Author Topic: Yeast Study on Chico Strains  (Read 2938 times)

Offline hopfenundmalz

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Yeast Study on Chico Strains
« on: August 08, 2020, 01:31:06 pm »
Nice paper. Dr. Maitreya Dunham at U. Washington presented on drift with consecutive pitches at HomebrewCon Portland. Our friend Tom Schmidlin PhD owns PostDoc in Redmond WA, where that study was done, and data from his brewery is in this paper too.

I found it interesting, as the Bell's House Strain is included, and it is a Chico strain, but has its own house character now.

There are two groupings of Chico yeast. One thing pointed out is that there may be an unknown ancestor.

Mark's post on WLP-051 jogged my memory on this paper. It loads slow for me be patient.

https://www.biorxiv.org/sites/all/libraries/pdfjs/web/viewer.html?file=/content/biorxiv/early/2020/06/29/2020.06.26.166157.full.pdf
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Offline Andy Farke

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Re: Yeast Study on Chico Strains
« Reply #1 on: August 08, 2020, 11:53:57 pm »
Super cool! Thanks for sharing this -- evolution in action! I've always thought it would be cool to see how the genetics of yeast cultures changes from pitch to pitch, especially for those strains where we're warned that characteristics change with repitches.

I like that they actually named the strains in the phylogeny. The lack of commercial strain names was (in my opinion) a significant drawback of the Gallone et al. 2016 paper (and if I was a reviewer or editor on it, I would have asked they provide this information to allow reproducibility!)...okay, climbing off my open science soapbox now.

I found a really nice thread on Twitter (https://twitter.com/DunhamLab/status/1277707293774065664) from the lab head, which gives some additional background information in (slightly) simpler language than the paper itself. Even though I have a Ph.D. in anatomy/paleontology, I get a bit lost in these "gene squeezing" papers sometimes, so it was nice to see a more conversational version. And I suppose the slides are available for AHA members, from the Portland presentation? I will have to check them out!

As an aside for anyone reading this, the paper is not yet officially published; this is a preprint, which means it's a mostly finished piece of work that has not yet been through formal peer review at a scientific journal. This doesn't mean it's unreliable, of course--just that it may change slightly between now and official publication. (or there is always a chance it will never make it through peer review, but that's pretty unlikely given the expertise of the workgroup!)
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Offline hopfenundmalz

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Re: Yeast Study on Chico Strains
« Reply #2 on: August 09, 2020, 01:46:55 am »
Super cool! Thanks for sharing this -- evolution in action! I've always thought it would be cool to see how the genetics of yeast cultures changes from pitch to pitch, especially for those strains where we're warned that characteristics change with repitches.

I like that they actually named the strains in the phylogeny. The lack of commercial strain names was (in my opinion) a significant drawback of the Gallone et al. 2016 paper (and if I was a reviewer or editor on it, I would have asked they provide this information to allow reproducibility!)...okay, climbing off my open science soapbox now.

I found a really nice thread on Twitter (https://twitter.com/DunhamLab/status/1277707293774065664) from the lab head, which gives some additional background information in (slightly) simpler language than the paper itself. Even though I have a Ph.D. in anatomy/paleontology, I get a bit lost in these "gene squeezing" papers sometimes, so it was nice to see a more conversational version. And I suppose the slides are available for AHA members, from the Portland presentation? I will have to check them out!

As an aside for anyone reading this, the paper is not yet officially published; this is a preprint, which means it's a mostly finished piece of work that has not yet been through formal peer review at a scientific journal. This doesn't mean it's unreliable, of course--just that it may change slightly between now and official publication. (or there is always a chance it will never make it through peer review, but that's pretty unlikely given the expertise of the workgroup!)

Thanks for the clarification Andy.

The Portland presentation was my conference favorite. Find if and give it a listen, I think it was recorded.
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Offline Saccharomyces

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Re: Yeast Study on Chico Strains
« Reply #3 on: August 09, 2020, 11:12:02 pm »
The PDF partially loads and the download quits with the error "Message: Unexpected server response (0) while retrieving PDF 'https://www.biorxiv.org/content/biorxiv/early/2020/06/29/2020.06.26.166157.full.pdf'," so will have to read it at another time.

Offline Saccharomyces

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Re: Yeast Study on Chico Strains
« Reply #4 on: August 09, 2020, 11:41:35 pm »
I believe that they have the wrong genetic ancestor from Ballantine.  They used Y-7408 when all roads point to the genetic ancestor to BRY-96 (a.k.a. Chico) being Y-7407.  It would be interesting if they re-ran the genetic test with Y-7407 because the Schalk Brothers brewery predates lager pure cultures.  BRY-96 does not form a head like Y-7408.  If one visits the link that I included in my WLP051 thread that points to my old thread about these yeast strains, one will see a photo that indicates that the strain Ballantine used for ale production was a top cropper and BRY-97 (Y-7408) is a top cropper.  I am willing to bet that BRY-96 came out of the Schalk Brothers' lager brewery that Ballantine acquired. All roads lead to the direction.  I wish that we could contact the researchers and have them compare Y-7407 against the BRY-96.  Siebel knows where these strains originated.
« Last Edit: August 10, 2020, 10:00:22 pm by Saccharomyces »

Offline Saccharomyces

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Re: Yeast Study on Chico Strains
« Reply #5 on: August 09, 2020, 11:42:31 pm »
Lallemand owns Siebel.

Offline hopfenundmalz

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Re: Yeast Study on Chico Strains
« Reply #6 on: August 10, 2020, 01:43:26 am »
I believe that they have the wrong genetic ancestor from Ballantine.  They used Y-7408 when all roads point to the genetic ancestor to BRY-96 (a.k.a. Chico) being Y-7407.  It would be interesting if they re-ran the genetic test with Y-7407 because the Schalk Brothers brewery predates lager pure cultures.  BRY-96 does not form a head like Y-7408.  If one visits the link that I included in my WLP051 thread that points to my old thread about these yeast strains, one see will see a photo that indicates that the strain Ballantine used for ale production was a top cropper and BRY-97 (Y-7408) is a top cropper.  I am willing to bet that BRY-96 came out of the Schalk Brothers' lager brewery that Ballantine acquired. All roads lead to the direction.  I wish that we could contact the researchers and have them compare Y-7407 against the BRY-96.  Siebel knows where these strains originated.

I thought you might see something, and have a good comment.

The picture on this site?
https://sites.google.com/site/pballantineandsons/skimmingale

I may have posted this link years back.
https://sites.google.com/site/pballantineandsons/

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Offline ynotbrusum

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Re: Yeast Study on Chico Strains
« Reply #7 on: August 10, 2020, 09:38:47 pm »
Great comments and links!  I can barely remember my dad having Ballantines...they were nearly ubiquitous way back when.
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Offline Andy Farke

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Re: Yeast Study on Chico Strains
« Reply #8 on: August 11, 2020, 04:12:10 am »
I believe that they have the wrong genetic ancestor from Ballantine.  They used Y-7408 when all roads point to the genetic ancestor to BRY-96 (a.k.a. Chico) being Y-7407.  It would be interesting if they re-ran the genetic test with Y-7407 because the Schalk Brothers brewery predates lager pure cultures.  BRY-96 does not form a head like Y-7408.  If one visits the link that I included in my WLP051 thread that points to my old thread about these yeast strains, one will see a photo that indicates that the strain Ballantine used for ale production was a top cropper and BRY-97 (Y-7408) is a top cropper.  I am willing to bet that BRY-96 came out of the Schalk Brothers' lager brewery that Ballantine acquired. All roads lead to the direction.  I wish that we could contact the researchers and have them compare Y-7407 against the BRY-96.  Siebel knows where these strains originated.

Interesting point -- agreed that it would be fun to see it re-run. I suppose you could contact the corresponding author listed on the PDF and ask about it? Although I wonder if it would ultimately make much of a difference in the overall tree topology for the more recently diverged strains that are nested more deeply within the phylogeny?
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Offline denny

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Re: Yeast Study on Chico Strains
« Reply #9 on: August 11, 2020, 01:53:41 pm »
I believe that they have the wrong genetic ancestor from Ballantine.  They used Y-7408 when all roads point to the genetic ancestor to BRY-96 (a.k.a. Chico) being Y-7407.  It would be interesting if they re-ran the genetic test with Y-7407 because the Schalk Brothers brewery predates lager pure cultures.  BRY-96 does not form a head like Y-7408.  If one visits the link that I included in my WLP051 thread that points to my old thread about these yeast strains, one will see a photo that indicates that the strain Ballantine used for ale production was a top cropper and BRY-97 (Y-7408) is a top cropper.  I am willing to bet that BRY-96 came out of the Schalk Brothers' lager brewery that Ballantine acquired. All roads lead to the direction.  I wish that we could contact the researchers and have them compare Y-7407 against the BRY-96.  Siebel knows where these strains originated.

Interesting point -- agreed that it would be fun to see it re-run. I suppose you could contact the corresponding author listed on the PDF and ask about it? Although I wonder if it would ultimately make much of a difference in the overall tree topology for the more recently diverged strains that are nested more deeply within the phylogeny?

And more important for me, will it make any difference to my beer?
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Offline Saccharomyces

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Re: Yeast Study on Chico Strains
« Reply #10 on: August 11, 2020, 10:37:21 pm »
Interesting point -- agreed that it would be fun to see it re-run. I suppose you could contact the corresponding author listed on the PDF and ask about it? Although I wonder if it would ultimately make much of a difference in the overall tree topology for the more recently diverged strains that are nested more deeply within the phylogeny?

I sent a message to a message to Maitreya today letting her know that there is a lot of evidence that points to Y-7407 being the parent strain. BRY-96  is unlike any other yeast strain that is used on brewing.  It will actively ferment colder than most ale strains and it is very lager-like when fermented cold.  The Schalk Brothers brewery on Freeman Street was built in 1856, which predates the isolation of the first lager pure culture, Carlsberg Unterhefe No. 1 (CBS 1501), by Emil Hansen in 1883 by 27 years.  Ballantine's acquisition of the Schalk Brothers Brewery in a 1879 predates Carlsberg Unterhefe, which means that the brewery was still using a mixed culture in when it was acquired by Ballantine.
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And more important for me, will it make any difference to my beer?

For me, it is about scratching an itch that I have felt for the better part of a decade.  Even if Y-7407 is not the parent culture for BRY-96, it will allow me to move on.
« Last Edit: August 13, 2020, 01:19:52 am by Saccharomyces »

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Re: Yeast Study on Chico Strains
« Reply #11 on: August 12, 2020, 02:08:41 pm »

Interesting point -- agreed that it would be fun to see it re-run. I suppose you could contact the corresponding author listed on the PDF and ask about it? Although I wonder if it would ultimately make much of a difference in the overall tree topology for the more recently diverged strains that are nested more deeply within the phylogeny?

I sent a message to a message to Maitreya today letting her know that there is a lot of evidence that points to Y-7407 being the parent strain. BRY-96 (and its descendants) is unlike any other yeast strain that is used on brewing.  It will actively ferment colder than most ale strains and it is very lager-like when fermented cold.  The Schalk Brothers brewery on Freeman Street was built in 1856, which predates the isolation of the first lager pure culture, Carlsberg Unterhefe No. 1 (CBS 1501), by Emil Hansen in 1883 by 27 years.  Ballantine's acquisition of the Schalk Brothers Brewery in a 1879 predates Carlsberg Unterhefe, which means that the brewery was still using a mixed culture in when it was acquired by Ballantine.
by Emil Han

And more important for me, will it make any difference to my beer?

For me, it is about scratching an itch that I have felt for the better part of a decade.  Even if Y-7407 is not the parent culture for BRY-96, it will allow me to move on.

Indeed.  We all participate in the hobby for our own reasons.
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Offline Andy Farke

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Re: Yeast Study on Chico Strains
« Reply #12 on: August 12, 2020, 06:09:13 pm »
And more important for me, will it make any difference to my beer?

For me, it is about scratching an itch that I have felt for the better part of a decade.  Even if Y-7407 is not the parent culture for BRY-96, it will allow me to move on.

After building and interpreting evolutionary trees for dinosaurs for the better part of 20 years now, I'm just excited that I can apply those skills to learn more about brewing. Definitely scratching an itch here, too.

And more practically, seeing the evolutionary relationships of the various strains will help me think more critically about substitutions across yeast distributors, dry vs. liquid subs, etc.
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Offline Saccharomyces

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Re: Yeast Study on Chico Strains
« Reply #13 on: August 12, 2020, 09:30:10 pm »
Well, Chris Large responded to the message that I sent to Maitreya, which humbles me because I am just a lowly amateur brewing scientist. There is new information.  To my chagrin, it appears that Y-7407 is a indeed a lager strain, at least genetically.  Secondly, the culture is a tetraploid (4 sets of chromosomes), not a diploid as originally claimed in Dunn and Sherlock's publication.  However, the most interesting part is that they are in touch with the Lallemand scientist who knows the history of BRY-96 and BRY-97 (Lallemand purchased the Siebel Institute several years ago).  It appears that their first sequence of BRY-97 may have been of a contaminant. However, they are currently sequencing a new culture from the original deposit of BRY-97 and it appears to align with Wyeast 1056.  From what I am led to believe, BRY-97 is an isolate from a brewery that acquired BRY-96 from Siebel that is superior to the original.  I do not know about you, but this information unbelievably cool to me. We are looking at brewing history through the lense of genetics.

I guess that the lesson to be learned here is that cultures will adapt to their environment.   I have seen that play out in my sourdough culture.  It was all over the place when I first started to make sourdough.  Now, it is developing into a more reliable culture.  In my humble opinion, every brewer should maintain a sourdough culture and bake sourdough bread.  It will give him/her a greater understanding of how the pure brewing cultures we enjoy today evolved.

By the way, here is a photo my gloved hand holding a Siebel culture from a few years ago.  If one Googles the address on the slant (6100 Royalmount, Montreal, Canada), one will discover that it is the Lallemand campus in Canada.

« Last Edit: August 12, 2020, 11:04:52 pm by Saccharomyces »

Offline Andy Farke

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Re: Yeast Study on Chico Strains
« Reply #14 on: August 12, 2020, 10:50:08 pm »
Well, Chris Large responded to the message that I sent to Maitreya, which humbles me because I am just a lowly amateur brewing scientist. There is new information.  To my chagrin, it appears that Y-7407 is a indeed a lager strain, at least genetically.  Secondly, the culture is a tetraploid (4 sets of chromosomes), not a diploid as originally claimed in Dunn and Sherlock's publication.  However, the most interesting part is that they are in touch with the Lallemand scientist who knows the history of BRY-96 and BRY-97 (Lallemand purchased the Siebel Institute several years ago).  It appears that their first sequence of BRY-97 may have been of a contaminant. However, they are currently sequencing a new culture from the original deposit of BRY-97 and it appears to align with Wyeast 1056.  From what I am lead to believe, BRY-97 is an isolate from a brewery that acquired BRY-96 from Siebel that is superior to the original.  I do not know about you, but this information unbelievably cool to me. We are looking at brewing history through the lense of genetics.

Wow!!!! That's *incredibly* cool...thank you so much for following up on that. I hope the new info will make it into the publication, and into a revised preprint too.
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