Colony Forming Units Explained: How to Interpret Probiotic and Pathogen Strain Counts

In microbiology, numbers can look deceptively simple. A product label may show millions or billions of bacteria, a trial result may report a ‘3-log reduction’, and a laboratory report may use colony forming units (CFU) or most probable numbers (MPN). These various terms help us understand whether a probiotic contains enough viable organisms, whether a pathogen challenge has genuinely been reduced, and whether we are fairly comparing products.

What Is the Difference Between Probiotic Species and Strain?

To understand how a microbe may perform, it is important to understand both the species and the strain (e.g Binda, et al. 2020). Even within the same bacterial species, different strains can behave in very different ways. For example, some strains of Staphylococcus aureus may live harmlessly on the skin, while others can cause infections. This is also true for probiotics: strains from the same species can vary widely in their beneficial effects.

• Species (the lineage): The broad group a microbe belongs to; it does not tell us the full story.
• Strain (the behavior): A specific version within a species; this detail can make all the difference.

This distinction is especially important for probiotics. It is not enough to say that a product contains Bacillus, Lactobacillus, or another familiar bacterial name.

Strain identifiers such as ATCC, DSM, NRRL, or NCIMB numbers act rather like a passport or fingerprint for the microbe, helping us know exactly which organism is being used.

What Are Colony-Forming Units (CFU), and How Do You Interpret Log Reductions?

Once we know which strain we are talking about, the next step is to determine how many viable cells are present. CFU is a measure of living bacteria that can grow into visible colonies under culture conditions. Results are usually expressed as CFU per gram, millilitre, or kilogram depending on the sample. CFU is commonly used for probiotics in animal feed, food, or even supplements; as well as for bacteria recovered from laboratory or field samples.

Bacterial numbers can become very large very quickly—a difference between 100,000 and 10,000,000 cells is hard to interpret at-a-glance. This is why microbiologists often use logarithmic (log) units.

• 1-log change = 10-fold change
• 2-log change = 100-fold change
• 3-log change = 1,000-fold change

So, when a pathogen count drops by 3 logs, that is not just a small improvement on a graph. It means the count has been reduced by a factor of 1,000.

This way of thinking is critical when interpreting trial results. If a treatment reduces Salmonella by nearly 4 log units, that represents an approximate 99.99% reduction. On a chart, this may appear as a few units on a vertical axis. In biological terms, however, it reflects a very large change in the number of viable bacteria. This is why the key message is simple: count in CFU but think in logs.

What Is Most Probable Number (MPN) in Microbiology?

MPN is another counting method used in microbiology (U.S. Food and Drug Administration, 2023). Unlike CFU, MPN is not a direct colony count. It is a statistical estimate based on whether growth occurs across a series of diluted liquid cultures. The pattern of positive and negative tubes is compared with probability tables to estimate the likely number of viable organisms, usually with confidence limits. MPN is particularly useful when bacterial levels are low or when colonies are difficult to count on plates.

Which is Better: CFU or MPN?

The answer depends on the question. CFU is generally preferred when viable bacteria are present at medium to high concentrations and can be counted directly. MPN is useful when concentrations are low, or the sample is difficult to plate reliably. Both methods estimate viable cells, but they do so in different ways and should not be confused.

What Makes a CFU Claim Meaningful?

Big numbers do not automatically mean better products. A high CFU claim should always prompt several questions:

• Is the count given per gram or per kilogram of product?
• What is the inclusion rate?
• How many organisms reach the final feed?
• How many survive processing, such as mixing or pelleting? And most importantly,
• Which strain is present?

As microbiology advances, culture-based counts will increasingly be complemented by microbiome analysis and we will be asking:

• How many bacteria are there?
• Which organisms are present?
• What are they doing?
• How does this affect animal health and resilience?

Turning Microbial Counts into Confident Decisions

Kemin connects strain-level microbiology, feed-processing validation and practical application expertise to help animal nutrition professionals assess what microbial counts mean in real-world conditions. Explore Kemin’s animal nutrition and health expertise or learn how the strain-specific science behind CLOSTAT^® or ENTEROSURE^™ supports a more resilient intestinal environment.

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References

Binda, S., Hill, C., Johansen, E., Obis, D., Pot, B., Sanders, M.E., Tremblay, A. and Ouwehand, A.C. (2020) ‘Criteria to Qualify Microorganisms as “Probiotic” in Foods and Dietary Supplements’, Frontiers in Microbiology, 11, p. 1662

U.S. Food and Drug Administration (2023) Bacteriological Analytical Manual Appendix 2: Most Probable Number from Serial Dilutions [online]. Available at: https://www.fda.gov/food/laboratory-methods-food/bam-appendix-2-most-probable-number-serial-dilutions (Accessed: 7 August 2026).