Techniques: Using a microscope to explore fermented foods

Many producers and home fermentors often ask me what simple DIY tools are available to better understand the microbiology of their products. Unfortunately, identifying most microbes is challenging and requires some expensive equipment, extensive experience, and access to DNA sequencing technologies. But the use of a simple microscope has the potential to teach you a lot about the microbes in your product. In this series of articles, I’ll explore how microscopy can be a useful tool for managing and monitoring the microbes in fermented foods.


What can I learn from looking at the microbial communities of my product under the microscope?
The diversity of cell morphology of microbes can be very limited, making microscopy not very useful for distinguishing one species from another. This is why most microbial identification relies on DNA sequencing technologies and not microscopy. But at broader biological levels, such as genus, family or phylum, microbes often produce distinct cell structures that can be used to track their abundances. These differences can be useful for tracking abundances of microbial populations within your fermented or aged microbial food.

At one of the coarsest levels of biological organization, across different kingdoms (note that kingdom is a bit outdated, but often still used in biology) one can easily see the difference between yeast, mold, and bacterial cells. Mold (more accurately called filamentous fungi) cells are usually quite large and form large tubular structures called hyphae. These hyphae are interconnected, so we call these microbes multicellular. Yeasts are also fungi, but they produce small circular cells that are unicellular. Bacteria are also unicellular, and look similar to yeast cells, but they are usually much smaller than yeast cells (~half to one tenth the size of a yeast cell).

A cartoon (left) and microscopic image (right) depict the main morphological and size differences between molds (filamentous fungi), yeast, and bacteria.

A cartoon (left) and microscopic image (right) depict the main morphological and size differences between molds (filamentous fungi), yeast, and bacteria.

At even finer scales, microbes can present useful morphological differences under the microscope. For example, some molds produce spores that have distinct morphologies. One example from cheese rinds is illustrated below, with spores of Aspergillus, Scopulariopsis, and Sporendonema. Aspergillus is a mold that is generally not desirable to have on the surface of your cheese, while the latter two genera contain species that are part of ‘normal’ rind microbial communities. These morphological differences can help you monitor whether undesirable species are present in your product or whether cultures you are adding to your product are actually growing in/on your product.

Examples of different spore morphologies that one can observe under a compound microscope.

Examples of different spore morphologies that one can observe under a compound microscope. Left shows Aspergillus, center shows Scopulariopsis, and right shows Sporendonema. All of these molds can be found on the rinds of cheese. Photos were taken at varying magnfiications from 400X to 1000X.

Before I go further, I want to make a really important note: to be absolutely sure about product safety, DO NOT rely on microscopy. Microscopy can only provide clues and coarse identifications of microbes. Send your product to a certified lab for testing for full identification.

Another useful way to integrate microscopy into your fermentation is to track specific stages in the life cycle of a microbe or look for patterns of colonization within a product. Some fermentations require microbes to get to certain stages of growth where they make specific structures. In some cases, you want to stop microbes from transitioning into another growth phase. One example is with the mold koji (Aspergillus oryzae). I recently looked at rice grains colonized by koji with Todd Bellomy of Dovetail Sake in Waltham, MA. Todd was interested in using microscopy to check how well the rice grains were colonized and how far his koji had penetrated into the rice. This allowed him to understand how strains he was using could impact product development and how his koji production could be manipulated.


What are the main types of microscopes available?
Stereomicroscopes (sometimes called dissecting microscopes) are useful for looking at larger objects that don’t require a lot of magnification. Cheese mites can be easily seen with a stereomicroscope. Closeup views of surfaces of fermented foods like cheeses and aged meats can be also obtained under a stereoscope and can provide potentially useful indicators of rind development. Cells of bacteria and fungi however, cannot be easily seen with a stereomicroscope. Only bigger structures produced by these microbes, such as gross morphology of conidiophores of molds, can be seen.


A steromicroscope (left) is useful for situations where you want to take a closer look at a microbial food, but don’t need to see cellular level detail. Two examples are cheese mites (top left) which can be seen here eating the molds that colonize the surface of a natural rind cheese. The mites are the shiny, beige, circular structures. The surface of a salami (bottom right) reveals colonies of bacteria (the white and yellow circular structures) and fuzzy mold mycelium. Photo of stereomicroscope from Wikipedia user GcG(jawp).


Light (also known as compound) microscopes, can see microbes at much finer resolution and have higher magnification power. When samples of a food are placed on a microscope slide and viewed under a light microscope, one can observe the cellular structures of the microbial community present. These microscopes come with different objective lenses, usually ranging from 10X to 100X. Combined with standard 10X ocular lens magnification, this can provide 100X to 1000X total magnification.

A typical light microscope. The left panel shows a kombucha SCOBY at 1000X magnification (10X ocular lens, 100X objective lens).

A typical light microscope. The right panel shows a kombucha SCOBY at 1000X magnification (10X ocular lens, 100X objective lens). Microscope photo from Wikipedia user “Moisey”


What features should I consider when buying a microscope?
If you are really interested in clearly seeing bacterial cells or looking at bacterial morphology, it will be critical to get a microscope that has a 100X objective lens. This will give you the magnification power to see bacterial cells and to observe differences in morphology of the bacterial cells. This 100X objective lens requires the use of oil immersion, which I will explain in a future techniques post.

Another thing to consider is whether you want to take photos of what you see under the microscope. If you are patient and skilled, it is possible to just put a digital camera up to the eyepiece of the microscope and take photos. But if you want high quality and consistent photos, you’ll want to invest in a camera adapter and digital camera. Check out this very detailed post over at MicrobeHunter about various ways to connect a camera to a microscope.


How much should I expect to pay for a basic microscope?
For a decent dissecting scope, expect to pay several hundred dollars. For a basic and fun stereoscope that is excellent for teaching and outreach activities, I love the USB microscopes from Dino-Lite. I used one of these inexpensive and quite easy-to-use microscopes to take the picture of the cheese mites above.

For a new light microscope that is both high-quality but also fairly basic, expect to pay around $900 to $1200. I recommend this Zeiss model (the Primo Star) to people looking for their first light microscope. I’ve used it in undergraduate teaching labs and while in the field working with cheese makers. Keep in mind that a camera adapter and camera will add to the cost.

If you are looking for used microscopes, two great sources are LabX and Cambridge Scientific.


In my next post in this series on microscopy in artisan fermented food production, I’ll review basic microscopy techniques and demonstrate how they can be used to look at the microbial communities of yeast, cheese, and salami. Stay tuned for more!

Post written by Benjamin Wolfe. Photos by Benjamin Wolfe unless otherwise noted.


Have you used a microscope to develop your artisan fermented food? I’d love to hear about your experience and possibly feature it in future pieces in this series.  Please comment below or get in touch via our Contact Us page.


There are 7 comments on this article

  • Lisa T says:

    I would love to be able to count the LAB bacteria in my ferments, too. However, I’ve come across literature that suggests it is difficult to obtain a true reading. This is due to requiring different culture medias depending on what type if LAB and because you are taking them out of their natural environment when counting them.

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    • Hi Lisa –

      What type of ferments are you working with? In vegetable ferments and things like kombucha, it is quite easy to see and count LABs with a microscope.



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  • Excuse me, but the link to the Zeiss Microscope is broken.
    What Zeiss model exactly is it, you recommend?

    Reply to this comment
    • Hello Jan –

      Thanks for pointing out the broken link. I just fixed it. The model is the Zeiss Primo Star.


      Reply to this comment
  • […] Foto Exploring Fermented Foods under a Microscope […]

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  • Awais Khan says:

    A great piece to read on. Thank you !

    Reply to this comment

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