Microbiology in Beer

Microbiology is a crucial part to every step of the brewing process. Enzymes release sugars in malt, yeasts metabolize the sugars, and bacteria can be used as accessories to adjust pH. From start to finish, microbiology dominates the brewing process. Understanding the role of bad and good microorganisms and their impact on beer is vital for breweries to maintain the quality and safety of their products.

Let’s start with several misconceptions by addressing a few common questions:

Q: Why should I worry about microbiology when the risks of health consequences are minimal?

A: Quality. The introduction of unwanted microorganisms can drastically change quality between beers. For flagship beers, consistency is key for consumer trust. A bad batch or recall ruins brand recognition.

Q: What are the problems microorganisms can cause in beer?

A: There are numerous concerns, some of which are unwanted pH changes, gushing, overattenuation, haze, biofilms, and off aromas.

Q: How can I afford a microbiology quality control program with limited resources?

A: Purchasing the right equipment can minimize the footprint in your brewery. In terms of cost, the associated price of a ruined batch is far more expensive than materials to start a microbiology monitoring program.

Identifying the Problems

The different species of microorganisms play diverse roles in brewing. We first must analyze a few of the most common microorganisms impacting beer:


Aspergillus Niger

Black mold is a common microorganism found in breweries. It is found across climates and can thrive under typical brewery conditions. The optimal growing temperature for black mold is 95.0°F - 98.6°F. Due to condensation on fermentation and lagering areas, black mold can grow fast and is a common nuisance in breweries. The high motility of the spores can persist on packaging and can even be found in the ring of cans, indicating poor brewery hygiene.


This common fungal disease impacts many cereal grains leading to damage, discoloration, and shriveling of the grains. These spores under a microscope have a banana-like shape. They produce dangerous mycotoxins and hydrophobin proteins (small peptides) which lead to gushing in bottled or canned beer.


Lactic Acid Bacteria

These bacteria are the double-edged sword of brewing. They are often utilized to drop pH and produce lactic acid. However, they prove difficult to eliminate between batches of beer. It takes only two cells of lactobacillus in 1mL of beer to create sourness in a matter of days.

Acetic Acid Bacteria

Acetobacter, Gluconobacter, and Gluconacetobacter gram-negative bacteria impact beer via digestion of ethanol and production of acetic acid. In oxygen-rich environments, these bacteria can further oxidize acetate, producing water and carbon dioxide. These bacteria primarily impact cask-conditioned beer during dispensing.


Wild Yeast

Yeast strains such as Brettanomyces or wild Saccharomyces can often produce off flavors in beer. While some breweries use these strains for wild beers, the consequences of unwanted yeast can ruin more subtle styles.

Ale and Lager Yeast

Always analyze re-pitched yeast to determine if they are viable for fermentation. The wrong yeast strain can create off flavors in your finished product. Under a microscope, lager yeast will appear large and smooth; ale yeast will appear smaller and rough in contrast.

Creating a Plan:

With a general understanding of some of the common problems microorganisms can cause in beer, a plan can be developed to identify problematic organisms and prevent damage to beer and equipment. A simple microscope can offer an easy solution for a number of these problems, but requires a clean space to ensure no false positives. A small laminar flow hood can be one tool to meet this requirement.

Knowing where to look and check for these potentially problematic microorganisms is one difficulty posed to plan development. These microorganisms can typically be found in the following:

Raw Materials

Check grain for fusarium, which manifest as discoloration and shrunken kernels in delivered materials. Check hops for fungal growth and damage.

Cold Wort

Take a sample of the cold wort following your mash. Use a petri dish at room temperature in a sterile environment and study the microbiology after 24-48hrs.

Yeast Starters and Slurries

Analyze the starters provided by your yeast manufacturer. Look for uniformity and get numbers regarding the yeast viability. Excessive yeast death may suggest a damaged pitch or manufacturing error.

There have been several high profile examples of contaminated yeast creating product loss. A recall is always more expensive and damaging to a brand than basic quality control.

Create testing centered around heat exchangers and between tanks. Running a basic wort stability test of your cold wort can help identity if further testing needs to be conducted upstream in your process.

Testing Methods for Common Problems

Some basic tests are summarized in the table below:

In most cases, knowing the signs and having a sterile area prepared is enough to handle microbiology in-house. This allows a brewery to address problems quickly and build a reputable, high quality regiment.

Microbiology requires sterile working conditions and certain equipment to avoid false positives, which waste time and money. Building a dedicated lab is one potential option for microbiology work, but often space and budgetary restrictions mean dedicated lab space is unfeasible for microbreweries.

Our Solution:

AirClean Systems offers a simple solution for microbreweries looking to develop quality control testing, but are limited by these constraints. Our ductless PCR Workstations provide an ISO 5 environment, offering you the microbiology capability of a clean room while remaining mobile.

The UV light destroys unwanted microorganisms in the unit in a matter of minutes, ensuring the environment keeps you from wasting time and money on false positives. The ISO 5 environment can even be used as a facility to propagate yeast strains individual to your brewery.

Microorganisms are an abundant part of the brewing process. From raw materials to finished products, microorganisms determine the flavor profiles of our favorite beers. By understanding some of the concerns of microbiology and developing plans, brands can maintain quality and consistency.


Bokulich, N. and Bamforth, C. The Microbiology of Malting and Brewing. Department of Food Science and Technology. Microbiology and Molecular Biology Reviews. Vol 77.

Retrieved at https://mmbr.asm.org/content/mmbr/77/2/157.full.pdf