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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) and to form biofilms and 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 fairly hop somewhat tolerant of hops (they can grow in beers with IBU's as high as 33-38) 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" />.
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" />.
Biofilm forming spoilage organisms include a much wider range and higher frequency in beer tap systems than in brewhouses. This is due to the availability of oxygen and higher temperatures at certain points in the tap system, as well as poorer hygiene in tap systems as well as the difficulty to effectively clean plastic hoses. Of particular concern here is the ability of ''E. coli'' serotype O157:H7 to survive in tap systems, which has had a couple of documented occurrences in contaminated apple cider. Another study showed that aerobic yeasts were able to grow in dispensing lines, as well as ''L. brevis'', and in many cases the draft lines were re-contaminated one week after cleaning, indicating that a contamination in draft lines is difficult to remove <ref name="storgards_2000">[http://www.vtt.fi/inf/pdf/publications/2000/P410.pdf Process hygiene control in beer production and dispensing. Erna Storgårds. VTT Publications 410. 2000.]</ref><ref name="Wirtanen_2001" />.
Sources for contamination in breweries can occur as "primary" contaminations (yeast pitching, and brewhouse related contaminations), or as "secondary" contaminations (packaging and cellaring), as well as in tap systems. They are usually not sudden occurrences, but a result of the continued growth of microorganisms in a problem area. Historically, re-pitching yeast was often a source of contamination, ; however, more recently this has become less of a source for contaminations due to better education and techniques. Typical sources for contamination also include unclean equipment such as thermometers, manometers, valves, dead ends, gas pipes, leaks in any part of the system (especially at heat exchangers), wort aeration equipment, and even worn floor surfaces. More than half of the documented contaminations come from the packaging system. These are typically the sealer (35%), the filler (25%), the bottle inspector (10%), dripping water from the bottle washer (10%), and the environment close to the filler and sealer (10%). In regards to the environment as a source of contamination, this has been found to be from airborne contaminants near the filler and crowner in open bottles on their way from the bottle washer to the filler and from the filler to the capper. The higher the humidity and the more airflow, the more chances of airborne contamination <ref name="storgards_2000" /><ref name="Vaughan_2005" />. For example, ''Pectinatus'', while mostly found in lubrication oils, water systems, floors, water condensed on ceilings, etc., it can also survive on [https://en.wikipedia.org/wiki/Aerosol aerosols] in the air and is thought to possibly transferred to beer that is being packaged via the air <ref name="Suzuki_2012" />. In tap systems at taverns, 'one-way' valves that are attached to kegs have been found to be a source of contamination, as well as the dispensing line <ref name="storgards_2000" /><ref name="Vaughan_2005" />.
See also:
* The [[Barrel#Sanitizing|Barrel]] wiki page.
* [http://mmbr.asm.org/content/77/2/157/F3.expansion.html Diagram overview of bacterial and fungal species reported at all stages of beer production.]