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[[File:Long_Fermentation.jpg|thumb|upright=2.5|Conceptual graph of traditional microbe and wort dynamics|Conceptual graph of traditional souring microbe and wort dynamics. Y-axis for each microbe group depicts relative activity which combines in a conceptual sense: growth, acidification of wort, attenuation and production of flavor compounds. Plot drawn by Drew Wham based on concepts discussed in American Sour Beer <ref> Tonsmeire, M. (2014). American Sour Beers. Brewers Publications </ref> and Wild Brews <ref> Sparrow, J. (2005). Wild Brews: Beer Beyond the Influence of Brewer's Yeast. Brewers Publications</ref> . ]]
====Primary Fermentation====
Primary fermentation by ''Saccharomyces'' is generally conducted in the same way for a sour beer as for a non-sour beer. Depending on the intended final result the brewer might select a neutral ale strain (WLP 001/Wyeast 1056, WLP036/Wyeast 1007) to provide a neutral background for the souring microbes to act on. Alternatively, the brewer may use a Belgian strain or a saison/farmhouse strain (see ''[[Saccharomyces]]'' page for a comprehensive list) to increase the ester and/or phenol characters of the beer which can then be acted on by ''[[Brettanomyces]]''. Primary fermentation with ''Saccharomyces'' also tends to lend to more glycerol production which increases the beer's mouthfeel (''Brettanomyces'' generally does not produce much glycerol <ref>[http://www.milkthefunk.com/wiki/Brettanomyces#Secondary_Metabolites Brettanomyces; Secondary Metabolites. MTF Wiki. Retrieved 06/23/2016]</ref>). However, the role of glycerol in creating mouthfeel is debatable in the wine world <ref>[https://www.winesandvines.com/features/article/68760 Tim Patterson. "Many Roads to Mouthfeel". Wines & Vines Magazine. Nov 2009. Retrieved 03/23/2018.]</ref>.This primary fermentation can take place in any vessel suitable for a normal ''Saccharomyces'' fermentation. As always fermentation temperature control is of critical importance and temperature profiles for this fermentation step should match those suggested for the strain of ''Saccharomyces'' selected for this step. Once active fermentation has subsided the mostly attenuated wort can then be moved on to the secondary fermenting vessel. There is some variation in common practice as to whether or not the primary fermentation yeast should be carefully settled out, moving over bright clear beer only, or if un-settled cloudy high yeast population wort is moved to the secondary vessel. New Belgium moves their lager primary fermented beer after centrifuging, indicating that this centrifuged beer exhibits cleaner characters from secondary fermentation faster than un-centrifuged beer, allowing the resulting sour beer to be ready for packaging more quickly <ref> The Sour Hour Episode 2 with Lauren Salazar from New Belgium Brewing Company ].</ref>. Concerns of yeast autolysis, however, have generally been minimized by most brewers (see [[Mixed_Fermentation#Secondary_Fermentation|Secondary Fermentation]]).
During both primary and secondary fermentation, a complex set of interactions occurs between the various yeast and bacteria species. Much of this is as yet unknown scientifically. For example, the production of [[Lactic Acid|lactic acid]] by lactic acid bacteria not only stresses and limits growth of ''S. cerevisiae'', but it can also turn off "glucose repression", meaning that instead of consuming simple sugars first, ''S. cerevisiae'' stops choosing which sugar types to consume first and consumes all sugar types indiscriminately. This can result in under-attenuation problems in the short run, but also more residual sugars for ''Brettanomyces'' (see [[Lactic Acid|lactic acid]] for details). Another example is that co-fermenting with brewer's yeast and ''Lactobacillus'' can create a different flavor profile than if they are staggered with a kettle souring method (see [[Lactobacillus#Effects_on_Mixed_Fermentation|effects of ''Lactobacillus'' on mixed fermentation]]). Another example is that some studies support that in nitrogen rich substrates, ''S. cerevisiae'' will synthesize simpler amino acids from the more complex nitrogen sources, and those amino acids contribute to the sustained survival of both ''Lactobacillus'' and ''Brettanomyces'' in the more stressful, post-fermentation environment <ref>[https://academic.oup.com/femsyr/article-abstract/17/4/fox018/3867021/The-influence-of-Dekkera-bruxellensis-on-the?redirectedFrom=fulltext The influence of Dekkera bruxellensis on the transcriptome of Saccharomyces cerevisiae and on the aromatic profile of synthetic wine must. Janez Kosel Neža Čadež Dorit Schuller Laura Carreto Ricardo Franco-Duarte Peter Raspor. 2017.]</ref><ref>[http://www.sciencedirect.com/science/article/pii/S2405471217303903?via%3Dihub Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow. Olga Ponomarova, Natalia Gabrielli, Daniel C.Sévin, Michael Mülleder, Katharina Zirngibl, Katsiaryna Bulyha, Sergej Andrejev, Eleni Kafkia, Athanasios Typas, Uwe Sauer, Markus Ralser, Kiran Raosaheb Patil. 2017.]</ref> (see also [https://www.facebook.com/groups/MilkTheFunk/permalink/1856920997669439/ this MTF thread]).