Contamination

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Contamination (or "infection") refers to the presence of unintentional microorganisms in a fermentation. A variety of different yeast, bacteria, and molds are known to contaminate beer and wine at various points in the process.

For beers that are dominated by offensive phenolic character, the most likely source of volatile phenols is metabolic activity of contaminating spoilage organisms. Most beer spoilage organisms fall into one of several categories: gram positive lactic acid bacteria, gram negative acetic acid bacteria, wild Saccharomyces yeast, and non-Saccharomyces yeast [100,101]. Lactic acid bacteria include a number of species within both the Lactobacillus and Pediococcus genera. While a number of species within these genera possess a PAD enzyme gene and can be considered POF+ (see Section 4.2), they are primarily known for spoilage by acidification of wort or beer through lactic acid fermentation, rather than for generating threshold levels of volatile phenols, although diacetyl formation is also a potential spoilage problem with Pediococcus [100]. Gluconobacter and Acetobacter are the most common brewery contaminants spoiling through metabolism of ethanol to acetic acid, but are also not known for detectable volatile phenol formation [100,102]. Most beer spoilage yeasts that have been characterized exhibit a POF+ phenotype, and volatile phenol production is a major mechanism of spoilage by yeasts. This includes wild strains of S. cerevisiae, as well as members of the Pichia, Candida, Toulaspora, Kloeckera, Brettanomyces, and Schizosaccharomyces genera most commonly associated with brewery contamination, although the degree of volatile phenol production varies widely among isolates [49,93,100,103,104]. A designation of POF+ is usually associated with an analysis of yeasts ability to metabolize HCA precursor compounds. Most POF+ strains are active for phenolic acid decarboxylase activity, leading to generation of vinyl derivatives (see Section 4.2). Among the strains tested, only Brettanomyces isolates have demonstrated vinylphenol reductase enzyme, completing HCA metabolism to ethyl derivatives, primarily 4-ethylphenol and 4-ethylguaiacol (Section 4.3). The ethyl compounds have comparable aroma and flavor thresholds, and are generally associated with less desirable characteristics of barnyard and creosote [3,71].

A few microbes encode a vinylphenol reductase (VPR) enzyme, which uses the vinyl intermediates as substrates to generate ethyl derivatives (Fig 2). Among brewing relevant organisms, a few Lactobacillus species (L. brevis, L. collinoides, L. plantarum), and P. damnosus, as well as members of the Brettanomyces yeast genus have active VPR enzymes. VPR activity appears to be rare among yeast species, but has been demonstrated for Pichia guilliermondii isolated from winery environments, although this activity is strain-dependent. The most common products are 4-ethylphenol and 4-ethylguaiacol, derived from p-coumaric acid and ferulic acid, respectively. These compounds have similar organoleptic properties to the vinyl substrates, but have somewhat lower aroma and flavor thresholds.

Possible signs of a contamination:

• Unexpected Pellicle (film)
• Unexpected flavors (especially phenolic, significant sourness, or acetic acid)
• Unexpected visual mold growth
• Unexpectedly high attenuation, or stuck fermentation in rare cases
• Unexpected haze or cloudiness

What to do

First, relax and take a deep breath so we can deal with this rationally.

Unexpected pellicle

A pellicle is a definite sign of wild microbes. (See Pellicle) If a pellicle is the only sign of contamination, anecdotally most of the time the wild microbes will have no noticable effect on the flavor.

Follow these simple steps:

1. Verify that fermentation has completed (e.g. take a hydrometer reading). This is to make sure it is safe to taste, since alcohol kills pathogens.
2. Smell and then taste the product.
3. If there are off flavors, see the appropriate section below.
4. If it smells and tastes normal, we recommend to treat it as normal.
   • Beer: go ahead and package it.
   • Wine, cider, mead, etc: consider using sulfite after fermentation.

Important caveats if bottling a contaminated beer:
Some wild yeast can consume sugar that brewers yeast leave behind, which may result in unexpected additional fermentation in the bottle. The likelihood of over-carbonation and eventual explosions is small, but some simple precautions are recommended just in case... Monitor the carbonation level every few days. If possible, move the bottles into the fridge once carbonated (this helps to slow down any wild microbe activity). Don't distribute bottles to friends/family/judges.

Unexpected off flavors

Wild microbes may cause a variety of flavors. If the unexpected flavor(s) are unpleasant, the beer/wine will most likely need to be wasted, with couple possible exceptions:

• If a beer/wine has hydrogen sulfide (rotten egg aroma), you should be able to remove it. See hydrogen sulfide for methods to remove hydrogen sulfide and certain other volatile sulfur compounds.
• If a beer is sour, it may be worth a try lowering the sour taste with sodium bicarbonate. However it likely won't taste good, and it may continue to sour after packaging. Use a bench trial to determine whether sodium bicarbonate will help.

Unexpected phenolic flavors in beer are a sure sign of contamination. These include clove, peppery, spicy, smoky, and medicinal flavors. There's no way to remove these flavors from the beer once they're present.

Unexpected mold growth

Mold growth is able to be visually identified.

Mold is allergenic and can produce toxins and/or carcinogens. Therefore if your beverage has mold growing on it, it should be dumped, even if it smells or tastes normal.

See Mold for more information.

High attenuation

Some wild yeast can eat sugars that pitched yeast leaves behind (in beer), or can tolerate higher levels of alcohol than pitched yeast (in wine).

Usually if a contaminating microbe is increasing the attenuation, it will do so slowly. However many factors can affect attenuation and fermentation rate, so diagnosing a contamination solely by the attenuation is not always definitive.

Generally the best way to prevent over-attenuation in a contaminated beverage is to keep it cold during storage such that the wild microbes are inhibited and stop any fermentation activity.

Cleaning

Equipment should be properly cleaned after every fermentation. Radical methods are generally not needed after a known contamination.

See Cleaning for more information.

Preventing contaminations

We don't brew in a sterile environment. Wild microbes are everywhere — on surfaces and floating around in the air. Invariably some unwanted microbes make it into our beverages at some point during preparation, fermentation, handling, or packaging. Fortunately, the anti-microbial effects of our processes and pitching strategies tend to prevent effects of contamination most of the time, but only when our processes are solid. Preventing contamination is one of the most important aspects of brewing beer, and also important in wine production to a much lesser degree.

• Clean your equipment thoroughly after use, and when you first receive it. See Cleaning.
• Store the equipment where it won't get dirty again.
• Use a quality no-rinse sanitizer on the equipment before use and just as importantly don't contaminate the sanitized equipment by touching it or touching it against anything unsanitary. See Sanitation.
• Sanitize ingredients. If you don't want wild microbes, don't use ingredients that aren't heat-pasteurized (besides yeast).
• Minimize open air exposure. Air is full of microbes.
• Pitch active healthy yeast without unnecessary delay.
• Minimize time in the fermenter. This reduces the likelihood that a biofilm will form.
• Consider avoiding risky processes, such as brewing with "no-chill" or no-boil recipes, repitching yeast, kettle souring, open fermentation, excessive numbers of transfers, secondary fermentation vessels, etc.

Bacterial contamination of water can occur at any time during storage, even at high temperatures. For example, contamination with thermophilic bacteria (such as Bacillus stearothermophilus) has been identified in hot-brewing liquor tanks held at 80°C.39

Terminology

"Infection" is not the best word for unwanted microbes in a fermentation, because an infection is a microbial invasion of a host organism. Contamination is the preferred term for beer, wine, etc., since the beverage is not an organism.

Furthermore, the term contamination should be reserved for unintentional introduction of microbes. Many times wild microbes are introduced intentionally, and the brewer should expect them to have some kind of effect. For example a wine made from unpasteurized fruit is expected to contain wild microbes, and therefore the appearance of a pellicle does not reflect "contamination".

Science

(In progress)

Diastaticus yeast is a group of variants of brewers yeast (Saccharomyces). They contain a gene called STA1, which encodes a secreted glucoamylase, an enzyme that breaks down dextrins/starches. Some strains with this gene can highly attenuate wort by breaking down the dextrins. Therefore it can be a problem if one of these strains contaminate a beer because it can cause phenolic off flavors or over-attenuation. Some strains that contain the STA1 gene express it minimally or not at all, and therefore may ferment dextrins slowly or not at all (the genotype does not always correspond to the phenotype). This is the most prominent contaminant in commercial breweries (due to inadequate cleaning processes). LCSM is useful QC to determine to presence of these strains, or of course PCR. Generally speaking, these Saccharomyces variants are not "contaminants" in wine because wine contains neither dextrins nor phenolic precursors.

Some Brett strains can break down dextrins, but how it does that is not well characterized.

• "The Microbiology of Malting and Brewing."
• "Selective-Differential Medium for Isolation and Differentiation of Pectinatus from Other Brewery Microorganisms"
• "Detection and Identification of Pectinatus Brewery Contaminants Based on the Gene for the Major Outer Membrane Protein."
• "Structural analysis of glucoamylase encoded by the STA1 gene of Saccharomyces cerevisiae (var. diastaticus)"
• "125th Anniversary Review: Microbiological Instability of Beer Caused by Spoilage Bacteria"
• "Botulism"
• "Non-Saccharomyces killer toxins: Possible biocontrol agents against Brettanomyces in wine?"
• https://www.homebrewtalk.com/threads/pellicle-photo-collection.174033/post-8923085
• see Handbook of Brewing 10.10

Fruit

• https://www.homebrewtalk.com/threads/possible-infection-in-peach-kettle-sour.636460/
• https://www.homebrewtalk.com/threads/raspberry-sour-infection.655560/
• https://www.homebrewtalk.com/threads/sulfur-smell-in-sour-raspberry-cranberry-berliner-weisse.654905/ (sulfite -> sulfide)
• https://www.homebrewtalk.com/threads/post-your-infection.71400/page-96#post-8563116
• https://www.homebrewtalk.com/threads/post-your-infection.71400/post-6268008
• https://www.homebrewtalk.com/threads/post-your-infection.71400/post-6270400
• https://www.homebrewtalk.com/threads/is-this-an-infection.679844/

Happy accidents

• https://www.homebrewtalk.com/threads/post-your-infection.71400/page-86#post-7696739
• https://www.homebrewtalk.com/threads/post-your-infection.71400/post-8927129
• https://www.homebrewtalk.com/threads/first-infected-beer.699953/

• https://onlinelibrary.wiley.com/doi/pdf/10.1002/j.2050-0416.2005.tb00221.x
• https://www.process-nmr.com/wp-content/uploads/2019/01/Dicaprio_Edwards-ACS-NERM-2013-NMR-Session-Talk.pdf
• https://onlinelibrary.wiley.com/doi/pdf/10.1002/jib.428
• https://www.researchgate.net/profile/Mathias_Hutzler/publication/287235582_Fermentation_and_spoilage_yeasts_and_their_relevance_for_the_beverage_industry_-_A_review/links/5c63c62f299bf1d14cc20a50/Fermentation-and-spoilage-yeasts-and-their-relevance-for-the-beverage-industry-A-review.pdf
• https://www.sciencedirect.com/science/article/pii/B9780127999548000149

Racking and nitrogen levels in wine do not affect Brettanomyces growth. https://ir.library.oregonstate.edu/downloads/f4752k49f