Microbrewery: 8 stages where microbiology can impact your beer's quality.

Starting a microbrewery is an exciting journey. You start everything from the beginning, join a community of passionate brewers, test, learn, and improve the quality of your beer. When your beer gains in popularity and is « exported » at some distance from the brewery, you're starting to face new challenges.

As you need to ensure a constant beer's quality, you need to manage different parameters. One parameter is critical if you to take a step further: Controlling microbiology to ensure beer's quality.

What is beer quality?

There are many aspects to consider as beer quality is measured by a complex set of sensory characters. These indicators are aroma, taste, texture, and appearance.

Together, they defined a sensory profile specific to your brand; this is what makes your beer unique. Preserving this quality at every sip builds your brand loyalty; it keeps your consumers excited about your craft beer. 

Dealing with a growing expectation for your craft beer

When production volumes increase, so does the expectation for a reproducible taste. Your consumers love your product and expect the same quality every time. Whether it is from a bottle or at the bar, they want to enjoy the same taste, texture, aroma, and appearance.

As your facility grows, so do the risks of microbial issues that can alter your beer's quality. Good brewing practices are available for large breweries, expressed in modern Quality Assurance terms, in documents approaching the subject from the HACCP or Hygiene monitoring perspective. As a still small brewery, where can microbiology impact the quality of your beer?

Microbiological contamination by wild yeasts, molds, and a wide variety of bacterial species can deteriorate the quality of your beer. It can cause off-flavors, souring of beer, over carbonation, the eruption of beer from bottles, and serious hazes.

8 stages where microbiology can impact your beer's quality



Microorganisms are everywhere, and a brewery working with yeast in a humid environment is the perfect place for microbial contamination. Beer provides nutrients for many undesirable organisms. Where should you start looking for preventing microbial contamination?

1. Barley, Malt, Grits

In the field, a vast variety of bacteria and fungi are present on the barley. Grinding, grit storage exposes the material to contamination by the environment, stimulated by humidity (condensation) and warmth.

Potential flora: Fusarium, Lactobacillus, ..

Impact: some mycotoxins survive the brewing process and can inhibit yeast growth during brewing, cause premature yeast flocculation, beer gushing/over foaming...

Prevention: store dry and low temperature, 

2. Water

For brewers, water is indispensable for many things, among which is used as a raw material.

Drinking water contains residual chlorine to prevent bacterial growth in the distribution piping. Treatments to remove scale, unwanted organic matter, and chlorine also removes this protection. Some treatment steps, such as carbon filtration or softeners, can promote the development of microorganisms.

Potential flora: Pseudomonads, Enterobacteria, Cladosporidium,..

Impact: biofilm formation upstream in the process, which contaminates downstream

Prevention: appropriate water treatment system design, techniques and maintenance, short storage, storage at low or high temperature to limit bacterial proliferation

3.Lines, fittings, holding tanks, …

Anything in contact with the product during the process is susceptible of affecting the product: condensation, incomplete draining, solid material caught on an inner asperity such as couplings can stimulate microbial growth. 

Potential flora, from water, brewing material and environment: Lactic-acetic bacteria, enterobaceriaceae, Gluconobacter,..

Impact: production of Acetaldehydes, diacetyl, ..

Prevention : components should be clean, undamaged and sterilized

4. Heat exchangers

The nutrient-rich wort leaving the kettle is vulnerable to spoilage organisms. Heat exchangers are challenging to clean because of their large internal surface and the tortuous channels the wort passes through. The retained organic material in a humid environment is favorable to the proliferation of microorganisms.

Potential flora: Enterobacteria, Lactobacilli, Pediococci, Yeasts

Impact: production of unpleasant flavors, inhibition of Saccharomyces growth

Prevention: proper cleaning and sanitation - rapid fermentation after cooling

5. Beer

Once Saccharomyces and hop are added to the wort, conditions become hostile to most microorganisms. However, when the beer is exposed to environmental contamination, some microorganisms can grow.

Potential flora: Hop-Resistant Lactobacilli, Pediococci, Acetic acid bacteria, Zymomonas (if adjunct sugar)

Impact: acidification, haze, unpleasant aroma

Prevention: Good hygiene practices upstream, limited exposure to the environment and to oxygen

6. Bottling equipment

Bottling is the last process step after which the live microbes escape the brewers' control. Controlling the sanitary status of that equipment means lowering the risk of undesirable fluctuations in beer stability.

Potential flora: the panoply described above, forming biofilms

Impact: shortened microbial stability

Prevention: proper cleaning and sanitation

7. Transportation and storage

It doesn't end when your beer leaves your facility! Beer storage areas should be free of food to prevent the growth of microorganisms that could spoil and alter your product.

Potential flora: Pectinatus spp, Megasphaera

Impact: Haze, Off-flavors

Prevention: limit exposure to temperature changes, light and turbulence 

8. In bars

When customers ask for your beer at their local bar, they expect the same quality. To ensure a high-quality beer, bar drains should be clean and flushed free of waste beer frequently. It helps prevent microbial growth and fruit flies.

Potential flora : Acetic bacteria, Lactobacilli, Pediococci,.. 

Impact: Haze, Off-flavors

Prevention: clean faucets, proper serving techniques

How can you start controlling your beer's quality?

What gets measured gets managed. To ensure a high-quality beer and prevent microbial spoilage, maintain audit regularly, and report your results.

Most of the controls conducted in industrial breweries require a laboratory and some expertise, not always available to small entities. Outsourcing these tests, on the other hand, does not offer the required reactivity and flexibility. 

Once a plan of control is established, we believe that every worker in a brewery should be able to control and prevent microbial contamination. That's why we created Pinqkerton.

Controlling and monitoring microbial activity easily anywhere and at any time could help artisans, managers, and entrepreneurs make high-quality products. With our first product, the "nomad" a self-contained device, you can start monitoring easily and get quantitative results.

We hope that these insights will help on your journey. Start measuring microbiology is not as difficult as it seems and can lead to tremendous results. For more information on how to measure microbial activity to maintain your beer's quality, you can subscribe to our mailing list or directly get in touch with us.


Further reading: The microbiology of Malting and Brewing - Nicholas A. Bokulich, Charles W. Bamfortha ; Best Practices Guide to Quality Craft Beer - Brewers Association

Autres articles:

Recovering from operations shut down is a unique experience. Can we limit the pain and find some gain ?


Operations may be slow now, but will ramp-up again sooner or later.

Very unusual circumstances caused the shut-down and the recovery will probably be also.

At Pinqkerton, our closest experience (from a previous life), to what we might be living soon, is a process transfer from one location to another. Based on that experience, we believe that this recovery will require a good dose of planning but is an opportunity to learn and progress.

In the case of a process transfer, most of the start-up (i.e. the recovery) at the receiving end depends on the shut-down and transfer of knowledge.

The differences with today are (i) this shut down was potentially organized in a bit of a rush (ii) the process understanding that was not developed before the shut down will not be available for the recovery.

We hope the experiences, information and advices collected from various sources (mainly from the food industry) and shared hereafter will provide you with at least one actionable idea that will help you recover faster and better.

So we start with an evaluation of the process state after shut down and quarantine, what we know about it and build the knowledge that is missing.


What do companies who go through seasonal shut-down pay attention to ?


A shut-down has a number of consequences: 

  • Water stops circulating : its quality drops
    That can be a concern since water is used among other things, for cleaning
  • Wet areas : humidity, condensation, residual water .. lead to microbial proliferation and development of biofilms
    72h is often used as a reference in the food industry as an action limit to trigger a re-washing. (max 24h is a target)
  • Dry areas : crusting takes place and standard washes are not enough to remove them
    Remaining crust will act as a anchor for new biofilm or other contamination
  • Pests : the facility has known unusual calm for an unusual long time and unusual visitors can be expected
  • Dryness damages seals or other parts…
  • Humidity favors contamination of the air system, vents…
  • Uncontrolled temperature leads to premature material aging, spoilage…

Good shut down practices in seasonal farming suggest measures that are generic and important for their restart. They include:
  • Empty/ purge all lines and containers
  • Apply the most thorough cleaning procedures e.g. alkali wash followed by acid rinse.If possible: allow to dry and close or leave in a protective solution e.g. peracetic acid
  • Close all networks (compressed air, water, CO2, etc.)
  • Disassemble all equipment that can be, prior to inspection and washing : unions, filter housings, heat-exchangers, etc
  • Scrub all accessible surfaces, including inside vats and silos, in safe conditions. 
  • Isolate and close packages of started materials, (if possible, put under vacuum)
  • Close the drains to avoid the rise of contaminating microorganisms
  • Install grids to avoid the rise or entry of rodents
  • Take stock and prevent looting / burglaries
If these steps were not taken during shut-down, they could or should be during recovery.


What do we know that is important for recovery ?


We know at least 2 things that are important: the process and the product susceptibility to contamination, the combination of which is reflected in the historical production yields and/or spoiled batches.

Hygiene by Design dictates that the exterior and interior of all equipment and pipework must be self-draining or drainable. In the case of external surfaces, any liquid must be directed away from the main product area. The design rules include choice of material of construction and other sometimes industry-specific considerations.

Some of our conception flaws can be detected by observation, such as areas of water stagnation which point at potential vulnerabilities to contamination.
Now is the opportunity to look, discover and improve.

Then, we also have our production history as a source of information.The documentation and/or personal experience tell us which intermediate or finished product, which particular tank, supplier or process step has been  most problematic.
If those production pain points present a higher risk of contamination in normal conditions, they probably hurt even more during recovery.

We can think of actions such as re-inforced inspection, avoidance (recover with manufacturing other « easier » products first, before manufacturing the more complicated ones) or upgrade the process.

This last option, in our experience, should be considered with care because of 2 conflicting propositions: 

  • First, if we have a known weak point in a chain and we know times ahead will be challenging, then dealing with the weak point might well increase our chances of success. It is good preparation.
  • On the other hand adding change to a crisis situation, when resources are spread thin and thinking clear not easy, could bring the entire organisation to a stop if anything unexpected happens. It is taking unnecessary risk.
    The decision might be taken considering a « risk/benefit » ratio, return on investment and our capacity to do it right the first time?






x 1 = Important

x 3 = critical

0 = Not Satisfactory  

2 = Very Satisfactory

Importance x Appreciation

Hygiene by Design 
applied to the process ?




Level of validation




History of problems




Cleaning during shut-down





Sum scores / Maximum score

56 %


Everything in this table is up for customisation, including the granularity for the criteria and evaluations. It may facilitate an assessment that can be explained, shared and feed a plan for recovery. A more comprehensive version can also be the starting point for a longer term Operational RoadMap, with annual objectives to improve the score.


How do we know we have recovered ?


For those processes and procedures that are validated, the key performance indicators are known, acceptable limits are specified etc.
Re-start could look like a walk in the park (relatively)

The answer to that question is made more difficult when we have insufficient or partial data history. If we don’t have measures or specifications to indicate what normal/satisfactory/improved are, we can remember Peter Drucker : If you cant measure it, you cant improve it »

The missing historical data can be built on this occasion.
Before the actual restart, we can test critical control points, points-of-use, water at various purification and storage steps, etc. which will give a reference point helpful to evaluate the efficiency of the cleaning and other recovery activities.
Chances are, that data will come useful again, and again for years to come

Preaching one second for our products: the nomad testers can really come handy in these circumstances.


A few points of attention

  1. Recent public debriefs from companies that have managed to function through this confinement period, one in Food and the other in PCP, both highlighted the importance of communication.

    Their point is that for a group to function in unusual conditions, everyone needs more than ever to be and feel listened to, considered and be lead rather than managed.
    In these experiences, the energy and creativity that were liberated really made the difference.


  1. Those large companies also had a wealth of experience and documentation i.e. a large toolbox from which they could draw. Here are some we thought might be helpful:

    • Beware of washing on biofilms or dry crusts well installed: start washing with a cold phase to remove organic and especially protein residues which hot coagulate on the walls and are very difficult to remove, and then form points of hook for subsequent deposits and biofilms.
    • Watch out for air systems, air intakes and introduction into the process.
    • Monitor fines (dust of various origins which are vectors of cross-contamination of the environment between zones ) in the workshops. Where are these fines generated? where do they circulate?
      Places where fines deposit risk harboring contaminations that might adapt, become resistant to the sanitation process,particulalrly in process dead-points.
    • Are there any plans to rework rework? how was it stored? Where will the rework be introduced in the process?
    • Atmospheres: has the temperature been lowered? Was it only when everything was dry? Has there potentially been any condensations?


      1. A scrupulous inspection is necessary before restarting

      In many cases, visual inspections are the main or only way to check that a particular criteria is met, even in normal activities.

      Training new personnel or standardizing the acceptable limits is not always simple for those visual controls. For that purpose,  building a library of different defects, labelled « acceptable » or « not » can be very useful. `

      There are rare occasions to enrich these libraries and a restart is probably one of them.

      We find that taking pictures with smartphone is a smart way of doing that. It does not cost much and can prove very valuable


      1. Gather data

      An unusually high level of testing might be desirable to satisfy yourself and potential auditors that the process is back under control.  

      In case of sensitive materials and or processes, swabs will be necessary if only to measure TVC (Total Viable Counts) and a few hygiene process specific indicators, at sensitive points identified during an inspection before recovery. 

      Same goes for equipment rinse water for equipment internal surfaces.

      Identification of the germs found would allow the use of cleaning agents well targeted for their specific efficacy and at the effective dose as well as doing some plant mapping. 

      Mapping is helpful to determine the origin and movements of contaminants in a site. If we know what flora is in the process water, what is typically from a raw material, and another form the skin, when we find  a contamination in a product, the origin of the contamination is easier to investigate.  

      This approach applied in routine can be a luxury for some activities, as a result of (i) the testing costs being to high compared to the product value and (ii) because the results of swabs or CIP rinse water test (before second washing and possibly post second washing), would not be known until after the manufacturing has resumed. The delayed results may expose to a difficult decision : what if a troubling result is found in retrospect, after the manufacturing restart, that is not part of the release criteria ?

      For that reason maybe, some manufacturers consider that the first batch, scrutinized, should be discarded no matter what.

      But such an approach might be acceptable in a recovery "study" mode during the upcoming start-up, to enhance our process understanding, which is a source of lasting future improvements and savings.


      Where are the opportunities in all that ?


      As a supply chain management expert pointed out this week, that we are living an opportunity to improve in a number of ways: 

      • Financially: because cash is priority number 1 right now, short term profitability left aside, if we look at our activity focussed only on current and future cash-flows, we may reveal improvements: contracting the supply chain, resizing batches and equipment, reconsider the value of a particular sales channel or customer type
      • Sales : some companies will probably not survive through this death valley unfortunately, which opens new markets for those who survive
      • Organisation : observe the time between taking important decisions and their realisation.
        What is slowing the process: communications, planning, adapting operations, lack of automation ?
      • Strategic : developing agility and resilience.
        What is our process for anticipation and decision making. How does it work when our vision of the future is not clear ?
        The post crisis consumer habits, behavior at work, economic models might be different : place bets on a few scenarios, prepare a response and pull the trigger when one of the bets becomes reality




      Several executives from reputable companies converge in the opinion that recovery is an opportunity to become more agile and resilient.

      This is consistent with our experience in process transfers.

      It starts with observing our processes, organisation and cash-flows to identify vulnerabilities. It continues with anticipating, adapting while measuring the progress.

      It may sound as the kind of conceptual thinking exclusive of large companies, but are these opportunities not real for all companies, whatever size and business ?

      Like for exceptional holidays, these exceptional days call for observing, taking pictures, comparing, so we can bring new habits and ideas home, on which to feed for a long time.

      Thank you for reading this. 
      If you would like more publications like this one, please "Like" or comment. 
      Wed love to read from you, share and help !
      As a token of our appreciation, enjoy free shipping on our products, with the code ILIKEBLOG4



      …and remember,

      Q: Why did the germ cross the microscope ? 

      A: To get to the other slide !

      4 contrôles avant d'utiliser un kit de terrain autonome microbien à votre satisfaction

      In our last article, we wrote about the usefulness of field kits and their potential applications, inspired by ISO 17381 « Selection and application of ready-to-use test kit methods in water analysis ».

      There are 4 main chapters in this standard we should consider:

      1. Define what will the kits be used for : that's the scope of applications
      2. Check the kit works, which is essentially making sure a component of the sample does not interfere with the detection technique
      3. Document what we do
      4. Train those who will do

      Since such kits are generally designed to be simple to use and are derived from lab techniques, the potential interferences (second chapter) are usually known by looking at the litterature and not much work is required.

      1-Define what we want the kit to do in practical terms

      What is the range of detection ?
      For example, a suppliers recommends an analytical limit for the equipment we just bought : « we cannot garantee the equipment will function properly if microorganism concentration is above XX ». We want a range of detection centered on that XX limit, +/- 1 log

      Is the product you want to test physically and chemically compatible with the kit technique?
      For example, if the product contains suspended matter or is opaque, a kit based on an optical detection may no be the simplest route to go down

      Will it be easy to live with once used in routine?

      Suggested topics to consider are:

        • The rapidity of set-up, of handling, of results
        • There is mobile and mobile. Should it hold in a pocket or in a briefcase?
        • Cost of initial (equipment) acquisition, cost per test, cost of ownership (training, maintenance, ..).
        • How much confidence in the results do we need to make the right decisions?
          For example a semi-quantitative may have the advantage of cost or rapidity, but generate more false positives and negatives than a quantitative technique. That can be OK …or not
        • Frequency of use for routine testing or for troubleshooting. Does (frequency x cost per test) fit with our budget?
        • Is a correlation with a reference or lab results critical, important or nice to have?
          The question can be particularly important with microbiology tests, since different techniques can give very different results.
        • Availability and ease of acquisition : if we opt for using a field kit, we don’t want to risk holding up our operations for a matter of supply.

      You decide what you want !

      « If one does not know to which port one is sailing, no wind is favorable. » Seneca

      2- Will it work?

      The biggest watch-out is for « interferences »

      With microbiology kits using a method by culture, preservatives or biocides will interfere with the microorganisms growth, since that is the reason for them being there.

      Chlorine is added to tap water to prevent microorganisms from multiplying in the distribution piping, preservatives are added to cosmetics, biocides to water baths used to wash solid products…

      Since field kits are often derived from lab techniques, how to deal with these situations is often public knowledge.A lab-developed solution is probably applicable to the field kit, for example neutralization of chlorine with thiosulfate, or sample dilution in other cases.

      A big watch-out, but not necessarily big work !

      3- Document

      The list of things we should document can be broken down:

          • The field of use: what do we want to measure, what range, what nature of products, how are interferences avoided, range of temperatures, pH, storage precautions, shelf life..
          • Usage: instructions on how to use the product, description of reagent and equipment, additional reagents & equipment.
          • Sampling: description of sample quantity, volume, handling.
          • Protocol: health and safety, step by step handling (pictogram), reaction time (& intervals), ascertainment of results, cleaning, and maintenance.
          • Results: methods for assessing the results, conversion tables, factors.
          • Disposal (waste).
          • Characteristic of the method, such as calibration, certificate of quality, controls (standards)
          • References to the procedure and additional information (possible applications).

      We can save time by adding this requirement to part 1, as a selection criteria for the kit. The last bullet is : « How much of the documentation can the kit supplier provide? »


      Our organization is responsible for ensuring the method is applied correctly, which implies the users are trained.
      Field tests are typically designed for use in unusual conditions: they are simple and robust.

      ISO points out that personnel must have undergone basic training (by supplier or company) and understands:

          • Test performance
          • Matrix influence
          • Limitations
          • Sampling
          • Dangers and how to avoid them
          • Disposal
          • Quality Assurance
          After what the protocols should be handy and in local language

      The documentation developed in part 3 provides the fundamentals for the training. All that’s left to do is to have samples and time to practice until the results are satisfactory.

      The ISO 17381 introduces itself by highlighting that the use of autonomous field kits can be very convenient.
      In most cases, it will be because the kit supplier is prepared for our requests.

      Remember : Microbiology is like cooking (just don’t lick the spoon)

      6 uses of microbial autonomous field kits that can make your life simpler

      We will discuss here the use of microbial test kits on-site or off-site in a regulated environment to justify company practices or to ensure the results obtained with an official test will pass.

      This article, inspired by the reading of ISO 17381 (Water quality - Selection and application of ready-to-use test kit methods in water analysis), addresses the context and the applications covered in the Standard.

      In water, food, cosmetic, …monitoring, appropriate standardized and sometimes mandatory procedures exist for practically every microbial parameter to be investigated. They constitute the reference methods and are largely based on culture methods.

      These test methods require a laboratory,  equipment and technical expertise that are not always available in all facilities. In such case, companies often chose to subcontract the minimum number of mandatory tests to external labs, who have these resources and skills.

      The limitations of outsourcing all your microbiology tests

      Outsourcing all of your microbiology tests can have limitations such as:

        • Having to adjust personnel and equipment schedule to the sampling schedule
          Don’t we prefer the other way round ?
        •  The analysis reports comply with the regulatory or best practice standards, but is not comprehensive for the production manager.
           It can be a bit like when you receive the results from your blood analysis and try to understand if you are sick or not.
        • Finally, an individual accurate report has value, but the real thing is to have enough results to constitute a baseline, with which  to set alerts when the trend in going in a worrying direction.
           A bit like a road radar : perfectly reliable but too rare to help control our driving speed at all times.

      So calling upon other test methods, more user friendly, can be helpful for day to day operations to complement internal or external lab tests.

      Using Ready-to-use methods as in ISO 17381

      ISO 17381 « Selection and application of ready-to-use test kit methods in water analysis » provides guidance on how to properly use such kits.

      The so-called "ready-to-use methods" are of increasing interest because, compared to standard methods, they allow fast and often inexpensive results for analytical problems. Under certain conditions these methods can be applied in routine control of water quality, provided they give reliable results.

      The methods are not intended as a substitute for other standards, which remain the reference method for use in a laboratory.

      The choice of the most suitable method depends upon the type of analysis required and the necessary quality of the results.

      Ready-To-Use methods are frequently based on standard methods that have been miniaturized to allow their direct application.

      This suggests that in many cases data, references, guidance, expertise required to start using an AFK are readily available from multiple sources and that with limited effort, the AFK results will probably be consistent with those from reference methods, since they are based on similar principles.

      We believe the recommendations put forth in this standard can be extended to applications beyond water quality testing and have inspired this article.

      The different use of Autonomous Field Kits which can ease your microbiological tests

          • 1. Screening : Preselection for samples for further analysis by a laboratory, due to their lower overall cost and easiness to deploy.
            Example : testing batches of intermediate product. When a change in counts or flora is observed, send the test for identification of the suspects.

          • 2. Screening : Selection of the most suitable analytical method due to their lower overall cost and easiness to deploy.Example : comparing CIP protocols and CIP rinse water collection methods prior to testing.

          • 3. Rapid detection after a potential incident due to the rapid availability of the test and consequently of the test results.  
            Example : evaluating the impact on a work environment after an accidental spill of waste product or the introduction of a potentially contaminated product / equipment in  clean area.

          • 4. Limiting the amount of damage after an incident due to the rapid availability of the tests and consequently of the test results 
            Example : after an incident, for monitoring the efficiency of the curative actions e.g. cleaning, disinfection. Like in the previous application, the time-to-result is shortened because the test kit is readily usable, the sample transport time eliminated

          • 5. Control measurements for monitoring/preparing compliance with the permissible concentration range for a given microbial parameters 
            Example : commissioning a piece of new equipment or preparing the validation of a process. Kits can constitute a convenient way for engineers to adjust equipment settings.

          • 6. Monitoring and controlling processes, facilities, production plants, water treatment and disinfection systems
            Example :  routine environmental or hygiene monitoring, equipment and process maintenance programs, quality plans, …

      So, the list of potential applications listed in this Standard covers the majority of a site auto-control testing activities, with the exception of the mandatory compliance tests.

      Considering the autonomy, savings (time and money) these kits can offer they can constitute an interesting adjunct to lab test methods…provided the kits do the job you expect from it.

      A glimpse of the next article : Implementing autonomous testing methods following the ISO 17381

      The second part of the ISO 17381 deals with how one should go about verifying a kit is suitable for a given application, which we will digest in an article to come.

      What are the highlights?

      1. Prove the test suitability for your applications.
      2. Meet requirements for example concerning safety, handling and documentation, because these tests are often used by non-specialists in microbiology
      3. Meet requirements concerning user training and supervision

      Remember : « microbiology is the only science in which multiplication is the same thing as division »