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Solving the Muri mystery

Last summer (2018), we published a paper on the ’Muri’ hybrid. This strain was isolated from a yeast culture that Bjarne Muri had produced when attempting to revive his grandfather’s old kveik culture. In the paper we did some genetic and phenotypic characterization of the strain (a single cell isolate from Richard Preiss). The strain turned out to be a Saccharomyces cerevisiae × Saccharomyces uvarum hybrid, with substantial contributions from Saccharomyces eubayanus as well. In addition to the characterization, we also attempted to reconstruct the hybrid through hybridization of closely related parent strains.

Interspecies hybrids have been found multiple times from beer; the most famous hybrid of course being lager yeast (S. cerevisiae × S. eubayanus). However, S. cerevisiae × S. uvarum from brewing environments have not really been reported (they have been found from wine and cider though). So this was already an interesting finding. The ‘Muri’ strain behaves very differently from other kveik strains, reaching very high attenuations (thanks to being diastatic) and producing phenolic off-flavours. Genome sequencing also revealed that the hybrid is not related to the other kveik isolates. So the question was, had this strain really been a part of the Muri family kveik culture or was this some contaminant that had unintentionally been propagated during Bjarne’s revival attempts?

As Lars mentioned in his recent article about the strain, it looked like we would probably never get the answer to this question. However, by chance, I stumbled upon an interesting finding when I was going through the recently uploaded sequence data linked to this pre-print on S. eubayanus and its hybrids from the Hittinger lab that had been deposited to NCBI-SRA. The sequence data of one strain, WLP351 Bavarian Weizen, was deposited under ‘Saccharomyces cerevisiae × Saccharomyces eubayanus × Saccharomyces uvarum’. This immediately caught my interest, and I downloaded the data. After trimming, aligning to a concatenated reference genome of S. cerevisiae, S. eubayanus and S. uvarum, and variant calling (see methodology in our 2018 paper), it became more and more evident that WLP351 might actually be Muri (or rather Muri was WLP351 or a similar strain).

First of all, based on the read coverage across the reference genomes, it appears as if the S. uvarum subgenome in both strains have the same S. eubayanus introgressions (Muri left, WLP351 right in the second image below). These are quite distinct to what has been reported in other studies for S. uvarum. If we perform phylogenetic analysis (together with other ‘Beer 2’/’Mosaic Beer’ strains) based on the SNPs present in the S. cerevisiae sub-genomes, we see that they are very similar in Muri and WLP351. Compared to the reference genomes, Muri and WLP351 share 86534 SNPs, and differ only at 470 sites.

So the evidence unfortunately points towards Muri actually being a contaminant and not a part of the original family kveik culture. Even with these new results, I still think the hybrid is very interesting, and the methods and analysis that we have performed in the paper are still relevant and valid.   

Phylogenetic tree of 1011+157 yeast genomes

A couple of weeks ago the main results of the 1002 yeast genomes project (which actually ended up as 1011 yeast genomes) were published in Nature. This amazing piece of work from the J Schacherer & G Liti labs offers insights into the evolutionary history of S. cerevisiae, and is also an amazing source of data for any yeast nerd (most of the data is freely available to download here). While browsing through the paper and the supplements, I noticed there wasn’t any phylogenetic tree available where the individual strains names were visible (yes I know, such a tree would be quite messy with the number of strains). The relatedness of different brewing yeast strains has been discussed in some of my previous posts and gathered much interest from readers, so I decided to put together a phylogenetic tree myself from the genome assemblies the authors have made available. As I’m a brewing yeast guy, I decided to also expand the tree with the 157 yeast genomes from the Gallone et al. 2016 study. I’ll get into the details below, and bring up some general observations. So, here it is, a phylogenetic tree of 1168 yeast genomes (click the image below to download the PDF):


First of all, sorry about the colors. It was difficult to find a good dark color palette (with 24+ colors) to differentiate the different strain origins and clades. I hope the tree is still readable. If not I will post a version with all the strains and branches is black.

The strains were originally named with their code names (3 letter code in 1011 yeast genomes, and XX### in Gallone et al. 2016). I’ve then replaced the code names with the strain names as listed in Supplementary Table S1 of the 1011 yeast genomes paper, and our decoded White Labs strains (only the medium to high confidence identifications). Here is a copy of the phylogenetic tree using only the original code names.

Many of the brewing strains sequenced in the 1011 yeast genomes paper are quite different from the Gallone et al. strains, but there is some overlap (e.g. Beer002, Beer003, WLP099 = Beer071, WLP570 = Beer085).

I think DBVPG6694 (Artois) and DBVPG6695 (Orval) might be mixed up in the paper, since Beer041 is reported as ‘Belgian Lager’ while Beer077 is reported as ‘Belgian Trappist’.

If CFG is Fermentis S-04 (and not S-40 as stated in the Table S1), then it interestingly doesn’t seem to cluster with the other Whitbread yeasts, but rather seems to be close to WLP006 Bedford and WLP013 London.

Fermentis S-33 and Lallemand Windsor are quite closely related.

The WLP530 isolate (CFC) sequenced in the 1011 yeast genomes paper is not at all where I was expecting it. Me and ‘qq’ were assuming Beer078 from the Gallone et al. paper would be WLP530 (which clusters together with several other Trappist beer strains), but instead WLP530 clustered together with Beer095-097 of unknown origin and WLP009 Australian Ale (Beer052). I’m not really sure what is going on here?

There are a couple of S. cerevisiae var. diastaticus strains (e.g. AEQ/CBS1782/NCYC361, YAG/YJM271, and AAQ/CLIB272_2) that cluster in the Beer 2 / Mosaic beer group (the genomes of which might be a source of good info for new identification methods).

There is probably a lot of observations I’m missing, so please feel free to comment 🙂

Quick summary of the methods:

Genome assemblies were downloaded and aligned to S288c using NUCmer through the NASP pipeline. SNPs were then called from each alignment. The resulting VCF was annotated with SnpEff, and filtered to only retain sites present in all 1167 strains, inside the coding region of a gene, and with a minor allele frequency greater than 0.25% (i.e. minor allele present in at least 2 strains). A maximum likelihood tree was then generated based on 462,842 filtered sites with IQ-TREE, using the GTR+F+R4 model and 1000 ultrafast bootstrap replicates.

Here is an archive containing the newick trees, FigTree NEXUS files, and the various strain maps (e.g. color map, code-to-strain name translation).


Gallone et al. 2016. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 166:1397 – 1410.e16
Peter et al. 2018. Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 556:339–344

The Perfect IPA?

Having just come home from our old apartment (where I did some last minute cleaning, before we have to hand it over to the new tenants), tired and exhausted, I decided I should reward myself with a beer. I take a quick look into my new dedicated beer fridge (which I will soon integrate into a bar counter; will probably make a post once I get it finished), and see a bottle of Firestone Walker’s Union Jack. The beer is bottled in the end of June, so it should be fresh (at least from a Finnish point-of-view). I pour up the beer, and the room already fills with citrusy and floral hop aroma. A beautiful beer. Strong hop aroma. Tones from C-hops, Amarillo and Simcoe. The flavor is perfectly balanced. A relatively light maltiness, combines with loads of citrus and resin from the hops, and ends in a lingering bitterness. The beer feels so smooth. Is this the perfect IPA? I think so.