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===Brettanomyces===
Although the exact pathway is not known in for ''Brettanomyces'' (several are proposed), the conditions for THP production are well documented. ATHP is produced by metabolizing the amino acid L-lysine or D-lysine <ref name="Grbin_2007" />, along with ethanol and a glucose or fructose molecule. Iron is also needed for THP production, although its exact role in biosynthesis is not known <ref name="Snowdon"></ref>. As with other amino acids, lysine is taken up by ''Saccharomyces'' during fermentation, and then released after fermentation. Levels of lysine fluctuate slightly throughout fermentation, but are generally high throughout a beer's lifetime (including after fermentation) <ref>[http://link.springer.com/article/10.1385/CBB:46:1:43 The α-aminoadipate pathway for lysine biosynthesis in fungi. Hengyu Xu, Babak Andi, Jinghua Qian, Ann H. West , Paul F. Cook. Sept 2006.]</ref><ref>[http://pubs.acs.org/doi/abs/10.1021/bi9829940 Lysine Biosynthesis in Saccharomyces cerevisiae: Mechanism of α-Aminoadipate Reductase (Lys2) Involves Posttranslational Phosphopantetheinylation by Lys5. David E. Ehmann , Amy M. Gehring , and Christopher T. Walsh. 1999.]</ref><ref>[http://onlinelibrary.wiley.com/doi/10.1002/j.2050-0416.2007.tb00249.x/abstract Elucidation of the Role of Nitrogenous Wort Components in Yeast Fermentation. C. Lekkas, G.G. Stewart, A.E. Hill, B. Taidi and J. Hodgson. May 2012.]</ref><ref>[http://www.sciencedirect.com/science/article/pii/S0308814699000710 Proteins and amino acids in beers, their contents and relationships with other analytical data. S. Gorinstein, M. Zemsera, F. Vargas-Albores, J-L. Ochoa, O. Paredes-Lopez, Ch. Scheler, J. Salnikow, O. Martin-Belloso, S. Trakhtenberg. 1999.]</ref>. Wheat generally has a slightly lower amount of lysine than barley, and oats have a slightly higher amount of lysine than barley <ref>[http://www.aaccnet.org/publications/cc/backissues/1983/Documents/chem60_461.pdf Amino Acid Composition of Six Grains and Winter Wheat Forage. Morey, D.D. 1983.]</ref><ref>[https://diy.soylent.com/ingredients/oats "Oats". DIY Soylent website. Retrieved 02/07/2017.]</ref><ref>[https://diy.soylent.com/ingredients/barley-malt-flour "Barley malt flour". DIY Soylent website. Retrieved 02/07/2017.]</ref><ref>[https://diy.soylent.com/ingredients/wheat-flour-wholegrain "Wheat flour, whole-grain". DIY Soylent website. Retrieved 02/07/2017.]</ref>. In red wine, yeast autolysis releases many amino acids including lysine (aging beer on trub and its effects on THP production has not been studied, but it might be a factor in beer as well) <ref>[http://oeno-one.eu/article/view/974 New trends on yeast autolysis and wine ageing on lees: a bibliographic review. Caroline Fornairon-Bonnefond, Carole Camarasa, Michel Moutounet, Jean-Michel Salmon. 2002.]</ref>.
Oxygen plays a key role and has a stimulatory effect in ATHP and ETHP production (particularly ATHP), but its exact role is not understood. It has been speculated that since ATHP production is associated with ''Brettanomyces'' growth, and ''Brettanomyces'' grows better under aerobic conditions, that this is why more ATHP is produced under aerobic conditions <ref>[http://www.brettanomycesproject.com/dissertation/introduction/ Yakobson, Chad. The Brettanomyces Project; Introduction. Retrieved 3/10/2015.]</ref><ref name="Grbin_2007">[http://pubs.acs.org/doi/abs/10.1021/jf071243e The Role of Lysine Amino Nitrogen in the Biosynthesis of Mousy Off-Flavor Compounds by Dekkera anomala. Paul R. Grbin, Markus Herderich, Andrew Markides, Terry H. Lee, and Paul A. Henschke. J. Agric. Food Chem., 2007.]</ref><ref name="Oelofse">[http://scholar.sun.ac.za/handle/10019.1/8437 Significance of Brettanomyces and Dekkera during Winemaking: A Synoptic Review. A. Oelofse, I.S. Pretorius, and M. du Toit. 2008.]</ref>. It has also been hypothesized that oxygen may have a direct effect on the THP molecules themselves <ref name="Snowdon"></ref>. ATHP production was also shown to increase when anaerobically precultured cells were transferred to an aerobic environment, indicating that oxygen has a direct role on the production of ATHP, not just a byproduct of ''Brettanomyces'' growth <ref name="Snowdon"></ref>. Limiting oxygen exposure during kegging/force carbonating is recommended for helping to reduce ATHP production; even very small amounts can have an effect (although the exact threshold of how much oxygen is required has not been determined). For example, the purity of the CO<sup>2</sup> supply should thus be taken into consideration when force carbonating. At 0.5% impurity (the impurity is air, 1/5 of which is oxygen) and at 2 volumes of CO<sup>2</sup>, ~1,420 ppb of O<sup>2</sup> would be added to the packaged beer, which is an exceedingly high amount of oxygen. The CO<sup>2</sup> supply should ideally be 99.990% pure or better (this would introduce 46 ppb of oxygen at 2 volumes of CO<sup>2</sup>). The method that the CO<sup>2</sup> is added can also determine how much oxygen is introduced into the packaged beer. Sparging CO<sup>2</sup> (bubbling it through the beer) dissolves significantly less oxygen due to Henry's Law (see reference), while injecting (flushing) dissolves significantly more oxygen <ref>[https://tapintohach.com/2014/01/27/how-the-purity-of-sparged-carbon-dioxide-affects-the-oxygen-concentration-of-beer/ How the Purity of Sparged Carbon Dioxide Affects the Oxygen Concentration of Beer. Tap Into Hach blog. 01/24/2014. Retrieved 06/29/2017.]</ref><ref>[https://tapintohach.com/2013/12/02/how-the-purity-of-injected-carbon-dioxide-affects-the-oxygen-concentration-of-beer/ How the Purity of Injected Carbon Dioxide Affects the Oxygen Concentration of Beer. Tap Into Hach blog. 12/02/2013. Retrieved 06/29/2017.]</ref>. Vessel purging methods with CO<sup>2</sup> are also less efficient than some might expect, and might still leave enough oxygen behind to stimulate THP production (see [http://www.homebrewtalk.com/showpost.php?p=8004741&postcount=3 this HomebrewTalk thread]). Pitching fresh ''Saccharomyces'' at bottling/kegging time and naturally carbonating the beer with sugar has reportedly reduced mousy off-flavor detection, perhaps because ''Saccharomyces'' metabolizes both the oxygen and sugar faster than ''Brettanomyces''. Different strains of ''S. cerevisiae'' might be more efficient than others at helping reduce THP. For example, Mitch Ermatinger from Speciation Artisan Ales anecdotally observed that switching from CBC1 conditioning yeast to EC1118 reduced THP off-flavors from 1 month to two weeks <ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/1839193092775563/?comment_id=1839266972768175&reply_comment_id=1839402709421268&comment_tracking=%7B%22tn%22%3A%22R7%22%7D Mitch Ermatinger. Milk The Funk Facebook group post on THP reduction using CBC1 and EC1118. 10/03/2017.]</ref> (see [[Packaging#Re-yeasting|Packaging]] for details on re-yeasting at packaging time).
[[File:THP path bacteria.JPG|thumbnail|right|[http://pubs.acs.org/doi/abs/10.1021/jf020341r Proposed pathway of APY and ATHP by ''L. hilgardii'' by Costello and Henschke (2002).]]]
Heterofermentative [[Lactobacillus]] spp., particularly ''L. hilgardii'' and ''L. brevis'', as well as ''Leuconostoc oeni'' <ref name="Grbin_1996" />, can also produce high levels of ATHP and APY from L-lysine/L-ornithine, ethanol (must be present), and iron. A strain of ''L. plantarum'' (L11a) was shown to produce relatively low amounts. L-lysine stimulates production of ATHP, and L-ornithine stimulates the production of APY <ref name="Costello">[http://pubs.acs.org/doi/abs/10.1021/jf020341r Mousy Off-Flavor of Wine: Precursors and Biosynthesis of the Causative N-Heterocycles 2-Ethyltetrahydropyridine, 2-Acetyltetrahydropyridine, and 2-Acetyl-1-pyrroline by Lactobacillus hilgardii DSM 20176. Peter J. Costello and Paul A. Henschke. 2002.]</ref><ref>[http://www.ajevonline.org/content/37/2/127.abstract Formation of Substituted Tetrahydropyridines by Species of Brettanomyces and Lactobacillus Isolated from Mousy Wines. Tamila Heresztyn. 1986.]</ref><ref>[http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0238.2001.tb00205.x/abstract Ability of lactic acid bacteria to produce N-heterocycles causing mousy off-flavour in wine. PETER J. COSTELLO1, TERRY H. LEE1, and PAULA. HENSCHKE. 2008.]</ref><ref>Sparrows, Jeff. ''Wild Brews''. Brewers Publications. 2005. Pg. 112.</ref><ref>[https://books.google.com/books?id=tFjsAuo5WocC&pg=PA348&lpg=PA348&dq=lactobacillus+Tetrahydropyridine&source=bl&ots=QUVyoFtIwK&sig=h1cdjB0r1pIRX2Bms8wVA0UiLk4&hl=en&sa=X&ei=4DX_VPz5CsH6oQSAzoGgBA&ved=0CEwQ6AEwCQ#v=onepage&q=lactobacillus%20Tetrahydropyridine&f=false Lahtinen, Ouwehand, Salminen, von Wright. Lactic Acid Bacteria: Microbiological and Functional Aspects, Fourth Edition. Pg 348.]</ref><ref>[http://ajevonline.org/content/37/2/127.short Heresztyn, Tamila. Formation of Substituted Tetrahydropyridines by Species of Brettanomyces and Lactobacillus Isolated from Mousy Wines.]</ref>. Acetaldehyde has a stimulatory effect on ATHP and APY production, but is not required. No studies have been done to show whether or not oxygen plays a role in ATHP/APY production in LAB <ref name="Snowdon"></ref>. Most species of [[Pediococcus]] do not create forms of THP, although a few species do produce relatively small amounts. In particular, these include ''P. pentosaceus'' <ref>[http://www.uniprot.org/uniprot/Q03HT0 UniProt article. Retrieved 3/10/2015.]</ref><ref>[http://www.uniprot.org/uniprot/U5ZF76 UniProt article. Retrieved 3/10/2015.]</ref>, and ''P. clausenii'' <ref>[http://www.uniprot.org/uniprot/G8PEU4 UniProt article. Retrieved 3/10/2015.]</ref> (note that commercial cultures of [[Pediococcus]] are normally ''P. damnosus''). ''Oenococcus oeni'' and ''Leuconostoc mesenteroides'' have also been associated with creating ATHP, APY, and ETHP all above threshold amounts. Since only heterofermentative species produce significant amounts of THP, it is thought that its production is linked to the heterolactic pathway, and thus the metabolism of sugars in LAB <ref name="Costello"></ref>. A pathway for APY and ATHP production in ''Lactobacillus hilgardii'' was proposed by Costello and Henschke, which involves the intake of lysine or ornithine, along with ethanol (which is broken down into acetaldehyde) to produce APY and ATHP <ref name="Costello" />. ''Lactobacillus pontis'' has been shown to break down proteins via proteolysis, yielding free amino acids such as ornithine which could serve as precursors to THP formation, and it might be [Lactobacillus#Foam_Degradation reasonable to presume] that other species of ''Lactobacillus'' could also free up ornithine as a precursor to THP <ref name="Adams_2005" />.
===Acetic Acid Bacteria and Mould===