Anyone Ever Tried Engineering Yeast Strains?

Hey all, this is my first post in these forums. I'm pretty new to brewing (have my second batch ever in the primary right now), but I've learned a lot pretty quickly.

To get right to the point, I have a unique (well, presumably so) strain of yeast that I have acquired. This is the strain that I have used to brew so far, and I intend to keep it that way.

However, I've had a thought. I'm planning on harvesting and reusing yeast (as opposed to making a starter from a slant every single time), and I was wondering if anyone had ever kept a persistent strain of yeast.

My thought is that each "major" type of beer that I brew could have its own specially adapted yeast cake associated with it. I could brew, say, my RIS, harvest and save the yeast cake, and use THAT yeast cake again when I brew the RIS. Repeat this process and I'll be placing some artificial selection pressure on the yeast, forcing them to adapt to the specific conditions of that beer.

Has anyone tried anything like this before?

tl;dr: I want to reuse the same yeast cake for a particular recipe, over and over again, until that yeast is perfectly adapted to that beer. Thoughts?

Isn't that what yeast labs do?

And, over generations (sometimes a few, sometimes many) yeast can degrade itself.

In theory I think it's great, but I just don't trust that a homebrew setting has enough control over major factors, especially cleanliness.

Also, how many separate yeasts would you want to maintain? If it's one per style, I hope you have a big fridge. Not to mention the shelf life - if you're trying to avoid doing starters, you'll need to constantly brew with each strain of yeast to ensure you have enough active cells to pitch into beer. If they sit around too long, your viability will dramatically decrease and you'll be required to make a starter.

But I like your thinkin here... I think your better bet would be to find a strain of yeast you like and use it in almost every beer. While it won't be adapted to a particular style/recipe you brew, at least it'll be selected for your brewery.

Yes, yeast labs engineer strains of yeast to be adapted to certain beer styles. I'm basically trying to turn myself into a yeast lab.

I'm basically looking at keeping 3 separate strains going, each one adapted to one of my 3 (planned) "flagship" brews. I'm not necessarily opposed to making a starter every time, just so long as I'm not staging up some ridiculous number of times. Starting with an inoculation from a slant is, well, time-consuming. I'd much rather pitch a whole ton of yeast to start with.

The main reason I want to do this is because, as I said, I have a unique strain of yeast that I'm using for my brewing. I like the concept of having a beer that I own almost entirely, down to the yeast. If I could, I'd grow my own hops and barley, and malt and roast it myself. Perhaps one day. In any event, I really want to stick with this unique yeast type and try forcibly adapting it.

I know that yeast cultures degrade with time (all microbial cultures degrade over time), and I'm prepared to do frequent passages to ensure that I always have a healthy population. Anyone know roughly how long a yeast cake stays viable? I would think not much longer than 6 months in cake form, but I know that slants can last a while. I'm thinking of making slants to serve as a backup to every cake that I make, just in case the cake dies before I use it. Thoughts?

In my humble opinion, I think that if you were to get serious about this, frozen cultures would be absolutely necessary. The only way to be assured that you have pure culture is to start from a pure culture. If you were to just repitch every time, you could not be assured that the yeast cake is 100% yeast. There are also other problems:

1) Repitching everytime builds up a lot of trub on the bottom. Even after two re-uses, I've seen my yeast cakes get about 6 inches thick. If you attempt to dig in there and only re-use a portion, you had better use a sterile hood. It is almost impossible to prevent some sort of contamination, especially over a long period of time.

2) There is an argument out there that deserves attention, with yeast going through, literally, hundreds of thousands of generations, there is a very very high chance of mutation or adaptation. With the former being more rare and more troublesome. Sure, it may not have a noticeable effect on the beer, but it can change other important things (pH tolerance, attenuation.. etc).

I also highly recommend storing tiny vials of the yeast with 30% glycerol in the freezer. You can get hundreds of starters from these with a lighter and a metal wire. Just dip the wire in ethanol and flame it to sterilize it. Then dip it in the frozen tube and just touch it to the frozen yeast. Now all you have to do is carefully touch the tip again to a starter solution. Wa-la- your yeast starter is going. And if we were careful enough, it will be close to 100% yeast.

toastermm said:

In my humble opinion, I think that if you were to get serious about this, frozen cultures would be absolutely necessary. The only way to be assured that you have pure culture is to start from a pure culture. If you were to just repitch every time, you could not be assured that the yeast cake is 100% yeast. There are also other problems:

1) Repitching everytime builds up a lot of trub on the bottom. Even after two re-uses, I've seen my yeast cakes get about 6 inches thick. If you attempt to dig in there and only re-use a portion, you had better use a sterile hood. It is almost impossible to prevent some sort of contamination, especially over a long period of time.

2) There is an argument out there that deserves attention, with yeast going through, literally, hundreds of thousands of generations, there is a very very high chance of mutation or adaptation. With the former being more rare and more troublesome. Sure, it may not have a noticeable effect on the beer, but it can change other important things (pH tolerance, attenuation.. etc).

I also highly recommend storing tiny vials of the yeast with 30% glycerol in the freezer. You can get hundreds of starters from these with a lighter and a metal wire. Just dip the wire in ethanol and flame it to sterilize it. Then dip it in the frozen tube and just touch it to the frozen yeast. Now all you have to do is carefully touch the tip again to a starter solution. Wa-la- your yeast starter is going. And if we were careful enough, it will be close to 100% yeast.

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Well, #2 is sort of moot because I'm TRYING to mutate the yeast. The idea is to dedicate one strain to one beer type.

I've been wondering about cryo-storage. I should throw this out there for a little reference: I'm a professional microbiologist, specializing in bacteriology. I know a good bit about cryo-storage of bacteria, but yeast is a different beast. I wasn't sure that they would do well in cryopreservation. Are you saying that a standard household freezer is sufficient for long-term storage? That would be a hell of a lot simpler than a -80C chest freezer or liquid nitrogen storage, I can tell you that.

Obviously, I have no idea how problematic contamination would be, but I'm pretty good with my open-air aseptic technique. A hood doesn't really do much for keeping a culture pure; the primary purpose is to separate the microbiologist from his work. I'm pretty confident that the minute airborne contaminants wouldn't be able to out-compete my yeast culture provided I take sufficient sanitary measures. Then again, I don't work with yeast routinely, so I'm not sure how readily they out-compete other contaminants.

As for your earlier question about viability, if you check out Mr Malty's pitching rate calc, it figures that if you save slurry from another batch, its viability decreases to 10% after about 8 weeks (and doesn't go any lower than 10%).

kanzimonson said:

As for your earlier question about viability, if you check out Mr Malty's pitching rate calc, it figures that if you save slurry from another batch, its viability decreases to 10% after about 8 weeks (and doesn't go any lower than 10%).

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Hm, so that would pretty much necessitate making a starter every time. That's sort of annoying, but not too bad.

What is so special about this yeast?

Half the fun of brewing is experimenting with different yeast strains. I don't know if you will have too much luck mutating the yeast, unless you are going to apply some reverse genetic techniques. For the most part you by adding pressure to your system you will just be selecting for variants all ready in your population, and for that part you will not be eliminating the traits you don't want but more over reducing their overall % in the total population.

Many Characteristics that yeast impart to beer are from the strain, but also you have to consider fermentation temperature and fermentation volume as well as many other factors.

A lot of brewery's have house strains of yeast,and like many of us home brewers, will re-use these yeast several times over the year. The brewers will uselessly have a lab such as White labs or Wyeast maintain that strain, and have them periodically grow them up a new starting batch that replace the old running stock with. Is this what you are looking to do?

It's an interesting idea. I think if you want to get into it, you need to start by reading up on how to slant yeast and how to plate out pure cultures. I think it's do-able in a kitchen setting, so long as you do everything in multiples so you can trash the inevitable contaminated strain.

I've kept yeast slants in the refrigerator door (I know, I know) well over a year and been able to reculture them into healthy starters and make good beer from them.

So, whats this "special" yeast you have? Yes, you can slant yeast. Most people do it as a money saving endeavor. Vials/smack packs cost $6 apeice. If you can get a few brews out of one pack, you save a lot of money. Unless you have a good microscope and good procedures, it will be quite hard to be sure you are saving the right, pure strain every single time. Thats why even most breweries pay Wyeast or White labs to maintain their cultures for them.

Aside from that, yeast mutations usually aren't favorable. Its not like a yeast will become super stout yeast, or awesome pale ale yeast after using them for that style a few times. Most yeast mutations affect how the yeast function on a biological level (as its been explained to me by a Seibel graduate and professional brewer). In the end, you end up with yeast that can't ferment any more, or will not attenuate properly. Some mutations also cause them to not reproduce.

TheWhaleShark said:

I've been wondering about cryo-storage. I should throw this out there for a little reference: I'm a professional microbiologist, specializing in bacteriology. I know a good bit about cryo-storage of bacteria, but yeast is a different beast. I wasn't sure that they would do well in cryopreservation. Are you saying that a standard household freezer is sufficient for long-term storage? That would be a hell of a lot simpler than a -80C chest freezer or liquid nitrogen storage, I can tell you that.

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Yep, I work in a micro lab with yeast. Storing them with 30% glycerol in a freezer with no defrost cycle works. As long as the tube isn't thawed and refrozen- then the viability drops significantly.

Obviously, I have no idea how problematic contamination would be, but I'm pretty good with my open-air aseptic technique. A hood doesn't really do much for keeping a culture pure; the primary purpose is to separate the microbiologist from his work. I'm pretty confident that the minute airborne contaminants wouldn't be able to out-compete my yeast culture provided I take sufficient sanitary measures. Then again, I don't work with yeast routinely, so I'm not sure how readily they out-compete other contaminants.

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Yeast are great competitors- they can outcompete and they will. I'm just worried that over time you will lose your unique culture. Who knows what will happen. If I wanted to be sure to keep my strain safe then I would at least keep one frozen copy in a freezer. I do this with my yeast strains and I'm close to not having to buy yeast, as I have a whole yeast library of every strain I've ever bought.

If this yeast is so special to you, that you absolutely need to be freezing/slanting as you go. If you keep it going by pitching slurry over and over, you will be carrying over traits that you don't want in your beer neccessarily (say high ester production). Besides ruining a batch of beer (if you are doing RIS, this might be hard knock by itself); your yeast culture might be unusable.

If you are freezing/slanting as you go along, you will have a catalog of your yeast as it is changing over time. If your yeast culture goes somewhere where don't like, you can go back to your freeze-downs/slants and propagate a yeast strain that you liked.

Its a good idea in theory but you need to be attentive to the details for it to work well...my 0.02....

TheWhaleShark said:

My thought is that each "major" type of beer that I brew could have its own specially adapted yeast cake associated with it. I could brew, say, my RIS, harvest and save the yeast cake, and use THAT yeast cake again when I brew the RIS. Repeat this process and I'll be placing some artificial selection pressure on the yeast, forcing them to adapt to the specific conditions of that beer.
tl;dr: I want to reuse the same yeast cake for a particular recipe, over and over again, until that yeast is perfectly adapted to that beer. Thoughts?

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It seems to me that in order for this to work, you would have to pitch
yeast into several batches of the same beer simultaneously, carry
out each fermentation at different temps around the house, then decide
which of those beers tastes best, and use yeast from that batch and
then repeat the process. I don't think you can brew enough beer
at home to do that. Otherwise you are just going to produce a yeast
that grows the best in that beer under those condititons, not the
yeast that produces the best taste.
Jim

For those wondering about the "special" yeast I have, I'll say that I isolated it from a chocolate syrup sample. These were bulk 5 lb cans of syrup purchased by an ice cream manufacturer. When I received the cans for analysis, they were at least 2 years expired. They were all heavily contaminated with yeast. From what I could tell (using staining, microscopy, and a few bouts of isolation on differential agar), the yeast was a monoculture, so I picked 3 colonies, struck each to an individual slant, and brought it home.

Essentially, the yeast had survived the canning process and somewhere in the neighborhood of 3 years in an extremely viscous environment with next to no nutrients. It fermented the syrup from the consistency of normal chocolate syrup to that of a chocolate liqueur. So, I said, "What the hell, let's try it," isolated it out, and decided to make beer with it.

The reason that I'm so set on using it is because, well, it's mine. It's exceedingly unlikely that anyone else on earth has this yeast, and that makes any beer I brew truly MINE. I could easily experiment with different strains from White Labs or Wyeast, but when I can isolate it and keep it myself, why bother? I figure that the heart of brewing is all about experimenting with the unknown and forging new ground (like any other art, craft, or what have you), so I really want to play around with this yeast.

As I said, it's already slanted, and I periodically transfer the slant to keep the culture healthy. If a standard household freezer is sufficient for cryopreservation, then that is definitely my next step. I'll keep a slant and a frozen representative of each iteration of each yeast cake, and see what happens.

Obviously, I have to be fairly attentive to the brewing conditions. I plan on keeping the fermentation temperature of each recipe fairly consistent batch-to-batch, or at least as consistent as I can make it. I don't have access to incubators - well, OK, I suppose I could do this at work, but that's extremely unethical and could get be fired like 6 times over - but I don't really think I'll need to be that strict for what I want to do.

@jdc2: Interesting idea, actually. I could do that, I suppose, but I actually like the taste that it produces right now. I fermented my RIS at about 70F, and it came out with a dry finish, and slight hint of some kind of dark fruit. I figure that if I ferment it warmer in, say, a saison, I'll have something that's a bit tart and fruity tasting.

So have you made any batches with it yet? Does it taste good?

Edcculus said:

So have you made any batches with it yet? Does it taste good?

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Yup. Brewed a Russian Imperial with it. 1.094 OG, 1.034 FG, clocks in at 8% ABV. The attenuation isn't what I expected there, but the recipe was mostly extract, so that probably had something to do with it.

The flavor is great. Granted, because of the style, it took about 3 or 4 months in the bottle to hit drinkability. Tastes great, has a dry finish and a hint of fruit (probably because I fermented a little on the warmer side).

TheWhaleShark said:

Yup. Brewed a Russian Imperial with it. 1.094 OG, 1.034 FG, clocks in at 8% ABV. The attenuation isn't what I expected there, but the recipe was mostly extract, so that probably had something to do with it.

The flavor is great. Granted, because of the style, it took about 3 or 4 months in the bottle to hit drinkability. Tastes great, has a dry finish and a hint of fruit (probably because I fermented a little on the warmer side).

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Yikes! when you go to test something, you go whole hog. I think I would have started with a starter and seen how that went. I wouldn't expect any greater attenuation level that what you got though. Beer yeast attenuates as well as it does because it's been selected for high attenuation. Your yeast has not.

Interesting story nonetheless. I am surprised yeast was able to grow in canned chocolate syrup....something is not right with that. Did you specifically check for botulism in your isolates? That would have been my first move given the conditions you describe. I think you might want to be darn sure you aren't somehow carrying botulism over in your isolates. Again, my 0.02.

Did you specifically check for botulism in your isolates?

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Correct me if I'm wrong, but isn't botulism only created by some specific sort of bacterium? I don't think botulism can be in yeast unless you mean that there is bacteria living alongside the yeast. Then that could be a problem. But I guessing he checked for this, or at least I hope he did.

toastermm said:

Correct me if I'm wrong, but isn't botulism only created by some specific sort of bacterium? I don't think botulism can be in yeast unless you mean that there is bacteria living alongside the yeast. Then that could be a problem. But I guessing he checked for this, or at least I hope he did.

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Yes, you are correct and it is my concern is that the botulism bacteria is growing alongside the yeast.

The thing that stands out to me is that yeast was found growing (and growing well) in canned chocolate syrup. I would have guessed that yeast could not grow in this because it would be an anaerobic environment. The bacterium that produces botulism toxin on the other hand...perfect conditions.

The other thing that is a concern is that although the OP may have tested for the presence of yeast (how ever it got there), he may not have tested for the absence of botulism. He may not be getting botulism growth in his yeast starters/beer (wrong conditions for botulism), but it might still be there (botulism form spores that can withstand some harsh conditions).

I'd be very careful with this.

TheWhaleShark said:

For those wondering about the "special" yeast I have, I'll say that I isolated it from a chocolate syrup sample.

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I have a similar story. I made a 10 gallon batch of sweet stout and when I split into 2 - 5 gallon kegs I added chocolate to one to make a Young's Double Chocolate Stout clone. For the chocolate I used Hershey's cocoa powder which I tried to boil in a small amount of water. The powder absorbed the water so quickly (and it evaporated) that I couldn't keep it wet. After about 30 minutes I figured that it had at least been hot if not boiling long enough to be okay, so I added it to the keg. It then sat there untouched for a few months and when I pulled a sample it was sour. Based on my sampling of other sour beers at different stages of development I would say that it is contaminated with Brett, and this isn't surprising since coffee and cocoa are often covered in it.

The beer tastes good even though the chocolate flavor is completely absent, the beer is thin in body, and the color and haze from the chocolate is a little unpleasant.

Anyway, I have isolated the strain, and I have thought about using it as my house "wild Hershey yeast" strain. Is botulism toxin something that I should be worried about here? If so, how do I test for it? I am also a microbiologist (virology) so I have the assets and skills to do the test.

I think the problem with continously using the same yeast over and over, is that you end up with a bunch of different yeast with a mix of mutations. Eventually you get enough different mutants in there and the population doesn't ferment as nicely.

One way around this (ie. more work) is after a couple batches with the same yeast, streak some out and pick a single colony and use it for a starter. Make several brews. Repeat. You could pick several colonies and use each of them separately if you're totally crazy.

BayouBrew said:

I have a similar story. I made a 10 gallon batch of sweet stout and when I split into 2 - 5 gallon kegs I added chocolate to one to make a Young's Double Chocolate Stout clone. For the chocolate I used Hershey's cocoa powder which I tried to boil in a small amount of water. The powder absorbed the water so quickly (and it evaporated) that I couldn't keep it wet. After about 30 minutes I figured that it had at least been hot if not boiling long enough to be okay, so I added it to the keg. It then sat there untouched for a few months and when I pulled a sample it was sour. Based on my sampling of other sour beers at different stages of development I would say that it is contaminated with Brett, and this isn't surprising since coffee and cocoa are often covered in it.

The beer tastes good even though the chocolate flavor is completely absent, the beer is thin in body, and the color and haze from the chocolate is a little unpleasant.

Anyway, I have isolated the strain, and I have thought about using it as my house "wild Hershey yeast" strain. Is botulism toxin something that I should be worried about here? If so, how do I test for it? I am also a microbiologist (virology) so I have the assets and skills to do the test.

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In your case you do not have to worry about botulism. Clostridium Botulinum is an obligate anaerobe so it will not grow in the presence of oxygen. Since you isolated your "wild Hershey yeast" from beer, you have nothing to worry about.

Your situation is different from the OP as they got their isolate from a can of chocolate syrup. The canning process removes oxygen, so Clostridium botulinum can grow if the proper precautions aren't taken.

In general, its not a good idea to go about isolating microbes from rotten foods for use in making new foods! Also, its not a good idea to isolate microbes from canned goods that have gone bad. Chance are they spoiled because of the action of some Clostridium subspecies.

pjj2ba said:

I think the problem with continously using the same yeast over and over, is that you end up with a bunch of different yeast with a mix of mutations. Eventually you get enough different mutants in there and the population doesn't ferment as nicely.

One way around this (ie. more work) is after a couple batches with the same yeast, streak some out and pick a single colony and use it for a starter. Make several brews. Repeat. You could pick several colonies and use each of them separately if you're totally crazy.

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One thing here, I don't think you want to use the term mutations here, but the term phenotype. Yeast genomes are fairly stable and don't spontaneously mutate over a few hundred generations. A population of yeast will have a mix of phenotypes (more floculent, less floculent, High EtOH tolerance, etc.) But these phenotypes are going to be present in the population from the start, and for the most part will not be acquired over a few generations. As you add pressure the one phenotype best suited for that environment will become the dominate phenotype.

That said, streaking out will be a good way to isolate that dominate phenotype. Also to assure there is not any bacteria in your Isolate, if you know how to identify yeast from bacteria, and you have sterile enough technique not to contaminate your isolate.

There is no C.bot in the yeast strain, believe me. C.bot contamination is fairly rare, actually, and is usually associated with canned products that have a high water activity. The canned syrup had next to no appreciable water activity.

Also, as I mentioned, I examined my isolated colonies microscopically. I observed only yeast cells. I saw no bacterial cells of any sort, especially not the bacilli that are associated with C.bot.

Also, like I said, I've used it to brew, and it tastes fine. Other than the ethanol, there are no toxins being introduced to the beer.

Also, I did make a starter before any of this. I suppose I should have clarified. I made 500 mL of a test wort using DME. It had a 1.095 OG, and after 20 days of fermentation, it bottomed out at a 1.020 FG. I didn't just jump right into brewing 5 gallons of RIS using a random yeast.

If you want to truly "engineer" a yeast strain, I would do it using molecular biology. I was very close to making yeast that secreted fluorescent jellyfish proteins, but I didn't want to pay for the experimental reagents and couldn't sell my boss on paying for it with his government money ;-).

Bendbiker said:

I was very close to making yeast that secreted fluorescent jellyfish proteins.

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That would be a great St. Patrick's day Beer, It would glow green under the black light!

I've never modified yeast, just bacteria and mammalian cell lines, would you electroporate or use a transfection reagent? Just Curious...

It's very similar to transformation of E. Coli with calcium chloride for cloning, but modified a bit for yeast. In addition, they have all those derivatives of GFP that are basically every color of the rainbow now, so that could potentially be very cool.

I never did it cause I'm sure my boss would've noticed that I had such a big side project....

TheWhaleShark said:

There is no C.bot in the yeast strain, believe me. C.bot contamination is fairly rare, actually, and is usually associated with canned products that have a high water activity. The canned syrup had next to no appreciable water activity.

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The lack of appreciable water activity should have prevented any yeast from propagating to begin with. A very very strange situation you have their...

Rushis said:

The lack of appreciable water activity should have prevented any yeast from propagating to begin with. A very very strange situation you have their...

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I'm betting it was externally contaminated with a culture of active yeast. They probably didn't divide at all in the syrup, especially given the anaerobic nature of the product. There was enough sugar for them to survive and ferment, but not to divide.

And yes, this is some strange yeast indeed. That's why I wanted to isolate it!

@Bendbiker: Well, OK, yes, molecular methods would be the best way to go about that. I'd like to minimize the abuse of state resources to support my hobbies, though. The taxpayers don't like that so much.

I would think that transforming yeasts would be more complicated than transforming E. coli. I imagine there aren't very many viral vectors with which you could transfect the yeast, right? As I said, I'm not a mycologist, so yeasts are a little strange to me.

Any more updates with making some special yeasties?? I just read this thread and it is indeed interesting.

Mutations in yeast, as in any other living organism is a crap shoot. For every "useful" or "good" mutation you get, there will probably be 1,000,000 or more either "bad" ones or indifferent ones. Trying to isolate that one"good"mutation I think would be next to impossible as a home brewer.