From the lab - family tree of White Labs yeast

[Northern_Brewer]

We now have the big one! NCYC have released 230 genomes as Project PRJEB42916 here :
https://ncbi.nlm.nih.gov/bioproject/PRJEB42916/
https://ebi.ac.uk/ena/browser/view/PRJEB42916

There's also now a genome field on their strain pages. I've extracted the equivalent NCYC numbers :
70,72,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,232,235,236,241,356,357,358,360,361,363,367,368,401,430,478,479,482,491,505,609,619,620,621,622,667,672,684,695,816,826,956,963,996,1001,1004,1006,1007,1010,1017,1023,1026,1030,1033,1037,1044,1052,1055,1064,1072,1097,1102,1111,1118,1132,1147,1151,1159,1163,1167,1179,1183,1190,1199,1211,1218,1228,1240,1243,1245,1260,1264,1270,1274,1280,1283,1286,1289,1292,1298,1308,1311,1315,1321,1337,1406,1407,1408,1409,1410,1413,1414,1415,1444,1529,1603,1681,1765,2397,2401,2402,2517,2587,2592,2695,2733,2737,2776,2777,2778,2779,2780,2798,2855,2945,2947,2967,2974,3025,3026,3028,3030,3031,3032,3033,3035,3036,3037,3038,3039,3051,3052,3076,3077,3114,3121,3122,3123,3124,3125,3126,3127,3265,3311,3313,3314,3315,3318,3319,3324,3325,3326,3331,3333,3334,3338,3339,3340,3341,3342,3343,3403,3406,3445,3447,3448,3449,3455,3456,3457,3458,3460,3461,3462,3464,3465,3467,3470,3472,3486,3487,3493,3497,3498,3499,3510,3511,3513,3514,3515,3516,3521,3522,3523,3528,3529,3546,3549,3552,3557,3612,3630,3997,4063,4068,4081

So if @suregork has nothing better to do....

Whilst we're on the subject, did anyone take a look at the genomes released by Brewlab and friends, of yeast from McEwan's stout recovered from a 1895 shipwreck and from two bottles of King's Ale, brewed by Bass to celebrate the visit to the brewery of King Edward VII?

They found Debaryomyces hansenii and Brettanomyces/Dekkera bruxellensis in all three of the shipwreck bottles, one had a couple of fungi including Metschnikowia pulcherrima, and one had viable Sacc, they also found Deb, Brett, (lots of ) Talaromyces rotundus in the Bass bottles, and Sacc in one of them. Given the historical importance of Bass and McEwan's, it would be fascinating to see how they fit in to the tree.

https://onlinelibrary.wiley.com/doi/full/10.1002/jib.641https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671797
@suregork - is there a quick and dirty marker for distinguishing Beer2 from Beer1?

 

[suregork]

We now have the big one! NCYC have released 230 genomes as Project PRJEB42916 here :
https://ncbi.nlm.nih.gov/bioproject/PRJEB42916/
https://ebi.ac.uk/ena/browser/view/PRJEB42916

There's also now a genome field on their strain pages. I've extracted the equivalent NCYC numbers :
70,72,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,95,96,97,232,235,236,241,356,357,358,360,361,363,367,368,401,430,478,479,482,491,505,609,619,620,621,622,667,672,684,695,816,826,956,963,996,1001,1004,1006,1007,1010,1017,1023,1026,1030,1033,1037,1044,1052,1055,1064,1072,1097,1102,1111,1118,1132,1147,1151,1159,1163,1167,1179,1183,1190,1199,1211,1218,1228,1240,1243,1245,1260,1264,1270,1274,1280,1283,1286,1289,1292,1298,1308,1311,1315,1321,1337,1406,1407,1408,1409,1410,1413,1414,1415,1444,1529,1603,1681,1765,2397,2401,2402,2517,2587,2592,2695,2733,2737,2776,2777,2778,2779,2780,2798,2855,2945,2947,2967,2974,3025,3026,3028,3030,3031,3032,3033,3035,3036,3037,3038,3039,3051,3052,3076,3077,3114,3121,3122,3123,3124,3125,3126,3127,3265,3311,3313,3314,3315,3318,3319,3324,3325,3326,3331,3333,3334,3338,3339,3340,3341,3342,3343,3403,3406,3445,3447,3448,3449,3455,3456,3457,3458,3460,3461,3462,3464,3465,3467,3470,3472,3486,3487,3493,3497,3498,3499,3510,3511,3513,3514,3515,3516,3521,3522,3523,3528,3529,3546,3549,3552,3557,3612,3630,3997,4063,4068,4081

So if @suregork has nothing better to do....

Whilst we're on the subject, did anyone take a look at the genomes released by Brewlab and friends, of yeast from McEwan's stout recovered from a 1895 shipwreck and from two bottles of King's Ale, brewed by Bass to celebrate the visit to the brewery of King Edward VII?

They found Debaryomyces hansenii and Brettanomyces/Dekkera bruxellensis in all three of the shipwreck bottles, one had a couple of fungi including Metschnikowia pulcherrima, and one had viable Sacc, they also found Deb, Brett, (lots of ) Talaromyces rotundus in the Bass bottles, and Sacc in one of them. Given the historical importance of Bass and McEwan's, it would be fascinating to see how they fit in to the tree.

https://onlinelibrary.wiley.com/doi/full/10.1002/jib.641https://www.ncbi.nlm.nih.gov/bioproject/PRJNA671797
@suregork - is there a quick and dirty marker for distinguishing Beer2 from Beer1?

Yeah I saw this earlier today, very cool! Will see what I can do, don't have that much extra time at the moment and that is quite a lot of data

 

[Northern_Brewer]

If it helps, I've matched a lot of the numbers to NCYC descriptions, first by doing a lookup on Seymour's list on Jim's and then by manually looking up the NCYC website. I got as far as NCYC3000 before getting bored which roughly corresponds to the millennium, by which time they were mostly collecting medical samples. I may get enthusiasm to finish it off, can't promise though!

A lot of their sequencing has been of the "a guy at Carlsberg or a hospital sent us this random sample a century ago, let's figure out what the hell it is" kind, also I wonder if they've been looking at the evolution of bread yeast given that it's something they regularly collect and have samples going back 100 years. But they bring it right up to date with some Voss and Hornindal strains.

NCYC 4081 is interesting - "Yorkshire Square Stone Type Ale yeast via USA. Reported as being very flocculent and producing a large head during fermentation. Only requires rousing once every six hours for half an hour, otherwise head production can be excessive." deposited December 2015.

NCYC70	Unknown 1933
NCYC72	Schmitt, Carlsberg Laboratorium.
NCYC74	Saccharomyces cerevisiae Hillman Hospital, Birmingham, Alabama, USA.
NCYC75	Unknown 1920
NCYC76	Unknown 1933
NCYC77	Baker's Yeast strain. Dr. A. Harden, Lister Institute, London
NCYC78	Unknown 1925
NCYC79	Fleischmann baker's yeast. 1942
NCYC80	Unknown 1930
NCYC81	Unknown 1942
NCYC82	Unknown A.Klöcker, Carlsberg Labs. Copenhagen.
NCYC83	Unknown Dr. A. Harden, Lister Institute. 1920
NCYC84	Barclay Perkins Brewery strain, Southwark, London, England, 1943.
NCYC85	Unknown Prf. A.J. Kluyver, Delft, Netherlands. Nov 1939 (!!!)
NCYC86	Unknown 'Old Process strain'. ATCC 7753
NCYC87	Distillery yeast. 1947 ATCC 9763
NCYC88	Ale strain. NCTC 6479, Thorne's Yeast S
NCYC89	Fleischmann's yeast cake
NCYC90	Unknown 1928
NCYC91	Ivory Coast Palm Wine, from Elaeis guineensis.
NCYC92	Unknown 1933
NCYC93	Unknown 1925
NCYC95	Unknown 1933
NCYC96	Unknown 1922
NCYC97	Unknown Dr. H.B. Hutchinson, Distillers Co. Ltd, Great Burgh, Epsom, UK. 1945
NCYC232	Strain S, an American brewery ale strain, 1951.
NCYC235	Whibread ZSC 169, anonymized British brewery ale strain, good head, 1953.
NCYC236	Whitbread ZSC 155, single-cell isolate of highly attenuative IPA strain, good head, 1951.
NCYC241	Whitbread SC16, Charrington Anchor Brewery, ale strain, good head, 1951.
NCYC356	Mead production strain
NCYC357	isolated from lees of Avize-Cramant Mead, north-eastern France, 1951.
NCYC358	isolated from lees of plum mead, 1951.
NCYC360	Distilling strain. D.R. Jackson, African Distillers (Rhodesia) Ltd.
NCYC361	Beer spoilage strain, from wort in Irish brewery. R.B. Gilliland 1952
NCYC363	anonymized historic stout production strain from an English Brewery, 1952
NCYC367	anonymized Yorkshire Square Stone system ale strain, good top-cropping characteristics, 1952.
NCYC368	anonymized Yorkshire Square Stone system ale strain, good top-cropping characteristics, 1952.
NCYC401	Burton type ale yeast, isolated from pressed brewer's yeast, 1953.
NCYC430	Saccharomyces cerevisiae, Reisling wine strain, 1955.
NCYC478	Saccharomyces cerevisiae, Sake production "Kyokai 6 strain" deposited by Dr. Sakaguchi, 1956.
NCYC479	Saccharomyces cerevisiae, sake production "Kyokai 7 strain" deposited by Dr. Sakaguchi, #9 in NCYC "Top Ten Yeasts" for commercial brewing, 1956.
NCYC482	Saccharomyces cerevisiae, Champagne yeast, 1956.
NCYC491	Single cell isolate from baking yeast.
NCYC505	Oranjeboom Brewery ale strain, Netherlands, good head, 1957.
NCYC609	Saccharomyces cerevisiae, isolated from West Indian molasses, deposited by Tate & Lyle, 1960.
NCYC619	Saccharomyces cerevisiae, Jerez Sherry production yeasts from Feduchy, 1962.
NCYC620	Saccharomyces cerevisiae, Jerez Sherry production yeasts from Feduchy, 1962.
NCYC621	Saccharomyces cerevisiae, Jerez Sherry production yeasts from Feduchy, 1962.
NCYC622	(Gilliland strain 1285) Guinness ale strain, under-attenuating strain unable to ferment malto-triose, 1960.
NCYC667	Unknown 1963
NCYC672	Saccharomyces cerevisiae, Sherry yeasts, 1964
NCYC684	Saccharomyces cerevisiae, Steinberg German wine yeast, 1965.
NCYC695	Unknown 1966
NCYC816	Saccharomyces cerevisiae, Australian Epernay wine yeast, 1974.
NCYC826	Unknown 1976
NCYC956	Genetically defined strain. Genotype: SUC2 mal gal2 CUP1. R.K. Mortimer, YGSC,
NCYC963	Saccharomyces cerevisiae, anonymized British Brewery Ale Strain 7, 1973.
NCYC996	Saccharomyces cerevisiae, US Patented baking yeasts, 1981.
NCYC1001	anonymized British Brewery ale strain, from historic Whitbread collection, good head, flocculent, 1958.
NCYC1004	anonymized British Brewery ale strain, intermediate head, non-flocculent, 1958.
NCYC1006	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1007	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1010	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1017	anonymized British Brewery ale strain, no head, non-flocculent, 1958.
NCYC1023	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1026	anonymized British Brewery ale strain, no head, flocculent, the renowned Whitbread B equivalent strain, #8 in NCYC "Top Ten Yeasts" for commercial brewing, 1958. Is Wyeast 1026 "British Cask Ale" related?
NCYC1030	anonymized British Brewery ale strain, no head, non-flocculent, 1958.
NCYC1033	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1037	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1044	anonymized British Brewery ale strain, no head, flocculent, 1958.
NCYC1052	anonymized British Brewery ale strain, intermediate head, flocculent, 1958.
NCYC1055	anonymized British Brewery ale strain, no head, flocculent, 1958.
NCYC1064	anonymized British Brewery stout strain, good head, non-flocculent, 1958.
NCYC1072	anonymized British Brewery ale strain, intermediate head, flocculent, 1958.
NCYC1097	anonymized British Brewery ale strain, no head, non-flocculent, 1958.
NCYC1102	anonymized British Brewery ale strain, good head, flocculent, 1958.
NCYC1111	anonymized British Brewery ale strain, no head, flocculent, 1958.
NCYC1118	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1132	anonymized British Brewery ale strain, good head, flocculent, 1958.
NCYC1147	anonymized British Brewery ale strain, no head, non-flocculent, 1958.
NCYC1151	anonymized British Brewery ale strain, good head, non-flocculent, 1958.
NCYC1159	anonymized British Brewery ale strain, good head, flocculent, 1959.
NCYC1163	anonymized British Brewery ale strain, intermediate head, non-flocculent, 1959.
NCYC1167	anonymized British Brewery ale strain, no head, non-flocculent, 1959.
NCYC1179	anonymized British Brewery ale strain, intermediate head, non-flocculent, 1960.
NCYC1183	anonymized British Brewery ale strain, no head, flocculent, 1959.
NCYC1190	anonymized British Brewery ale strain, no head, flocculent, 1960.
NCYC1199	anonymized British Brewery ale strain, good head, flocculent, 1961.
NCYC1211	anonymized British Brewery ale strain, intermediate head, flocculent, 1962.
NCYC1218	anonymized British Brewery ale strain, good head, flocculent, 1963.
NCYC1228	anonymized British Brewery ale strain, good head, non-flocculent, 1964.
NCYC1240	anonymized British Brewery ale strain, no head, non-flocculent, 1966.
NCYC1243	anonymized British Brewery ale strain, intermediate head, non-flocculent, 1966.
NCYC1245	anonymized British Brewery ale strain, no head, fairly flocculent, high attenuating, modern non-top-cropping behavior well-suited to conical fermentors, good flavour, a popular historic English ale production strain, #3 in NCYC "Top Ten Yeasts" for commercial brewing, 1965.
NCYC1260	anonymized brewery ale strain, no head, flocculent, for use in tower continuous fermentors, 1968.
NCYC1264	anonymized British brewery ale strain, no head, flocculent, 1968.
NCYC1270	anonymized brewery ale strain, no head, flocculent, 1969.
NCYC1274	anonymized British brewery ale strain, good head, non-flocculent, 1969.
NCYC1280	anonymized British brewery ale strain, flocculent, 1969.
NCYC1283	anonymized British brewery ale strain, good head, non-flocculent, 1970.
NCYC1286	anonymized British brewery ale strain, good head, flocculent, 1970.
NCYC1289	anonymized British brewery ale strain, good head, flocculent, 1970.
NCYC1292	anonymized British brewery ale strain, no head, flocculent, 1970.
NCYC1298	anonymized British brewery ale strain, good head, flocculent, 1970.
NCYC1308	anonymized British brewery ale strain, no head, non-flocculent, 1971.
NCYC1311	anonymized British brewery ale strain, no head, flocculent, 1971.
NCYC1315	anonymized British brewery ale strain, no head, flocculent, 1972.
NCYC1321	anonymized British brewery ale strain, intermediate head, flocculent, 1973.
NCYC1337	anonymized British brewery stout strain, good head, non-flocculent, 1974.
NCYC1406	Wine production strain. Isolated from Grape must. Japan
NCYC1407	Sake strain isolated from moromi mash, Japan, 1982.
NCYC1408	Mesophilic wine production strain. Isolated from grape must. Japan
NCYC1409	Wine production strain. Japan
NCYC1410	Wine production strain. Japan
NCYC1413	Sauternes wine production strain.
NCYC1414	Tarragona wine production strain.
NCYC1415	Tokay 22 wine production strain.
NCYC1444	Ale production strain. UK 1982
NCYC1529	Active dried baker's yeast. 1984
NCYC1603	anonymized British brewery ale strain, 1986.
NCYC1681	bottom-cropping ale strain, used in pilot scale fermentors, 1987.
NCYC1765	Bakers yeast 1987
NCYC2397	British ale strain called Darley's ale yeast, fast fermentation, good head, Gilliland Type IV loose flaky/clumpy sediment, 1991.
NCYC2401	Saccharomyces cerevisiae, Sri Lankan palm wine strains, 1992.
NCYC2402	Saccharomyces cerevisiae, Sri Lankan palm wine strains, 1992.
NCYC2517	Burgundy strain UCDavis
NCYC2587	Saccharomyces cerevisiae, sake strain, 1994.
NCYC2592	Distiller's production strain. CBS 1200
NCYC2695	Saccharomyces cerevisiae, cider production strain "Rankine's 350" used commercially in Australia, deposited by University of California, Davis, USA, 1996.
NCYC2733	anonymized British brewery ale strain, 1985.
NCYC2737	anonymized British brewery ale strain, 1997.
NCYC2776	Saccharomyces cerevisiae, Vaginal isolate from patient recently treated with Clotrimazole, Antwerp, Belgium, 1997.
NCYC2777	Saccharomyces cerevisiae, Vaginal isolate from patient recently treated with Clotrimazole, Antwerp, Belgium, 1997.
NCYC2778	Oral isolate from patient, Antwerp, Belgium.
NCYC2779	Oral swab from patient, Antwerp, Belgium.
NCYC2780	Vaginal swab from symptomless patient, Antwerp, Belgium.
NCYC2798	From mouth of AIDS patient, Germany.
NCYC2855	Wine production strain. CECT 1478 Tokaj22
NCYC2945	Distiller's yeast CBS 1508
NCYC2947	Wine production Bulgaria
NCYC2967	Saccharomyces cerevisiae, isolated from a stool sample in Notingham City Hospital, UK, 2000.
NCYC2974	Human throat UK 2000
NCYC3314	Saccharomyces cerevisiae, isolated from barrel fermentation in Napa Valley, USA, 2005.
NCYC3315
NCYC3318	Saccharomyces cerevisiae, isolated from wine fermentation in Maule Region, Chile, 2005.
NCYC3319	Saccharomyces cerevisiae, isolated from wine fermentation in Maule Region, Chile, 2005.
NCYC3406	anonymized British brewery ale strain, 2006.
NCYC3445
NCYC3447	Saccharomyces cerevisiae, isolated from grapes in Australia, 2007.
NCYC3448	Saccharomyces cerevisiae, isolated from Fruit of Opuntia stricta, Bahamas, 2007.
NCYC3460	Saccharomyces cerevisiae, isolated from Ragi (sake type wine), Japan, 2007.
NCYC3461	Saccharomyces cerevisiae, isolated from nectar of Bertam Palm, Malaysia, 2007.
NCYC3462	Saccharomyces cerevisiae, isolated from nectar of Bertam Palm, Malaysia, 2007.
NCYC3529	Human clinical isolate, from sputum. UK
NCYC3546	Saccharomyces cerevisiae, multi-strains from "Norwegian Kveik yeast blend. Traditional mixed brewing yeast sourced from kveikstokk (yeast log) Vos", 2009. #2 Rivene
NCYC3549	Saccharomyces cerevisiae, multi-strains from "Norwegian Kveik yeast blend. Traditional mixed brewing yeast sourced from kveikstokk (yeast log) Vos", 2009. #2 Rivene
NCYC3552	Saccharomyces cerevisiae, multi-strains from "Norwegian Kveik yeast blend. Traditional mixed brewing yeast sourced from kveikstokk (yeast log) Vos", 2009. #2 Rivene
NCYC3557	Mat a/alpha derivative of DBVPG6040
NCYC3612	Mat alpha derivative of YIIc17_E5
NCYC3630	Mat alpha derivative of Y12
NCYC3997	Single strain isolate from NCYC 3995, Traditional Norwegian Kveik Brewing yeast culture, Voss, Norway. #1 Sigmund
NCYC4063	Traditional Norwegian Kveik Brewing yeast, Hornindal, Norway. #5 Hornindal
NCYC4068	Traditional Norwegian Kveik Brewing yeast, Hornindal, Norway. #5 Hornindal
NCYC4081	Yorkshire Square Stone Type Ale production yeast.

 

[Andre3000]

don't have that much extra time at the moment and that is quite a lot of data

Where's the link to your GoFundMe .

 

[Northern_Brewer]

Where's the link to your GoFundMe .

Yeast people use OnlyFAN...

Don't get your hopes up too high - the NCYC started with brewing yeast, in particular a load of yeast from Whitbread, but in recent years has been more involved with gathering clinical samples from British hospitals, so there's a lot of those in this list.

 

[Northern_Brewer]

There's a new preprint out from the Dunham lab in Seattle that is mostly looking at what happens to yeast genomes as they are repitched, but they also sequenced all the Chicos they could find to get an idea of the background diversity....

There's also a ton of detail on how yeast genomes change over time, but that's another story....

If anybody's interested, Escarpment are holding a webinar with Dunham about the Chico stuff, and in particular its evolution on repitching, tomorrow-evening-ish. Unfortunately it's 1am my time so I will probably pass, but if anybody's interested it's at :
https://www.crowdcast.io/e/mutant-beer-yeast-evolution/register

 

[Northern_Brewer]

I've just come across an interesting paper - random lab guy at brewery doing next-gen sequencing as you do (turns out Matt Cottrell has 89 papers to his name from his former life as a marine microbiologist, this is not his first rodeo) - that is the first published confirmation I've seen that BRY-97 is a Chico. In fact he used interdelta 12/21 to distinguish the 1056 subgroup (including Imperial A07 and Omega OYL-004) from the US-05 subgroup, and BRY-97 grouped with 1056/A07/OYL-004. Which rather supports the idea that "Imperial M44" in the chart above is MJ M44 West Coast, and that the latter is repacked BRY-97. Which kinda fits with previous suspicions based on lag times.

The paper is mostly looking at how repeatable interdeltas are for yeast ID - they work great for WLP001 out to 18 repitchings, but he had some problems with Belle Saison, albeit mostly that seemed to be sequencing problems rather than yeast related.

https://www.tandfonline.com/doi/full/10.1080/03610470.2022.2110645

These do correlate with @isomerization 's 12/21 interdeltas - US-05 is V in slide 3, you can see those clear 4 bands from 200-600bp even if it's not resolving the ones up at ~1300bp. 1.5% gel helps I guess.

In other, completely unrelated news, the first full hop genome - Cascade - was published 2 years ago, they're still polishing it up but it's at :
https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20072https://www.ncbi.nlm.nih.gov/bioproject/PRJNA562558/Project home is at HopBase but it's a bit fragile, lots of it doesn't work for much of the time...

 

[dmtaylor]

@Northern_Brewer Thank you! This is indeed confirmation of our suspicions based on "Imperial M44" and the fact that Mangrove Jack repacks *something*. No updates to my sheet will be necessary, but this bolsters. Good to have someone like you who understands the lab stuff to help interpret, thanks again.

 

[joshbuhl]

There's now an update with a bunch of Wyeast and dry strains, albeit not all of them :
http://beer.suregork.com/?p=4030

Some key points -
S-04 is nothing to do with Whitbread, it's closest to 006 Bedford and 013 London
BRY-97 is absolutely nothing to do with the Chicos but is a distant cousin of S-33/Windsor

I've just come across an interesting paper - ….. that is the first published confirmation I've seen that BRY-97 is a Chico. In fact he used interdelta 12/21 to distinguish the 1056 subgroup (including Imperial A07 and Omega OYL-004) from the US-05 subgroup, and BRY-97 grouped with 1056/A07/OYL-004. Which rather supports the idea that "Imperial M44" in the chart above is MJ M44 West Coast, and that the latter is repacked BRY-97. Which kinda fits with previous suspicions based on lag times.

So, the two papers contradict each other re. BRY-97 is or is NOT a chico? Sorry, don‘t understand much of the nitty gritty of this…

 

[Northern_Brewer]

So, the two papers contradict each other re. BRY-97 is or is NOT a chico?

BRY-97 is a Chico, the early sequencing had some kind of problem with the wrong labels or whatever.

 

[joshbuhl]

BRY-97 is a Chico, the early sequencing had some kind of problem with the wrong labels or whatever.

Ok, thx. And have I read the results correctly that BRY-97 is in fact a much more closely related Chico-Relative than US-05? I in my naivity up until now had believed that US-05 was Chico. My understanding now is that there are several closely related Chico-Siblings, one of which is BRY-97. Is there an „original“ Chico, the Chico?

Cheers!

 

[McMullan]

What difference does it make? A brewer should choose a yeast that produces beer he or she is happy with regardless of its hypothesised genetic ancestry. Even genetically identical (by descent) yeast can behave differently based on how they interact with the environment. So, in theory, two genetically identical yeast cells separated at budding, sent to different breweries and remaining genetically identical (without mutation) could still diverge behaviourally over time, because of heritable non-genetic factors. Epigenetics. If there’s one thing biologists have learnt over the last 20 years or so, it’s how genetics is just one layer of biological organisation, not so much the ‘blueprint’ it was once thought, but more a set of loose guidelines how to build living things, which are clearly more than just genetics.

It’s best to view most of these publications as low-value ‘technical reports’ lacking sufficient scientific integrity to warrant publication in science journals. The published phylogenies are mainly untestable hypotheses beyond low resolution phylogeography. Drilling down into higher resolution analyses, e.g., variants of strains (therefore at least some strains or perhaps all, depending on samples and molecular markers), gets too noisy. Establishing, for example, genetic identity by decent and direction of gene flow, are impossible in most cases and merely fudged by assumptions like ‘the simplest path is correct’. In most cases, without solid independent evidence to support ‘genetic’ conclusions, it borders on pseudoscience and even fantasy feeding biased narratives in the wrong hands. Academic stamp collecting. All that matters really is brewers are happy with the yeast they choose to pitch.

 

[Northern_Brewer]

Ok, thx. And have I read the results correctly that BRY-97 is in fact a much more closely related Chico-Relative than US-05? I in my naivity up until now had believed that US-05 was Chico. My understanding now is that there are several closely related Chico-Siblings, one of which is BRY-97. Is there an „original“ Chico, the Chico?

Stop thinking there's One True Chico. Look at the pictures below which are all of the same person, but which show him with different body sizes, all the cells will have been replaced, some will be genetically mutated compared to the original fertilised egg (notably in his prostate recently), his hair is different - which is the Charles?

So it is with yeast - they evolve and change just through the process of being repitched in a brewery. You can't say that the original ($$$) BRY-96 is "the" Chico - as it had never been anywhere near California when it went into a freezer at Siebel. In as much as there was ever a One True Chico, it existed for a fleeting moment after a few generations of arriving at Sierra Nevada and adapting to the conditions there. But now Sierra Nevada makes their beer with a yeast that has changed since that time.

Yeast are in a state of constant change, sometimes those changes matter to a brewer, often they don't. But changes are inevitable. Brewers try to simplify things for themselves by using names like Chico which don't capture the changes, and marketeers are even worse.

But your One True Chico does not exist. If you want to make a beer like Sierra Nevada's 2024 beers, then harvest yeast from their beer, they condition with the production strain. Assuming BRY-97 is the "Imperial M44" in the family tree above, then it's more closely related to US-05 than either of them are to WLP001 or BRY-96. Whilst I disagree with McMullan on the importance of taxonomy, I would agree with him on this - don't worry so much about the detailed taxonomy, and use the strain that works best for you.

 

[joshbuhl]

Stop thinking there's One True Chico….

But your One True Chico does not exist. …. and use the strain that works best for you.

Cheers NB.

I‘m definitely fine with using what turns out to work best and am not on a quest of the Holy Grail of The One True Chico, rather I‘m at the stage where I‘m just starting to compare same recipe with different yeast strains, and am trying to figure out which one are worth comparing.

My actual yeast quest at the moment is with the London Ale III family, how similar (or different?) Verdant, 1318, London Fog and Imperial Juice actually are, whether it‘s worth trying out the expensive liquid yeasts or if Verdant is „good/simllar enough“ and what the heck is actually in M66. Wouldn‘t happen to have any imput on that, would you?

cheers!

Josh

 

[McMullan]

Whilst I disagree with McMullan on the importance of taxonomy

I’m not questioning the importance of good taxonomy. Quite the opposite. These ‘domesticated’ yeast phylogenies are a fuzzy branch of taxonomy fogged by being artificial populations with insufficient reliable info re sources (and sinks). Therefore the samples are poorly ‘labelled’ regardless of good practices followed in any lab. They’re going to mainly remain untestable hypotheses. Sequencing DNA is easy. And cheap these days. Confirming the hypothetical phylogenies with independent (non-genetic) evidence is the tricky bit in most cases. That’s what good taxonomy is about.

 

[duelerx]

Stop thinking there's One True Chico. Look at the pictures below which are all of the same person, but which show him with different body sizes, all the cells will have been replaced, some will be genetically mutated compared to the original fertilised egg (notably in his prostate recently), his hair is different - which is the Charles?

So it is with yeast - they evolve and change just through the process of being repitched in a brewery. You can't say that the original ($$$) BRY-96 is "the" Chico - as it had never been anywhere near California when it went into a freezer at Siebel. In as much as there was ever a One True Chico, it existed for a fleeting moment after a few generations of arriving at Sierra Nevada and adapting to the conditions there. But now Sierra Nevada makes their beer with a yeast that has changed since that time.

Yeast are in a state of constant change, sometimes those changes matter to a brewer, often they don't. But changes are inevitable. Brewers try to simplify things for themselves by using names like Chico which don't capture the changes, and marketeers are even worse.

But your One True Chico does not exist. If you want to make a beer like Sierra Nevada's 2024 beers, then harvest yeast from their beer, they condition with the production strain. Assuming BRY-97 is the "Imperial M44" in the family tree above, then it's more closely related to US-05 than either of them are to WLP001 or BRY-96. Whilst I disagree with McMullan on the importance of taxonomy, I would agree with him on this - don't worry so much about the detailed taxonomy, and use the strain that works best for you.

View attachment 842984View attachment 842985View attachment 842986View attachment 842987View attachment 842988

Of all the Chicos which one is your favorite?

 

[Franktalk]

My favorite is Chico and the man!

 

[SkiHazy]

Cheers NB.

I‘m definitely fine with using what turns out to work best and am not on a quest of the Holy Grail of The One True Chico, rather I‘m at the stage where I‘m just starting to compare same recipe with different yeast strains, and am trying to figure out which one are worth comparing.

My actual yeast quest at the moment is with the London Ale III family, how similar (or different?) Verdant, 1318, London Fog and Imperial Juice actually are, whether it‘s worth trying out the expensive liquid yeasts or if Verdant is „good/simllar enough“ and what the heck is actually in M66. Wouldn‘t happen to have any imput on that, would you?

cheers!

Josh

Hey Josh, wondering if you have any results to share on the comparison of the London Ale III family. Very interested in this as well. Cheers

 

[joshbuhl]

Hi Ski,

Sorry for the delay in replying..I'm not here very often...

No, my research & brewing have been on hold since february due to a knee replacement surgery, so no further results.

If all this interests you, then you shound check out the "yeastmaster" resource from @dmtaylor as well äs this thread:

https://www.homebrewtalk.com/threads/from-the-lab-family-tree-of-white-labs-yeast.642831

Cheers,

Josh

 

[dmtaylor]

If all this interests you, then you shound check out... this thread:

https://www.homebrewtalk.com/threads/from-the-lab-family-tree-of-white-labs-yeast.642831

Oops, that's a circular reference.

Here is one link that I haven't seen on this thread yet ( ):

http://tinyurl.com/yeastmaster

Josh, I hope all has gone well with your knee replacement. My dad has had both his knees done and after the therapy he is LOVING the results.

 

[rtstrider]

Of all the Chicos which one is your favorite?

At the top of the list would be propped up yeast from Sierra Nevada Pale Ale. It's dog slow to ferment initially though. Second would be WLP001. Wyeast 1056 is closer to US-05 than SNPA or WLP001 on my palate at least. At the end of the day though it's really all about personal preference.

With that said there's a pack of bry-97 laying around here I want to play around with and also want to play around with propping up 3 year old chico (still good as I used another tube of this for a red a few months ago) fermenting something in the 1.040-1.045 range then transfer a Cascade pale ale straight onto the yeast cake and see what happens in regards to fermentation speed.

 

[Northern_Brewer]

New paper from the Schacherer lab in Strasbourg with 3,034 yeast genomes :
https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkae245/7904545

 

[CascadesBrewer]

New paper from the Schacherer lab in Strasbourg with 3,034 yeast genomes :

I only skimmed the paper...it looked pretty dense...are there new strains in here that map to common brewing yeasts?

 

[Northern_Brewer]

I only skimmed the paper...it looked pretty dense...are there new strains in here that map to common brewing yeasts?

Not had a chance to look closely, but I think they were mostly trying to broaden geo/ecological coverage, so probably not a lot of direct relevance to brewing.

 

[dmtaylor]

I only skimmed the paper...it looked pretty dense...are there new strains in here that map to common brewing yeasts?

I took some time tonight (several hours), but I didn't find any big revelations relevant to homebrewers. Very few commercial strains are named in the data, and the ones that are named are just repeats of previous studies by Gallone, Fay, etc. Still, it prompted me to take a deeper look at things, which resulted in a couple tweaks to my table (which weren't really new information but things that I should have incorporated a while ago already). All interesting nonetheless to see how tiny a slice that beer (and wine) are to the Sacch. c species as a whole. I mean, here's the two slices from a big circle of life:

(the darker red clade is "12. Belgium Beer 1"), and

(the yellow super clade is "S2. Beer" which includes most of the yeasts we use today).

One tidbit that is kind of interesting to me is that some of the oddest Belgian yeasts we use (from "12. Belgium Beer 1") are very closely related to the yeasts typically found in...

French cheeses.

That I thought was pretty cool. I wonder if they have some capability of eating lactose? Maybe that's why most of these have such high apparent attenuation in the 90-95% range or thereabouts?

Have a good night, and a good Thanksgiving to those who celebrate.

 

[kmarkstevens]

@dmtaylor can you share a link to the magnum opus yeast strain spreadsheet you have been carefully cultivating and confirming for the past several years (decades?) ?

 

[dmtaylor]

@dmtaylor can you share a link to the magnum opus yeast strain spreadsheet you have been carefully cultivating and confirming for the past several years (decades?) ?

Since 2019.

YEAST MASTER Perma-Living by Yours Truly