Microbial Testing in Cannabis: Navigating the Basics and Beyond with LIMS

The Role of LIMS in Microbial Testing in Cannabis

As cannabis gains legal ground across various states in the United States, the absence of universal federal regulations has created a diverse landscape of testing standards, with each state marching to its own set of rules. Amid the budding promise of legalized cannabis, the lack of standardized methods for microbiology testing has repercussions echoing across state lines, evidenced by product recalls in states such as Oregon and Arizona due to fungal and bacterial contamination. The stakes are high, particularly for the vulnerable population turning to medical cannabis for relief. With no standardized safety net, immunocompromised patients face an elevated risk of severe illness or worse, death, from contaminated cannabis products. 

In this blog post, we look under the hood to unravel microbial testing in cannabis — understanding its significance, identifying prevalent microbial contaminants such as bacteria and fungi, exploring current testing methods, and more.

What is Microbial Testing?

Microbial testing in cannabis is a process designed to assess the presence of microorganisms, such as bacteria, molds, fungi, and yeast, in cannabis products. The goal of microbial testing is to ensure the safety and quality of cannabis for consumers, particularly in the medical cannabis space where patients may have compromised immune systems.

The testing typically involves analyzing samples from cannabis plants, flowers, or related products to detect and quantify microbial contaminants. Common contaminants targeted in microbial testing include harmful bacteria like Escherichia coli (E. coli), molds such as Aspergillus, and various types of fungi and yeasts. These microorganisms can pose health risks, especially when inhaled or ingested, making it essential to identify and control their presence in cannabis products.

What are Some Common Microbial Contaminants in Cannabis? 

Cannabis plants and products can harbor a variety of bacterial and fungal microbes that are detrimental to human health. There are two primary ways in which these microbes can pose threats. The first involves active infection, wherein the rapid proliferation of the microbe induces cellular damage, toxicity, and an alarmingly excessive activation of the immune system. The secondary pathway is attributed to toxins generated by certain species of microbes. These toxins can induce illness even when the bacterial or fungal cell responsible for toxin production is no longer viable. 

  • Mold and Fungal Contamination: The most significant threat to human health in cannabis products arises from mold and fungal contamination. Among the prevalent fungal species identified in cannabis, Penicillium and Aspergillus are notable for producing aflatoxins. Additionally, Fusarium, another common fungal species, generates mycotoxins, referred to as fumonisins. Regarded as carcinogens, these toxins have been associated with toxicity and the induction of cell death in the liver, kidneys, and neurons. Cannabis contaminated with Aspergillus may trigger allergic responses in individuals without underlying health issues, and it has been explicitly associated with pulmonary aspergillosis—a serious condition affecting immunocompromised patients.
  • Bacterial Contamination: While less frequent than fungal contamination, bacterial contamination in cannabis products has been identified in several studies. Escherichia coli, Listeria monocytogenes, Salmonella, and Clostridium are human pathogens commonly associated with cannabis. Escherichia coli can induce various illnesses, encompassing gastrointestinal symptoms such as vomiting, diarrhea, and meningitis. Both L. monocytogenes and Salmonella species can lead to foodborne illnesses characterized by gastrointestinal symptoms, posing heightened risks to individuals with weakened immune systems. Additionally, Clostridium botulinum produces the potentially lethal botulinum toxin.
  • Filth Matter: Apart from mold, fungal, and bacterial contamination, cannabis products are also tested for filth matter, broadly defined as any substance that shouldn’t be present in food or edible products, encompassing rodent feces, insects, insect fragments, parasites, and other extraneous materials that may inadvertently enter a product during processing and storage. Consuming cannabis contaminated with filth matter can lead to a range of adverse health effects, such as gastrointestinal symptoms like nausea, vomiting, abdominal pain, and diarrhea. Additionally, depending on the nature of the contaminants, there is the potential for more severe health consequences, including infections or allergic reactions.

Microbial Testing Techniques in Cannabis

Key techniques that ensure the purity and safety of the final product in cannabis microbial testing include:

  • Culture Plating-Based Methods: Culture plating is a traditional and widely used method in microbial testing. This technique involves taking a sample from a cannabis product and placing it on a specialized growth medium that supports the growth of specific microorganisms. The sample is spread or streaked onto the medium, and under controlled conditions (temperature, humidity), microorganisms present in the sample proliferate and form visible colonies. These colonies are then counted and identified, providing information on the types and quantity of microorganisms in the sample.
  • Polymerase Chain Reaction (PCR) Methods: PCR is a molecular biology technique used to amplify and analyze DNA. In microbial testing, PCR is employed to detect the presence of specific genetic material from microorganisms in a cannabis sample. A small amount of DNA is extracted from the sample, and specific target sequences related to the microorganisms of interest are amplified using PCR. This amplification allows for the detection and quantification of the microorganisms present in the original sample.
  • Most Probable Number (MPN) Methods: MPN methods are statistical techniques used to estimate the number of microorganisms in a sample based on the presence or absence of growth in a series of tubes or wells. Multiple tubes or wells with different dilutions of the sample are inoculated with the microbial culture medium. The presence or absence of growth in each tube is then used to statistically estimate the most probable number of microorganisms in the original sample.

Contrasting Culture Plating and Molecular Methods

Culture plating-based methods can be time-consuming and require skilled analysts to interpret results. Total organism counts, such as yeast and mold counts, are determined through culture plating, but issues like plant material interference can affect accuracy. Notably, Aspergillus, a significant contaminant, may be under-reported using these methods. The cut-off for passing this test doesn’t distinguish harmless from harmful organisms. Additionally, water activity levels serve as a proxy for contamination, with inadequately dried cannabis buds potentially supporting microbial growth. Recognizing the time constraints, labs are increasingly adopting molecular methods like quantitative polymerase chain reaction (qPCR) for faster and more specific results, albeit with concerns about accuracy, especially for yeasts and molds.

How Does a Laboratory Information Management System (LIMS) Support Microbial Testing in Cannabis?

A LIMS can be an invaluable asset for laboratories engaged in cannabis microbial testing. A LIMS efficiently manages and organizes vast amounts of data generated during microbial testing, ensuring accurate record-keeping and traceability. The interoperability with testing equipment provides a seamless workflow, reducing the risk of errors and expediting the testing process. A cannabis LIMS is instrumental in quality control. It automates workflows, minimizing manual interventions, and maintaining consistency in testing protocols. The system’s robust reporting capabilities enable laboratories to generate detailed and customizable reports, facilitating analysis and meeting regulatory requirements. Furthermore, a LIMS is not only a cornerstone in optimizing microbial testing processes but also helps laboratories align with the stringent standards outlined in ISO 17025.


Microbial testing, crucial for ensuring the safety and quality of cannabis products, detects the presence of harmful microorganisms such as bacteria, molds, fungi, and yeast. The prevalence of contaminants such as Escherichia coli, Aspergillus, and Penicillium poses significant health risks, especially in medical cannabis where patients may have compromised immune systems.

While traditional culture plating methods of microbial testing have their merits, molecular methods such as PCR are gaining traction for their speed and specificity despite concerns about accuracy.

Furthermore, the integration of LIMS emerges as a crucial tool in optimizing cannabis microbial testing. A LIMS not only streamlines data management but also enhances workflow efficiency, minimizes errors, and ensures compliance with stringent standards.

In a continually evolving scheme of things marked by regulatory variations and advancing testing methodologies, the call for standardized federal regulations in cannabis microbial testing is imperative. It is not only a matter of ensuring product safety but also safeguarding the well-being of those who rely on cannabis for medicinal purposes.

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