Isolated Yeast (Tree House): How to Identify and Characterize?

[StinkyBeer]

Does anyone have access to qPCR currently who reads/posts in this thread? If so, how about taking up the challenge!?

is it possible to use the data from ‘famouslastworts’ research to save some time? His gels/lines look nice and clear (unsmudged)...could be cool to figure this out once and for all.

 

[Clyde McCoy]

Does anyone have access to qPCR currently who reads/posts in this thread? If so, how about taking up the challenge!?

is it possible to use the data from ‘famouslastworts’ research to save some time? His gels/lines look nice and clear (unsmudged)...could be cool to figure this out once and for all.

You're confusing qPCR and PCR...but yes, I am planning something. There will be a delay due to COVID.

 

[StinkyBeer]

You're confusing qPCR and PCR...but yes, I am planning something. There will be a delay due to COVID.

Amazing. Thanks for the PCR correction. Would you care to share your thoughts/approach?

 

[Clyde McCoy]

Amazing. Thanks for the PCR correction. Would you care to share your thoughts/approach?

There are some differences in the findings posted above that I will try to reproduce.

 

[stickyfinger]

I have access to a qPCR right now. What would you like to have tested? I can have my wife do it. She is a geneticist/cell biologist.

 

[isomerization]

I have access to a qPCR right now. What would you like to have tested? I can have my wife do it. She is a geneticist/cell biologist.

What you really want is next gen sequencing (NGS), that would really open up the information flow.

I’m not sure how much info qPCR is going to provide here. You’d need known DNA sequences unique to each strain in order to look at population dynamics.

 

[Clyde McCoy]

What you really want is next gen sequencing (NGS), that would really open up the information flow.

I’m not sure how much info qPCR is going to provide here. You’d need known DNA sequences unique to each strain in order to look at population dynamics.

Agreed, I think there is some misunderstanding about terminology here. Certainly no one is trying to compare gene expression across strains. qPCR could be useful for CNV analysis if Tree House was using a hybrid strain, but (1) relative analysis isn't trivial and (2) the banding patterns you've already shown argue against that possibility. I am going to assume these posters are referring to PCR unless otherwise corrected.

 

[stickyfinger]

I have access to next gen sequencing as well. no problem.

 

[Clyde McCoy]

I have access to next gen sequencing as well. no problem.

It will cost you thousands of dollars to perform whole genome sequencing on several saccharomyces cerevisiae strains. Is this what you are offering to do?

157 strains have already been sequenced (link below), but you would need to isolate colonies from a Tree House beer to find a match.

https://www.cell.com/fulltext/S0092-8674(16)31071-6

 

[beervoid]

It will cost you thousands of dollars to perform whole genome sequencing on several saccharomyces cerevisiae strains. Is this what you are offering to do?

157 strains have already been sequenced (link below), but you would need to isolate colonies from a Tree House beer to find a match.

https://www.cell.com/fulltext/S0092-8674(16)31071-6

Time for a crowdfunding round?

 

[Clyde McCoy]

Time for a crowdfunding round?

Whole genome sequencing is hugely overkill for figuring out which yeasts are in TH beers. It could potentially be useful for identifying any mutations unique to their house strain(s), but the number of genetic differences could range from tens to thousands, so actually identifying a casual variant isn't really possible. I.e. needle in a hay stack. Besides, I think it's extremely unlikely that the actual strains they use are unique on a genetic level. I do not think they are using a hybrid strain based on existing evidence.

Much more reasonable is the PCR-based interdelta fingerprinting that has already been done. I do think given two conflicting reports that some follow-up would be useful. Especially isolating more colonies from their beers. Of course, even if there is convincing evidence that TH is doing mix-yeast fermentations, which it appears they likely are, we still don't know the pitch rate or schedule.

Unfortunately, no genetic analysis is going to point to an obvious way to clone their beers.

 

[NJGeorge]

Whole genome sequencing is hugely overkill for figuring out which yeasts are in TH beers. It could potentially be useful for identifying any mutations unique to their house strain(s), but the number of genetic differences could range from tens to thousands, so actually identifying a casual variant isn't really possible. I.e. needle in a hay stack. Besides, I think it's extremely unlikely that the actual strains they use are unique on a genetic level. I do not think they are using a hybrid strain based on existing evidence.

Much more reasonable is the PCR-based interdelta fingerprinting that has already been done. I do think given two conflicting reports that some follow-up would be useful. Especially isolating more colonies from their beers. Of course, even if there is convincing evidence that TH is doing mix-yeast fermentations, which it appears they likely are, we still don't know the pitch rate or schedule.

Unfortunately, no genetic analysis is going to point to an obvious way to clone their beers.

 

[elgee]

I get some similar esters from Trillium from time to time. Has anyone done the same type of plate streaking or other methods with their beers. Sometimes I get almost an identical nose on their and TH beers, but not taste. There is speculation they use 1318 but I don’t taste that.

 

[StinkyBeer]

Just having a look at all of isomerisations images above, I couldn’t confidently say there are any matches at all. No slight against you by the way! When I look at famouslastworts images the correlation or lack there of is crystal clear.

Would it not make sense to:

- obtain a can of Julius
- obtain a sachet of every Fermentis and LalBrew dry yeast
- cycle through all this again with the aim of producing clear unsmudged banding

I fully understand the possibility of process intricacies never being known BUT...it would be nice to definitively know what yeasts are in there. Currently IMO we only know WB06 is which isn’t a great basis to attempt any ‘cloning’.

 

[Clyde McCoy]

Just having a look at all of isomerisations images above, I couldn’t confidently say there are any matches at all. No slight against you by the way! When I look at famouslastworts images the correlation or lack there of is crystal clear.

Would it not make sense to:

- obtain a can of Julius
- obtain a sachet of every Fermentis and LalBrew dry yeast
- cycle through all this again with the aim of producing clear unsmudged banding

I fully understand the possibility of process intricacies never being known BUT...it would be nice to definitively know what yeasts are in there. Currently IMO we only know WB06 is which isn’t a great basis to attempt any ‘cloning’.

I've ordered US-05, S-04, K-97, S-33, WB-06, and T-58. Once the world reopens, I'll spend some time on it.

 

[NJGeorge]

Why is there assumption that they only use dry yeast? It literally could be anything. The WB-06 banding in the other study is very close but not perfect. Didn’t they also test S04 and T58? Not trying to be negative Nancy here but I guess it wouldn’t hurt to double check. I recently fermented with omega kviek and the beer has esters similar to TH. I’m definitely not saying they use that but there are sooo many possibilities and types of yeast that need to be retested.

 

[isomerization]

Just having a look at all of isomerisations images above, I couldn’t confidently say there are any matches at all. No slight against you by the way! When I look at famouslastworts images the correlation or lack there of is crystal clear.

Would it not make sense to:

- obtain a can of Julius
- obtain a sachet of every Fermentis and LalBrew dry yeast
- cycle through all this again with the aim of producing clear unsmudged banding

I fully understand the possibility of process intricacies never being known BUT...it would be nice to definitively know what yeasts are in there. Currently IMO we only know WB06 is which isn’t a great basis to attempt any ‘cloning’.

No offense taken, can’t let your data become personal in science!

With that said, I don’t agree with you, at all.

My biggest issue with the famouslastworts data is choice of interdelta primers. This person was apparently not aware of this thread, which is unfortunate. Would have been great to see an actual replication attempt. It is pretty funny that the only strain with overlap was WB-06 though.

High % percentage agarose gels are very tricky and this was done on a shoestring budget in spare time. Here are two images of previous gels cropped to (hopefully) better show comparability:

 

[isomerization]

Why is there assumption that they only use dry yeast? It literally could be anything. The WB-06 banding in the other study is very close but not perfect. Didn’t they also test S04 and T58? Not trying to be negative Nancy here but I guess it wouldn’t hurt to double check. I recently fermented with omega kviek and the beer has esters similar to TH. I’m definitely not saying they use that but there are sooo many possibilities and types of yeast that need to be retested.

I bet @Clyde McCoy would be happy to test every strain you want to purchase and send his way, this stuff isn’t free!

Tongue in cheek comment aside, you attempt to replicate previous observations first, then move onward. If banding patterns (using same DNA primers) match up well using the same commercial strains, then we have confidence that the process is working the same in both lab settings.

Also when were kveik yeasts introduced to the US? It would be shocking to me if a US brewery had adopted them that early, but you never know.

 

[NJGeorge]

I bet @Clyde McCoy would be happy to test every strain you want to purchase and send his way, this stuff isn’t free!

Tongue in cheek comment aside, you attempt to replicate previous observations first, then move onward. If banding patterns (using same DNA primers) match up well using the same commercial strains, then we have confidence that the process is working the same in both lab settings.

Also when were kveik yeasts introduced to the US? It would be shocking to me if a US brewery had adopted them that early, but you never know.

I’d love to help out in anyway I can! I’ve been on this thread since the beginning and would love to see some new developments. Here is an article in regards to kveik being introduced to Omega. https://growlermag.com/rise-of-the-super-yeast-kveik/ The thing with this yeast is it needs to be fermented super warm to get those esters and we have no idea what TH current fermentation temp is like. There was a picture of the temp control panel from back in the day, but that was much cooler temps.

 

[couchsending]

Their yeast is predominantly S04. Without a doubt in my mind. Esters are identical. Has that weird bready off putting aroma that crushes everything. So hard to actually pick out the hops.

I’d be more interested in how they accomplish the mouthfeel and softness. The intensity of hop flavor and texture that hits the front of your palate then disappears I don’t think anyone else can accomplish.

For me the aroma is the last thing about their beers I’d like to copy.

edit: Also interesting to me that based on other observations from the yeast genome study like the fact that VT Ale and 1968 look almost identical on the PCR and they’re on the same “branch” of the yeast genome tree. Yet WLP644 (Sacch Trois) is on the same “branch” as WB-06 but the PCR is completely different. I don’t think there is any way there’s any WB-06 in their beers but I’d be much more likely to believe there’s some Sacch Trois.

 

[NJGeorge]

@couchsending I don’t remember it’s been a while, but do you have access and drink their beers often? Is there a way to coax banana and fruity aromas from S04? I haven’t experimented with it much and when I did I wasn’t a huge fan. I always get overripe banana from their house yeast when smelling their beer. Maybe it’s a function of the yeast and type of hop they use? As for water and mouthfeel, I’m with you there.

 

[couchsending]

Alright I’m finally inspired enough to see if these things are still alive... these are the original isolates @isomerization sent me almost three years ago. I revived some 2 year old yeast recently with surprising ease so I’ll give these a shot.

 

[couchsending]

@couchsending I don’t remember it’s been a while, but do you have access and drink their beers often? Is there a way to coax banana and fruity aromas from S04? I haven’t experimented with it much and when I did I wasn’t a huge fan. I always get overripe banana from their house yeast when smelling their beer. Maybe it’s a function of the yeast and type of hop they use? As for water and mouthfeel, I’m with you there.

I have someone send me some of their beers few times a year (generally only when it’s cold out) and I’ve visited the brewery once a year for a while. So I don’t drink them “often” but enough. Just had 8 cans two weeks ago I think.... and they all smelled exactly the same.

You can get isoamyl acetate from a lot of yeasts by way underpitching. I know someone that makes a “Hefe” with 1318 way underpitched and fermented warm with very little o2.

It’s weird I don’t get the banana esters in their beer at all... Everyone uses the “juicy fruit” descriptor for when their beers are firing. I find you can definitely get “bubble gum” at times from Mosaic and Simcoe.

 

[isomerization]

View attachment 675789 Alright I’m finally inspired enough to see if these things are still alive... these are the original isolates @isomerization sent me almost three years ago. I revived some 2 year old yeast recently with surprising ease so I’ll give these a shot.

Ah yes, I recall those leaked out the threads during transit, didn’t account for the elevation change maybe? How were they stored? Good luck!

 

[isomerization]

Their yeast is predominantly S04. Without a doubt in my mind. Esters are identical. Has that weird bready off putting aroma that crushes everything. So hard to actually pick out the hops.

I’d be more interested in how they accomplish the mouthfeel and softness. The intensity of hop flavor and texture that hits the front of your palate then disappears I don’t think anyone else can accomplish.

For me the aroma is the last thing about their beers I’d like to copy.

edit: Also interesting to me that based on other observations from the yeast genome study like the fact that VT Ale and 1968 look almost identical on the PCR and they’re on the same “branch” of the yeast genome tree. Yet WLP644 (Sacch Trois) is on the same “branch” as WB-06 but the PCR is completely different. I don’t think there is any way there’s any WB-06 in their beers but I’d be much more likely to believe there’s some Sacch Trois.

I wouldn’t put a ton of stock in that WLP644 data, it was provided to me in the mail and not in the original package. Had some other issues with yeast strains in the same shipment (cross-contamination) that it may not actually be WLP644.

 

[lowtones84]

Their yeast is predominantly S04. Without a doubt in my mind. Esters are identical. Has that weird bready off putting aroma that crushes everything. So hard to actually pick out the hops.

I’d be more interested in how they accomplish the mouthfeel and softness. The intensity of hop flavor and texture that hits the front of your palate then disappears I don’t think anyone else can accomplish.

I agree that there is a bready, even doughy thing going on with all of their IPAs, and it's definitely the first thing that I notice. I do get some fruitiness/juiciness but I also believe the mouthfeel enhances some people's perception of that.

The brewery in my town gets a similar profile across all of their NEIPAs, but not quite that next-level mouthfeel. When the taproom opens back up I'll see if I can pick their brains a little.

Disclaimer: I've only bought from them a couple of times, but when I did I walked out with $250+ worth of beer. Have done some trades/gifted a bit here and there other than that.

 

[couchsending]

Ah yes, I recall those leaked out the threads during transit, didn’t account for the elevation change maybe? How were they stored? Good luck!

In the fridge with all the other yeasts. I don’t have much faith but you never know. Don’t have much else to do.

 

[StinkyBeer]

Go Team!

 

[beervoid]

Isnt it possible the bready thing comes from the malt bill?

 

[suregork]

If someone has the TH isolates left, and an extra 125 USD per strain, then I recommend the whole genome sequencing route. MiGS does 625 Mb Illumina sequencing (50x coverage for yeast) for 125 USD.

https://www.migscenter.com/sequencing

I'd be happy to do the analysis and figure out the closest matches if someone orders the sequencing. The interdelta route will get you in the ballpark, but WGS if you want a more precise answer (provided the commercial strains have been sequenced as well; but very many have).