of sugar was left at that stage to allow carbonation. Still happens in the UK with cask conditioned ales, but all beer was “cask conditioned” before tanks of industrial CO2 were available. Ron’s got some specific examples of where he has brewery records and analysis of purchased beer where there’s quite a difference in “final” gravity.

    You also have to remember that apparent attenuation in the 19th century is as much about malt as yeast, the malt wasn’t as well modified as modern malts so attenuations will look lower.

  12. Johnny H


    Very good points, thanks! I had been aware of lower malt qualities and modification levels but hadn’t thought of differences due to early racking.

    In theory, not much residual sugar is needed for carbonisation, though. At 10°C, you need roughly 5-6 g sugar/l to fully carbonate the beer. Assuming a “standard” 12°P beer, that’s roughly a difference of 0.6% in terms of gravity, i.e. thus 5% in AA% terms. Who knows how accurate they were with this though, and at which point the beer was racked with perhaps subsequent release of CO2 later (as does happen in the UK, as you said).

    Drinking habits might also have to be considered: beer was much more a food component rather than drunk specifically for inebriation purposes. Some of the beers with AA% below 50% would probably be considered too sweet today but were perhaps more normal in the 19th century.

    I wonder whether we will see any Saaz strains ever again. It’s probably difficult to say how technologically significant they were in the first place.

  13. PhillC

    Bit late to comment, but wanted to add that in his book, “Historic German and Austrian Beers for the Home Brewer”, Andreas Krennmair noted that in the late 19th Century, the Bavarian legal limit for attenuation was a low 48%. He goes on to highlight two cases of beers with only 41.86% and less than 44% attenuation.

    “In 1891, Colosseum brewery in Munich was found to be in violation of this limit, as their beer only had an attenuation of 41.86% even after 3 months of fermentation and maturation. Only after a court-appointed expert was able to determine that even lager beer from the state-run Hofbräuhaus brewery had an attenuation below 44%, all charges were dropped and the court proceedings suspended.”

    Krennmair cites Michel, Carl. Geschichte des Bieres von der ältesten Zeit bis zum Jahre 1899. Augsberg, 1899.

    As an aside Krennmair’s book is currently available, as of a couple of days ago, at no cost on Amazon as a kindle download.

  14. Charles Sweet

    This is amazing work! I’m both a microbiologist and a brewer, so a hearty thanks for putting this out on the web – it’s a thing of beauty.

    This resolves some old questions and raises new ones (like what is up with Lallemand 97? And WLP530? Though the latter matches my experiences that 3787 and 530 are not interchangeable )

  15. qq

    For those who’ve not seen, the Dunham lab have a fun paper drilling down into the relationships within the Chico family, tracing different mutations within it :

    And apparently there’s a pers comm from Maitreya saying that the assignment of BRY-97 to the mixed group looks like a mix-up, supposedly it is a derivative of BRY-96 (not a separate strain from Ballantines) and hence another distinct lineage within the Chico family.

    There’s a good thread over on the AHA forum.

  16. Ed

    Curious about the changes with respect to WY1469 in this version from the prior version in 2018. In the latter, 1469 is adjacent to WLP022 whereas in this version it is quite far apart. Is there any explanation for this?

  17. Ed

    Regarding Wyeast 1469, it was very close to WLP022 in the 2018 version but seems to have move quite far away in this 2019 version. Can you provide any insight on why that happened?

  18. suregork Post author

    Hi Ed, sorry I didn’t see your comment(s) earlier. I’ll need to check more closely, but the strains sometimes move around a bit e.g. if some higher quality sequence data becomes available for the strain or depending on the mutations that are included in the analysis.

  19. Vladimir

    Soviet Union used A(8)II strain for lager production known for high SG.
    You would get 5-7 AVB on 20% SG beer, perhaps it was SaaZ strain.

  20. Russell

    Great work although I can’t seem to open the perma link. I was wondering if anyone could suggest a time line for this as well?

  21. qq

    @Russell The original Gallone paper suggested that Beer 1 and 2 both split off around 1600, personally I think it was probably a bit earlier than that but it gives you an idea of the kind of timescales.

    The Hittinger lab have just released an epic preprint where they’ve sequenced mitochondria from 1600 Sacc strains across the genus, and genome sequenced 163 of them to try and give better coverage and tease out more of the evolutionary history (there’s lots of gene transfer) plus phenotyping a lot of them as well – it’s very cool.

    I’m just working my way through their spreadsheet of strains – there’s the original Gallone Be ones,

    WLP001, WLP002, WLP004, WLP013, WLP023, WLP028, WLP099, WLP775, WLP800 (Borneman 2016)
    Wy3463, Wy4766
    Wy1026, WY1084, Wy1187, Wy1338, Wy1728, Wy2124, Wy2308, Wy2533, Wy2565, Wy2633, Wy3638, Wy3724
    WLP380 (yHAB35), WLP300 (yHAB49), WLP550 (yHAB52)
    Wy1007 (yHAB219), WY1028 (yHAB27), WY1318 (yHAB42), WY3787 (yHAB43), WY2001 (yHCT134), Wyeast2112 (yHCT135) (Langdon et al 2020)

    Plus some familiar faces like Lalvin EC1118.

    I’ve not checked but it feels like none of these are new except maybe Wy3463 Forbidden Fruit and Wy4766 cider, I can’t quite work out whether they’ve reassembled reads they got from Langdon?? (they’re in Table 2 and the others aren’t) So maybe less relevant to brewing but still a fascinating big picture view of “the cousins”.

    The coordinates are charmingly erratic – WLP001 is located to the hills east of Fresno, 265 miles south of Chico; WLP002 is a Sainsburys distribution depot in Daventry, some 80 miles north of London, WLP004 is roughly the middle of Ireland, 60 miles west of Dublin, WLP013 London grew up brewing smack in the middle of Trafalgar Square, WLP023 is on Horninglow St in Burton (famously the home address of Marston) and WLP028 is apparently from next door to Waverley station and the Balmoral hotel in Edinburgh.

    Table 6 has the phenotyping – glucose at different temperatures, various sugars at different concentrations at 22C, and a couple of others like 30% grape must. The Belgians and 1007 will eat almost anything, whereas 1318 is quite picky, it’ll eat maltose but not maltotriose nor raffinose.

  22. Erik Vermeulen

    It wouldn’t surprise me if WLP515 and WLP838 were swapped. Belgian pale ales (De Koninck, Ops-Ale etc) are brewed using yeasts of British origin and WLP838 walks and talks like a true lager strain.

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