Yeasts Aint Yeasts

Lately I’ve been reading about how some recent discoveries have shown that some yeasts we thought were hybrids aren’t and some we thought we’re aren’t.

Now I’m just a brewing guy who studied biochemistry a while ago so I am going to probably stuff some of this up compared to people more well-versed in this topic than I am, but here goes…

What I mean by hybrids is that brewing yeasts in the Saccharomyces species fall into two main categories – “Lager” or pastorianus yeast, or “Ale”, cerevisiae yeast. Pastorianus is actually a hybrid of Cerevisiae with another yeast, Eubayanus, that gives it is low temperature and other characteristics that set it apart from the normal Ale type yeasts.

With recent advances in biotechnology including the practicality of PCR and gene sequencing it’s been shown that at least two yeasts and probably more used for a long time as lager / ale brewing yeasts aren’t actually what they seem. WLP800, which is a single strain isolate purportedly from Pilsner Urquell has been shown to be an ale yeast, and WLP051 California V Ale yeast has been shown to be a pastorianus yeast.

There’s still some debate out there about WLP800 which led me to search out for some extra data, as well as working out how else we could get some additional evidence. I jumped onto the NCBI SRA site and searched for WLP800, hoping to at least find some extra data that I could point someone at, and I must have got lucky as there was a huge collection of SRA data uploaded around 31st August to the NCBI site, from a whole number of commercial yeasts.

Turns out it’s for an upcoming study by Hittinger Lab, one of the world’s foremost yeast genomics labs into hybridisation of brewing yeasts, the paper is yet to be released but they have done a huge favour to everyone by releasing this data. From the descriptions of the short reads I could see a hybrid species identification had already been done – showing WLP800 was plain Cerevisiae, WLP029 was Cerevisiae x Eubayanus hybrid, as well as a couple of other interesting categorisations that go against common knowledge. E.g. WY1187 Ringwood being a lager, WLP838 S.German lager being an ale!

Now I don’t really have that much background in these matters so I reached out to a couple of people who I thought might help. One was Suregork, aka Kristoffer Krogerus, yeast researcher at VTT Finland, who’s got a heap of knowledge in the area for sure, even knowing how to make hybrids and study them, and the other was the owner of the data, Quinn Langdon.

That led to two things… Kristoffer agreed with me about how interesting it was, told me a little about how the identification would work and then wrote up this article where he found the WLP351 sequencing matched the sequencing they did on the Muri Kveik.

The owner of the data then got back to me and explained a couple of things… one was that the paper I thought the data was from wasn’t that, and this was for an upcoming paper, and the other thing was that the identifications came from a tool they developed called sppIDer run over the short sequences.

So this tool they released last year known as sppIDer is for analysing genomic content of short read gene sequence data. There’s a paper over here explaining the program:

It takes short read data, and analyses its fit to a reference set of genomic data. You can then set up different genomic data to refence with, and the typical example with this would be S cerevisiae, S uvarum and S eubayanus to determine fit to the different hybrid genomes you’d find in a saccharomyces’ gene sequence. It can then also determine some level of ploidy by interpreting the data to see how much material maps to the different genomes, so this would be useful for identifying Frohberg (ie German) lager strains vs Saaz (ie Bohemian / Danish) lager strains.

I managed to the sppIDer program running. Being Docker makes it easy for me as I work with Docker containers constantly as part of my job at work, the program is based on R, Python and a number of bioinformatics programs such as bwa to process the short read data.

I don’t want to say too much about the results so as not to tarnish the full result release contained in that upcoming paper, but here’s an example of WLP029 short read data being fed into it, the analysis shows there’s plenty of Eubayanus DNA in there.

Once the paper’s released I will do some more analysis, and also Suregork is working on an updated yeast family tree. It’s going to be very interesting seeing where WLP838, 800 and some of these other strains end up in the tree!

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