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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 form biofilms and survive in beer and make a potential impact on the beer's flavor by producing acidity, phenols, and turbidity with just a few surviving cells. Adaption to the brewing environment also makes them more able to survive the harsh environment of beer. These species include [[Brettanomyces|''Brettanomyces'']] species, numerous [[Lactobacillus|''Lactobacillus'']] species, ''Pediococcus damnosus'', ''Pectinatus cerevisiphilus'', ''P. frisingensis'', ''Megasphaera cerevisiae'', ''Selenomonas lactifex'', and [[Saccharomyces#Saccharomyces_cerevisiae_var._diastaticus|''Saccharomyces cerevisiae'' var. ''diastaticus'']]. In sour beers with a pH below 4.3, only the lactic acid bacteria, ''Brettanomyces'', and some wild ''Saccharomyces'' 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. Other species of microbes do not grow in beer but can become contaminants earlier on in the brewing process (for example during kettle souring). These species include enterobacteria such as ''Clostridium'' species, ''Obesumbacterium proteus'' and ''Rahnella aquatilis'', and wild ''Saccharomyces'' that might not be able to grow in finished beer. 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'', and ''Klebsiella'' species, as well as aerobic yeasts <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>.
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 after just one week of 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 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 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. The higher the humidity and the more airflow, the more chances of airborne contamination. 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" />.
===Biofilms===