Changes

'''Saccharomyces''Saccharomyces' is considered a yeast, although this term is historical and ill-defined. ''Saccharomyces'' is a genus of fungus including many species. The distinct species of ''Saccharomyces'' are revised frequently as more research is done. All species are unicellular and capable of fermentation. ''Saccharomyces cerevisiae'' is the most well-known species of yeast. It is used in the fermentation of beer, wine, and sake, and as a leavening agent in bread. It is commonly referred to as "ale yeast", "wine yeast" (see [[Saccharomyces#Killer_Wine_Yeast|Killer Wine Yeast]] below), or "bread yeast". ''S. pastorianus'', known as lager yeast, is a hybrid closely related to ''S. cerevisiae'' but is not a true species. ''S. cerevisiae'' is commonly studied as a model organism and was the first eukaryote to have its genome entirely sequenced. In rare cases, ''Saccharomyces'' can form a [[pellicle]].

''Saccharomyces cerevisiae'' is the type species of the genus ''Saccharomyces'', although ''Saccharomyces paradoxus''and is well-known and highly studied. it is used in industrial production of baking and fermentation as well as bioenergy and biomedical fields. Wholke-genome sequencing was completed in 1996, and since then the body of scientific knowledge on the species of ''S. cerevisiae's'' closest relative, is likely older and more globally ubiquitous higher than any other eukaryotic system. More recently, whole-genome sequencing has also been performed on other species of ''S. cerevisiaeSaccharomyces''. , which has resulted in models for studies on population genomics, as well as insight into the evolution of this genus <ref>ref needed<[https://academic.oup.com/femsyr/article/20/3/foaa013/ref> Many previously recognized species 5810663 Haya Alsammar, Daniela Delneri, An update on the diversity, ecology and biogeography of the Saccharomyces have been consolidated or reassigned to another genus, commonly ''Zygosaccharomyces''FEMS Yeast Research, Volume 20, Issue 3, May 2020, foaa013, https://doi.org/10.1093/femsyr/foaa013.]</ref>.  Species of ''Saccharomyces'' other than ''S. cerevisiae'' (and only certain strains of ''S. cerevisiae'') are generally unable to efficiently ferment maltotriose, although some can ferment maltose (such as ''S. eubayanus'') <ref name="Cubillos_2019">[https://onlinelibrary.wiley.com/doi/10.1002/yea.3380 Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. F.A. Cubillos, B. Gibson, N. Grijalva‐Vallejos, K. Krogerus, J. Nikulin. 2019. DOI: https://doi.org/10.1002/yea.3380.]</ref>.

* [https://www.youtube.com/channel/UCEyCSmOUfkp_QPH1PClAxVQ/videos Escarpment Labs video presentations on yeast basics] and [https://www.youtube.com/watch?v=d5TFluCM3_4 Why do yeast cells need oxygen? | Yeast Basics 2: Lecture 1].

** [https://www.nature.com/articles/s41586-018-0030-5 Genome evolution across 1,011 Saccharomyces cerevisiae isolates, by Peter et al (2018), which indated indicated that domestication of yeast might have begun in Asia.] See also [https://www.theatlantic.com/science/archive/2018/04/yeast-sequencing-china/557930/ this article] and the [https://www.facebook.com/groups/MilkTheFunk/permalink/2056777254350478/ associated MTF thread].** [https://www.nature.com/articles/s41586-020-2889-1 A yeast living ancestor reveals the origin of genomic introgressions.] ''From Dr. Bryan Heit:'' "This study may interest some here. A lot of yeast evolution is driven by introgression - interspecies hybridization which gets "cleaned up" by back-crosses with one of the parental species (but leaving pieces of the other parental species genome behind). But it's always been a bit of a mystery of how these hybrids can back-cross, since these hybrids are usually unable to reproduce sexually. These scientists found a '''living''' ancestor of a hybrid between ''S. cereveseacerevisiae'' and ''S. paradoxus'' that gave rise to many modern ''S. cereveseacerevisiae'' strains, and may have figured out how it regained the ability to reproduce with its parental species <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/4055441394484044 Dr. Bryan Heit. Milk The Funk post on a new study that found a living ancestor of a hybrid between ''S. cereveseacerevisiae'' and ''S. paradoxus'' that gave rise to many modern ''S. cereveseacerevisiae'' strains. 11/12/2020.]</ref>."** [https://www.sciencedaily.com/releases/2019/03/190305153648.htm Modern beer yeast emerged from mix of European grape wine, Asian rice wine yeast, by Science Daily. The two explanations of beer yeast ancestry are: beer yeasts might have evolved from a mix of European wine strains and Asian fermentation strains during trade on the Silk Route, as well as an unknown ancestor. The second explanation is that European wine strains themselves descended from Asian strains (whether European wine strains desceneded descended from Asia or were developed in Europe has not been clear and needs more research).]

** [https://www.nature.com/articles/s41559-019-0998-8 Fermentation innovation through complex hybridization of wild and domesticated yeasts] - Hittinger lab sequencing of commercial and homebrew strains of yeast, analysing analyzing their hybrid species makeup using WGS.

Various other yeast species have the ability to produce toxins that effect a range of other yeasts (but generally not bacteria), including species from the genera ''Candida'', ''Cryptococcus'', ''Debaryomyces'', ''Hanseniaspora'', ''Hansenula'', ''Kluyveromyces'', ''Metschnikowia'', ''Pichia'', ''Ustilago'', ''Torulopsis'', ''Williopsis'', ''Zygosaccharomyces'', ''Aureobasidium'', ''Zygowilliopsis'', and ''Mrakia'' <ref name="Buyuksirit">[http://waset.org/publications/9999528/antimicrobial-agents-produced-by-yeasts Antimicrobial Agents Produced by Yeasts. T. Buyuksirit, H. Kuleasan. 2014.]</ref><ref name="Stewart_2018" />. For example, strains of the yeast species ''Candida pyralidae'' <ref name="Buyuksirit"></ref>, ''Wickerhamomyces anomalus'', ''Kluyveromyces wickeramii'', ''Torulaspora delbrueckii'' and ''Pichia membranifaciens'' have been found to produce toxin that inhibits ''Brettanomyces'' <ref name="Ciani_2016">[https://www.researchgate.net/publication/301581233_Yeast_Interactions_in_Inoculated_Wine_Fermentation Yeast Interactions in Inoculated Wine Fermentation. Maurizio Ciani, Angela Capece, Francesca Comitini, Laura Canonico, Gabriella Siesto and Patrizia Romano. 2016.]</ref><ref>[https://www.mdpi.com/1422-0067/24/2/1309 Agarbati A, Ciani M, Esin S, Agnolucci M, Marcheggiani F, Tiano L, Comitini F. Comparative Zymocidial Effect of Three Different Killer Toxins against Brettanomyces bruxellensis Spoilage Yeasts. International Journal of Molecular Sciences. 2023; 24(2):1309. https://doi.org/10.3390/ijms24021309 .]</ref>. In addition, the toxin produced by ''Wickerhamomyces anomalus'' and ''Williopsis markii'' have been found to inhibit a wide range of spoilage and pathogenic fungi <ref name="Hatoum2012"></ref>. Killer strains of ''S. cerevisiae'' and other yeast can occur naturally in the wild on fruit and can have a negative impact on other flora that are found in the same environment <ref name="Buyuksirit"></ref>. Strains of ''Torulaspora delbrueckii'' have been shown to kill killer strains of ''S. cerevisae'' (wine strains), as well as to kill ''Pichia'' species <ref name="Ciani_2016"></ref>. The occurrence of killer strains of yeast in the wild is also wide spread. For example, out of 210 yeasts from various genera isolated from molasses, 13 of them were killer strains. Out of 1,000 isolates of various ''Candida'' species isolated from human skin, 52 were killer strains. Out of 65 strains of various yeasts isolated from fermented foods, soil samples, and spoiled fruits/vegetables, 12 were killer strains <ref name="Bajaj_2017" />. It has been hypothesized that toxin production is ubiquitous throughout nearly all genera of yeast; the more studies that have been done on a particular genus of yeast, the more likely it is that toxin production has been found by species and strains within that genus. Yeasts that produce toxins have been found on every continent and in every natural habitat of yeast, including leaf surfaces, leaf litter, tree slime fluxes, fruits, cactus stems and cladodes, insect guts, mammal feces, leaf-cutting ant nests, lake water, ocean sediment, soil, wine, bakeries, and dairy products <ref name="Boynton_2019" />.

Scientists have used genetic modification to create ''S. cerevisiae'' strains that produce various killer toxins that can assist in completing fermentation in the baking, wine, distillation, and beer making processes. These yeasts are able to inhibit undesired yeast contaminants, preventing various off-flavors and other unwanted characteristics in the finished products. Ale and lager strains that have been modified to release these toxins have reportedly retained the positive fermentation and flavor characteristics of the original strains <ref name="Bajaj_2017" />. Branco et al. (2017 and 2019) discovered several strains of ''S. cerevisiae'' that excrete a biocin toxin that is active against several other genera of yeast, including ''Brettanomyces bruxellensis''. The toxin is composed of peptides derived from the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is a protein that serves many different roles in different species of microbes and animals. This toxin is produced by some strains of ''S. cerevisiae'' as they enter the stationary phase after primary fermentation. However, the amount of the toxin needed to inhibit ''B. bruxellensis'' was 10 times the amount that is produced naturally during fermentation. The researchers later genetically modified a strain of ''S. cerevisiae'' to over-produce the toxin, which they named "saccharomycin", at levels required to completely inhibit ''B. bruxellensis'' when co-pitched at a 1:1 ratio (10^5 cells/ml for both). This toxin was also reported to be highly active against ''Hanseniaspora guilliermondii'', ''Kluyveromyces marxianus'', ''Lactobacillus thermotolerans'' (inhibited at 250 μg/ml of toxin), while inhibition of ''Torulaspora delbrueckii'' and ''B. bruxellensis'' required very high amounts of the toxin (500 μg/ml and 1000-2000 μg/ml) <ref>[https://link.springer.com/article/10.1007%2Fs00253-016-7755-6 Antimicrobial properties and death-inducing mechanisms of saccharomycin, a biocide secreted by Saccharomyces cerevisiae. Patrícia Branco, Diana Francisco, Margarida Monteiro, Maria Gabriela Almeida, Jorge Caldeira, Nils Arneborg, Catarina Prista, Helena Albergaria. 2017. DOI: 10.1007/s00253-016-7755-6.]</ref><ref>[https://link.springer.com/article/10.1007/s00253-019-09657-7 Biocontrol of Brettanomyces/Dekkera bruxellensis in alcoholic fermentations using saccharomycin-overproducing Saccharomyces cerevisiae strains. Patrícia Branco, Farzana Sabir, Mário Diniz, Luísa Carvalho, Helena Albergaria, Catarina Prista. 2019.]</ref>. They later demonstrated that using 1.0 mg/mL of saccharomycin with 25 mg/L of SO₂ in grape must fermentation completely eliminated ''B. bruxellensis'' <ref>[https://www.mdpi.com/2076-2607/9/12/2528#cite Branco P, Coutinho R, Malfeito-Ferreira M, Prista C, Albergaria H. Wine Spoilage Control: Impact of Saccharomycin on Brettanomyces bruxellensis and Its Conjugated Effect with Sulfur Dioxide. Microorganisms. 2021; 9(12):2528. https://doi.org/10.3390/microorganisms9122528]</ref>.

* [https://www.homebrewtalk.com//forum/threads/from-the-lab-wine-yeast-pof-and-killer-status.648095/ List of killer strains as well as phenol production (4VG and 4VP) in various wine yeasts, compiled from a scientific study Hisamoto et al. (2010).]

Cheaper methods of doing PCR are recently becoming available, and could help breweries with smaller budgets sufficiently detect this as a contaminant (see [[Laboratory_Techniques#PCR.2FqPCR|PCR Lab Techniques]]). A recent study used agar plates with 15 g/L^-1 of starch as the only nutrient with 40 mg/L^-1 bromophenol blue in anaerobic conditions to detect the fermentation of starch (a pH drop from 5.2 to 4.6-3.0 will change the color of the agar plate to blue/violet). For some of the slower growing strains, 14 days were required to verify that they were ''STA1+'' while other strains grew as quickly as two days and most strains grew after five days. The yeast cells had to be thoroughly washed of all other carbohydrate material and starved in order to avoid false positives. Using dextrin agar plates instead of starch also led to false positives <ref name="Meier-Dörnberg_2018" />. This starch media has been recommended by Richard Preiss from [[Escarpment Laboratories]] and Justin Amaral from [[Mainiacal Yeast]] <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/2149139905114212/?comment_id=2150763631618506&comment_tracking=%7B%22tn%22%3A%22R%22%7D Richard Preiss and Justin Amaral. Milk The Funk Facebook thread on plate media for diastatic ''cerevisiae''. 06/26/2018.]</ref>. Note that diastatic ''S. cerevisiae'' cells look the same under a microscope as regular ''S. cerevisiae'', so cell morphology is not an effective way to identify ''STA1+'' strains <ref name="Begrow_MBAA">[https://www.mbaa.com/education/webinars/Pages/webcast.aspx?vid=diastaticus Wade Begrow. "S. cerevisiae var. diasttaicus". MBAA webinar. July 2018.]</ref> (~8 minutes in). Other methods of detection include using a Durham tube/fermentation tube test to see if the beer produces CO² after fermentation, although this method does not identify the cause of the additional fermentation <ref name="Begrow_MBAA" /> (~18 mins in). More recently, Krogerus et al. (2019) developed more precise PCR primers to detect ''STA1'' active, ''STA1'' non-active, and non-''STA1'' based on their discovered role of an ''STA1'' promoter called ''1162 bp'' that is required for the ''STA1'' gene to be effective at producing the glucoamylase enzyme, however, PCR and qPCR have limited detection rates of 10^-4 and 10^-5 cells (see [http://beer.suregork.com/?p=4068 this Suregork Loves Beer blog post] and [https://www.facebook.com/groups/MilkTheFunk/permalink/2697088176986046/ this MTF thread posted by Kristoffer Krogerus]). Detection of ''STA1+'' strains of ''S. cerevisiae'' as a contaminant can be difficult. While using PCR to detect the ''STA1'' gene and the promoter gene, the presence of the promoter gene alone does not completely explain the wide variance of diastatic power between strains. Additionally, PCR genotyping is sucseptable to user error or DNA detection from dead cells. Detection of the presence of starch degrading enzymes can come from other contaminants such as ''Brettanomyces'' <ref name="Omega_diastaticus_2020" />. Some agar media products and even starch/dextrin materials have been suspected to contain small amounts of glucose or other simple sugar contaminants that can support the growth of non-diastatic yeasts <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/3308119659216225/ Lance Shaner and Joshua Mayers. Milk The Funk Facebook thread on Omega Yeast's STA1+ detection methods. 03/04/2020.]</ref>. [[Omega Yeast Labs]] reported that a slight alteration to the classic LCYM media recipe had significantly more reliable detection than classic LCYM and the proprietary Weber diastatic agar for all ''STA1+'' strains in Omega's collection, including detecting slow growing strains within 2-3 days and strains with the non-active promoter genes as per Krogerus et al (2019) and limited false positives. See [[Laboratory_Techniques#Saccharomyces|''Saccharomyces'' agar plates]] for the recipe and [https://www.facebook.com/groups/MilkTheFunk/permalink/2874530432575152/ this MTF thread] by Laura Burns from Omega Yeast Labs, as well as their [https://omegayeast.com/news/improved-functional-assays-and-risk-assessment-for-sta-strains-of-saccharomyces-cerevisiae associated peer reviewed study on recommended detection methods)] <ref>[https://www.tandfonline.com/doi/full/10.1080/03610470.2020.1796175 Laura T. Burns, Christine D. Sislak, Nathan L. Gibbon, Nicole R. Saylor, Marete R. Seymour, Lance M. Shaner & Patrick A. Gibney (2020) Improved Functional Assays and Risk Assessment for STA1+ Strains of Saccharomyces cerevisiae, Journal of the American Society of Brewing Chemists, DOI: 10.1080/03610470.2020.1796175 .]</ref>. A summary of the Omega Yeast Lab detection methodology findings by Lance Shaner is available [https://www.facebook.com/groups/MilkTheFunk/permalink/3308119659216225/ here on MTF]. Escarpment Labs built upon the work by Burns et al. and developed a modified version of the Omega LCYM, and they reported it to have less false positives for non-diastatic strains and it has reportedly been used for growing beer strains of ''Brettanomyces'' and ''Pichia''. See the [[Laboratory_Techniques#Saccharomyces|Escarpment SCCM media]].

Detection of ''STA1+'' strains of ''S. cerevisiae'' as a contaminant can be difficult. While using PCR to detect the ''STA1'' gene and the promoter gene, the presence of the promoter gene alone does not completely explain the wide variance of diastatic power between strains. AdditionallyIn 2022, PCR genotyping is sucseptable to user error or DNA detection from dead cells. Detection of the presence of starch degrading enzymes can come from other contaminants such as ''Brettanomyces'' <ref name="Omega_diastaticus_2020" />. Some agar media products Ida Uotila and even starch/dextrin materials have been suspected to contain small amounts of glucose or other Kristoffer Krogerus developed a simple sugar contaminants that can support the growth of non-diastatic yeasts <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/3308119659216225/ Lance Shaner and Joshua Mayers. Milk The Funk Facebook thread on Omega Yeast's STA1+ detection methods. 03/04/2020.]</ref>. [[Omega Yeast Labs]] reported technique that a slight alteration to the classic LCYM media recipe had significantly more reliable detection than classic LCYM only requires basic lab equipment (pipettes, centrifuge, and the proprietary Weber diastatic agar for all ''STA1+'' strains heat block), gives results from beer or yeast samples in Omega's collection75 minutes, including detecting slow growing strains within 2-3 days and strains with the nonaccuracy as good as traditional PCR-active promoter genes as per Krogerus et al (2019) and limited false positivesbased methods. See [[Laboratory_Techniques#Saccharomyces|''Saccharomyces'' agar plates]] for the recipe and [https://wwwThe test result can be visualized on a lateral flow strip.facebook.com/groups/MilkTheFunk/permalink/2874530432575152/ this MTF thread] by Laura Burns from Omega Yeast LabsFor more information, as well as their [https://omegayeast.com/news/improved-functional-assays-and-risk-assessment-for-sta-strains-of-saccharomyces-cerevisiae associated peer reviewed study on recommended detection methods)] <ref>see [https://www.tandfonlinebiorxiv.com/doiorg/fullcontent/10.10801101/036104702022.202011.1796175 Laura T23. Burns, Christine D. Sislak, Nathan L. Gibbon, Nicole R. Saylor, Marete R. Seymour, Lance M. Shaner & Patrick A. Gibney 517627v1 their published paper] (2020) Improved Functional Assays and Risk Assessment for STA1+ Strains of Saccharomyces cerevisiae, Journal of the American Society of Brewing Chemists, DOI: 10.1080/03610470.2020.1796175 .]</ref>. A summary of the Omega Yeast Lab detection methodology findings by Lance Shaner is available [https://www.facebook.com/groups/MilkTheFunk/permalinkposts/3308119659216225/ here on 6360775983950562 associated MTFthread]).

It was first isolated and described in 2011 growing within ''Nothofagus'' trees in Patagonia, Argentina. Since then, strains of this species have also been found in cold regions across the globe, including Tibet, China, the United States, Chile, and New Zealand. It has also been isolated from the wild in Ireland <ref>[https://academic.oup.com/femsyr/article/22/1/foac053/6874782 Sean A Bergin, Stephen Allen, Conor Hession, Eoin Ó Cinnéide, Adam Ryan, Kevin P Byrne, Tadhg Ó Cróinín, Kenneth H Wolfe, Geraldine Butler, Identification of European isolates of the lager yeast parent Saccharomyces eubayanus, FEMS Yeast Research, Volume 22, Issue 1, 2022, foac053, https://doi.org/10.1093/femsyr/foac053.]</ref>. ''S. eubayanus'' has been described as being cold-tolerant, and can grow between 4–25°C. It has been suggested that this trait was inherited by lager yeast.

For a long time the origins of the hybrid were unknown and were postulated to be a hybrid between ''S. cerevisiae'' and ''S.uvarum'', or ''S. cerevisiae'' and ''S.bayanus''. Recent work eg. Libkind et al 2011 proved that the hybridisation was between ''S. eubayanus'', which had been recently found in South America and ''S. cerevisiae'' <ref name="libkind_2011" />. Further work points to a Tibetan lineage of ''S.eubayanus'' being the most likely from those discovered in the wild so far <ref name="bing_2014" /> (see also [https://www.facebook.com/groups/MilkTheFunk/posts/6399366356758191/?comment_id=6399963343365159 this MTF post]). It is hypothesized that the hybridization event occurred in a Bavarian brewery (Hofbräuhaus in Munich has been proposed as the most likely site for the hybridization event) in the 16th century by the chance interaction of ''S. eubayanus'' with ale yeast; however, an alternative hypothesis is that bottom-fermentation with ''S. eubayanus'' was in practice before lager yeast was created <ref>[https://academic.oup.com/femsyr/article/doi/10.1093/femsyr/foad023/7142826 Mathias Hutzler, John P Morrissey, Andreas Laus, Franz Meussdoerffer, Martin Zarnkow, A new hypothesis for the origin of the lager yeast Saccharomyces pastorianus, FEMS Yeast Research, Volume 23, 2023, foad023, https://doi.org/10.1093/femsyr/foad023.]</ref>.

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===[[Bootleg Biology]]/[[Spot Yeast]]===

===[[Jasper Yeast LLC]]===

| JY029 JY008 - Saint Nicholas, Belgian Wit Ale I || Hoegaarden Poperinge, Belgium || 70-77 78 || Low Med-High || 6368-76 78 || Spicy he yeast is very fruity and phenolicdoes well on a wide range of temperatures. At the lower temperatures maltiness comes more forward, with a nice estery finishand at the higher range yeast esters are more pronounced. <ref name="Jasper_Yeast">[https://jasperyeast.com/yeast/belgian "Belgian Yeast Strains". Jasper Yeast Website. Great for witbier]</ref>|-| JY011 - Belgian Ale II || Antwerp, Grand CruBelgium || 73-78 || Med-High || 62-style wit 74 || Rumored to originate from a famous brewery in Antwerp. Comparatively clean and specialty beersversatile. Produces less aromatics than other Belgian Stylesyeasts, mainly and is therefore more suited for malt-driven beers and Belgian Wit and Grand-Crustyle pale ales, but does well in Blondestill carries the Belgian aromatic flair. <ref name="Jasper_Yeast" />|-| JY027 - Belgian Ale V, Scourmont || Belgium || 76-81 || Med-High || 62-74 || Trappist yeast from one of the six Trappist breweries from Belgium. Strong fruity esters at elevated fermentation temperatures, Belgian Tripel but more subdued and Specialtyspicy at lower fermentation temperatures. <ref name="Jasper_Yeast" />

===[[Mainiacal Yeast]](CLOSED)===

Homebrew Methods# [https://suigenerisbrewing.com/index.php/2022/09/20/optimizing-yeast-starters/ "Optimizing Yeast Starters" by Dr. Bryan Heit.]