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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 CO² 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. Biofilm forming spoilage organisms include a much wider range in beer tap systems due to the availability of oxygen and higher temperatures at certain points in the tap system. 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 <ref name="storgards_2000Wirtanen_2001">[httphttps://www.vttresearchgate.finet/infpublication/pdf/publications/2000/P410273439407_Disinfectant_testing_against_brewery-related_biofilms.pdf Process hygiene control in beer production and dispensing Disinfectant testing against brewery-related biofilms. Erna Storgårds. VTT Publications 410, Gun Wirtanen. 20002001.]</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 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" />.

Bacteria and yeast form a biofilm in two stages, which are determined by a number of variables. In the first stage, the microbes remain in their [http://www.dictionary.com/browse/planktonic|"planktonic"] form (floating around in the liquid), but they begin to adhere on surfaces and to each other as those surfaces. Other species of microbes can also be adhered to during this phase. The second stage is where the microbes start producing exopolysaccharides (EPS) which helps them bind together in a matrix, along with any available proteins and exopolymers produced by the bacteria. A large portion of biofilms is actually water (80-80%) as this allows the microbes to remove waste and consume nutrients. This matrix helps the microbes resist antibiotics, UV radiation, and cleaning chemicals. Gene exchange also occurs more frequently. At the end of this second stage, the microbes become attached to surfaces in such a way that is permanent without the use of cleaning chemicals. This is known as the microbe's [http://www.dictionary.com/browse/sessile|"sessile"] form (immobile). Bacteria in this form continue to multiply, and upon maturation of the biofilm, eventually, planktonic cells begin to be produced and released from the biofilm to find new homes. They also display different phenotypes, which might contribute to their ability to resist cleaning chemicals. Rough or surfaces, scratched surfaces , jagged edges, and pores are more prone to biofilm formation due to the higher surface area. Hydrophobic surfaces, such as Teflon and other plastics) , are more prone to biofilm formation than hydrophilic surfaces (glass and metalstainless steel). Nitrile butyl rubber (NBR) was found to inhibit biofilm formation when new, but as the material breaks down biofilms are able to grow <ref>Biofilms in the Food and Beverage Industries. P M Fratamico, B A Annous, N W Guenther. Elsevier, Sep 22, 2009. Pp 4-14.</ref>. Biofilm formation is strain specific rather than species specific; some strains can form thicker biofilms than others within the same species and faster, and some strains of lactic acid species are not good biofilm producers. Full biofilms can form within 2-4 days for some strains, while 10 days is required for significant biofilm formation in other strains. For example, one strain of ''Lactobacillus brevis'' isolated from draft beer did not form any biofilm, while another strain of ''L. brevis'' tested was a strong biofilm producer. Similar results were observed for ''Brettanomyces'' strains . In general, mixed cultures form stronger biofilms than single cultures. The presence of soil (biological residue) encourages biofilm formation <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>.

The goal of cleaning is to remove as much biomaterial as possible, while the goal of sanitizing is to reduce the population of viable microbes as much as possible and prevent them from growing on surfaces during the non-production time. It's been shown that chemical cleaners are better at removing biofilms than sanitizers and disinfectants, and sanitizers that kill cells in suspension may not be effective at killing cells within biofilms. Complete removal of unwanted microbes within biofilms can be achieved by first using a cleaning agent followed by a sanitizing agent. CIP procedures may not be enough to remove biofilms without high turbulent flow with spray nozzles and the use of heat (low cleaning temperatures are not effective at removing biofilms). Chlorinated alkaline detergents were found to be the most effective at removing biofilms <ref name="Wirtanen_2001" />. Below is a typical CIP process according to [http://www.vtt.fi/inf/pdf/publications/2000/P410.pdf Erna Storgårds (2000)]; CIP processes at room temperatures are not adequate enough to remove biofilms, so use hot temperatures when possible and maximum times to applicable. Also, the higher the velocity of the cleaning fluid through the system, the more effectively remove efficient it is at removing biofilms:

Open surfaces such as bottle inspectors, fillers, and conveyor belts in the packaging line should be first rinsed with water, then cleaned with a foaming agent, rinsed again with water, and then sprayed with a disinfectant solution and a final rinse. Components that cannot be visually inspected should be dismantled and inspected . Rubber gaskets and sealings have been found to house biofilms, especially after deteriorating, and so they should be inspected and replaced as needed. NBR rubber has been found to inhibit biofilms when new, and EPDM rubber has been found to be anti-bacterial towards some bacteria <ref name="Wirtanen_2001" />.