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update to Pectinatus
Any microorganism that is introduced into a beer unintentionally and can survive in the beer is considered a "beer spoiler". While most microorganisms cannot survive in beer due to the hops, low pH, alcohol content, relatively high carbon dioxide, and shortage of nutrients, certain species are considered to be beer spoilage organisms due to their ability to adapt to brewing conditions (namely hops, ethanol, and low pH) and sometimes form biofilms that help them resist cleaning. Some are able to survive in beer and make a potential impact on the beer's flavor by producing acidity, phenols, turbidity/ropiness via exopolysaccharides (EPS), and/or super-attenuation (which can cause gushing or in extreme cases exploding bottles/cans) with just a few surviving cells. These effects can sometimes manifest days or even weeks after packaging, and longer storage or non-refrigerated storage can increase the potential for beer spoilers to negatively impact the beer. Bacteria species that have adapted to the brewing environment tend to be hop tolerant, but strains of the same species found outside of breweries are not tolerant of brewing conditions. It is thought that these species evolved to carry the genes to adapt to brewing conditions during the 5th to 9th centuries when hops were first being used in brewing, and that this evolution gave them a specialized adaption to the brewing environment where few competitors can survive <ref name="Suzuki_2012">[https://onlinelibrary.wiley.com/doi/abs/10.1002/j.2050-0416.2011.tb00454.x 125th Anniversary Review: Microbiological Instability of Beer Caused by Spoilage Bacteria. Ken Suzuki. 2012. DOI: https://doi.org/10.1002/j.2050-0416.2011.tb00454.x]</ref>. Hop tolerant lactic acid bacteria have been found on the surfaces of many places in the brewing environment, including the fermentation area, bottling area, and cold storage. Hop tolerant lactic acid bacteria have been isolated from the air in at least one brewery in the fermentation and bottling areas <ref>[https://www.tandfonline.com/doi/abs/10.1094/ASBCJ-2017-4294-01?src=recsys Distribution of Lactobacillus and Pediococcus in a Brewery Environment. Jorge Hugo Garcia-Garcia, Luis J. Galán-Wong, Benito Pereyra-Alférez, Luis C. Damas-Buenrostro, Esmeralda Pérez, and Juan Carlos Cabada. 2017. DOI: https://doi.org/10.1094/ASBCJ-2017-4294-01.]</ref>.
Species of yeast and bacteria that are considered beer spoilers include [[Brettanomyces|''Brettanomyces'']] species, numerous [[Lactobacillus|''Lactobacillus'']] species, ''Pediococcus damnosus'', ''Pectinatus'' species (anaerobe responsible for 20-30% of bacterial contaminations that produces acetic acid, [https://en.wikipedia.org/wiki/Propionic_acid propionic acid], acetoin, and 'rotten egg' like odors in contaminated beer), ''Megasphaera cerevisiae'' (7% of bacterial contaminations; inhibited below pH 4.1 and 2.8% ABV but can produce considerable amounts of [[Butyric Acid|butyric acid]] along with smaller amounts of acetic acid, caproic acid, [[Isovaleric Acid|isovaleric acid]], acetoin, and hydrogen sulphide), ''Selenomonas lactifex'', ''Zymophilus'' spp., [[Saccharomyces#Saccharomyces_cerevisiae_var._diastaticus|''Saccharomyces cerevisiae'' var. ''diastaticus'']], and some species from the ''Candida'' and ''Pichia'' genera. Most wild yeasts that can grow in beer in lab conditions are not considered largely impactful because of their limitatons to growing in the presence of ethanol or lack of oxygen, but they can become impactful on barrel aged beers where oxygen is present (''Candida'' species, ''Pichia'' species, ''Torulaspora delbrueckii'', ''Issatchenkia orientalis'', ''Kluyveromyces marxianus'', ''Debaryomyces hansenii'', ''Zygosaccharomyces bailii'', ''Zygosaccharomyces bisporus'', ''Schizosaccharomyces pombe'', and ''Kloeckera apiculata'') <ref name="Bokulich_2013">[http://mmbr.asm.org/content/77/2/157.full The Microbiology of Malting and Brewing. Nicholas A. Bokulich and Charles W. Bamforth. 2013. DOI: 10.1128/MMBR.00060-12]</ref>. Hop tolerant lactic acid bacteria make up the majority of contamination issues in breweries, with ''L. brevis'' making up more than half of the reported contaminations, and all lactic acid bacteria making up 60-90% of reported contaminations. A new species of ''Lactobacillus'' was recently identified called ''L. acetotolerans'' and was [https://www.facebook.com/groups/MilkTheFunk/permalink/1363048380390039/ responsible for contaminating Goose Island's Bourbon County Stout], which is 60 IBU and 11% ABV. In sour beers with a pH below 4.3, only some lactic acid bacteria, ''Brettanomyces'', and some wild ''Saccharomyces cerevisiae'' strains (which sometimes produce phenols, haze, over-attenuation, and/or over-carbonation) have the potential for unwanted growth, while beers with low alcohol, a small amount of hops, lower CO<sup>2</sup> volumes (cask ales and beers dispensed with nitrogen, for example), and higher pH (4.4-4.6) are the most susceptible to contamination <ref name="Vaughan_2005">[https://onlinelibrary.wiley.com/doi/full/10.1002/j.2050-0416.2005.tb00221.x Enhancing the Microbiological Stability of Malt and Beer — A Review. Anne Vaughan, Tadhg O'Sullivan, Douwe Van Sinderen. 2005. DOI: https://doi.org/10.1002/j.2050-0416.2005.tb00221.x.]</ref>. ''Pectinatus'' and ''Megasphaera'' are Gram-negative anaerobic species that produce a number of off-flavors in ales but not lagers (probably due to their preference for warmer temperatures). They are somewhat tolerant of hops (they can grow in beers with IBU's as high as 33-38with one strain isolated from pickles reported to grow in beer up to 5% ABV and 80 IBU <ref>[https://www.sciencedirect.com/science/article/pii/S0740002020300514 Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains. Timo Kramer, Philip Kelleher, Julia van der Meer, Tadhg O’Sullivan, Jan-Maarten A.Geertman, Sylvia H. Duncan, Harry J. Flint, Petra Louis. 2020. DOI: https://doi.org/10.1016/j.fm.2020.103462.]</ref>) and often survive within the biofilms of other species in the brewing environment where the biofilm creates an anaerobic environment for them. They are sometimes found contaminating low ABV beers (under 5.2%) during packaging. They are not tolerant of pH below 4 and are killed at relatively low temperatures (58–60°C for one min) <ref name="Suzuki_2012" />. ''Zymomonas mobilis'' is a microaerophilic Gram-negative acetic acid bacteria that can withstand hops and can grow in bottled beer or casks where priming sugar is added and small amounts of air is present and produces high levels of acetaldehyde and hydrogen sulphide <ref name="Vaughan_2005" />. While the Gram-positive ''Staphylococcus xylosus'' bacteria, which grows on the skin of humans and animals, is not normally considered a beer contaminant, one strain was isolated from craft beer and was identified as the cause of increased turbidity, lactic acid, and succinic acid. It could grow at a pH between 3-7 (although only produced turbidity at a pH of 4-7), a temperature between 4–37°C, and as much as 8% ABV. This demonstrates that it is possible for species to adapt to living in beer other than the more typical beer spoilers <ref>[https://onlinelibrary.wiley.com/doi/pdf/10.1002/fsn3.1256 Beer‐spoilage characteristics of Staphylococcus xylosus newly isolated from craft beer and its potential to influence beer quality. Zhimin Yu, Qiuying Luo, Li Xiao, Yumei Sun, Rong Li, Zhen Sun, Xianzhen Li. 2019. DOI: 10.1002/fsn3.1256.]</ref>.
Other species of microbes do not grow in beer but can become contaminants earlier on in the brewing process prior to primary fermentation (for example during kettle souring). These species include enterobacteria such as species of ''Clostridium'', ''Obesumbacterium'', ''Citrobacter'', and ''Rahnella aquatilis'', and wild ''Saccharomyces'' species that might not be able to grow in finished beer. These microbes produce [[Dimethyl Sulfide|dimethyl sulfide]], organic acids, and 2,3-butanediol in high amounts which gives the beer an unpleasant rotting fruity or vegetal aroma <ref name="Bokulich_2013" />. Other species are considered "indicator" species because they do not directly cause spoilage of beer, but indicate that there is a hygiene problem. These include ''Acetobacter'', ''Gluconobacter'', ''Escherichia '', and ''Klebsiella'', as well as aerobic yeasts, all of which usually don't have an impact when present unless oxygen is also present. They can also produce slime that protects other microorganisms that can have a greater impact on the beer's stability <ref name="Wirtanen_2001">[https://www.researchgate.net/publication/273439407_Disinfectant_testing_against_brewery-related_biofilms. Disinfectant testing against brewery-related biofilms. Erna Storgårds, Gun Wirtanen. 2001.]</ref><ref name="Bokulich_2018">[https://www.tandfonline.com/doi/abs/10.1094/ASBCJ-2012-0709-01 A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. Nicholas A. Bokulich, Charles W. Bamforth & David A. Mills. 2018.]</ref>. Some species can contaminate yeast pitches. ''Pediococcus damnosus'' is frequently the cause of such contaminations and can cause diacetyl problems, as well as ''Pediococcus inopinatus'', ''Pediococcus claussenii'', ''L. casei'', ''Selenomonas lacticifex'', and ''Zymophilus raffinosivorans'' (although these are rarer to find in finished beer). ''Obesumbacterium proteus'' (which gives a parsnip-like smell and flavor) and ''Rahnella aquatilis'' can contaminate yeast pitches, and can inhibit fermentation and result in the beer finishing at a higher pH <ref name="Vaughan_2005" />.