Observing bacteria under the light microscope

Can one see bacteria using a compound microscope? The answer is a careful “yes, but”. Generally speaking, it is theoretically and practically possible to see living and unstained bacteria with compound light microscopes, including those microscopes which are used for educational purposes in schools. There are several issues to consider, however.

Why bacteria are difficult to see

Bacteria are difficult to see with a bright-field compound microscope for several reasons:

  • They are small: In order to see their shape, it is necessary to use a magnification of about 400x to 1000x. The optics must be good in order to resolve them properly at this magnification.
  • Difficult to focus: At a high magnification, the bacterial cells will float in and out of focus, especially if the layer of water between the cover glass and the slide is too thick.
  • They are transparent: Bacteria will show their color only if they are present in a colony. Individual cells present on the slide are clear. Regular bright-field optics will only show the bacteria if one closes the condenser iris diaphragm. This is due to the difference in the refractive index between the water and the bacterial cells.
  • Difficult to recognize: An untrained eye may have problems differentiating bacteria from small dust and dirt which is present on the slide. Some bacteria also form clumps and therefore it is difficult to see the individual cells.

Research organizations and advanced amateurs use phase contrast optics to see bacteria. This system converts the differences of the refractive index of the bacteria into brightness. The transparent bacteria can then be seen dark on bright background. In bright-field, closing the condenser iris diaphragm will also make the bacteria appear darker, but at the same time one also introduces artifacts (“fringes”) around the individual cells. This is because of the diffraction of light. One possibility is to stain the bacteria, but in this case the fixing and staining process may introduce other artifacts, and it kills the bacteria.

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How to observe bacteria

Most people do not have a phase contrast microscope, which makes it much easier to see bacteria. It is still possible to see them, if your microscope has a condenser. Here are some suggestions.

  • Use the 40x objective: With the 10x eyepiece you get 400x total magnification. This is enough to see them. Of course you have to start focusing with the 4x and 10x objective first and then work your way upwards.
  • Completely close the condenser: This will increase contrast and depth of field. If your microscope does not have a condenser, then you might not be able to see them. In this case I suggest that you buy some ready-made slides with stained bacteria.
  • Use very little water: When making the slide, use very little water and make sure that there are no larger particles under the cover glass. There must be a thin film of water beneath the cover glass. Otherwise the bacteria can float vertically and go out of focus. The cover glass should not float on the water. As a matter of fact, it is better if the water is so little that it is not even able to spread beneath the whole cover glass.
  • Keep bacterial density low: If there are too many bacteria in the sample, then they will overlap and you will only see a clump.

What is a safe source of bacteria?

For recreational or educational purposes, one should never use spoiled food or (heaven forbid!) use bacteria obtained from the human body and grown on agar plates. The risks involved are simply not worth it, especially when working with students. Other sources, such as soil or humus have other disadvantages. The impurities make it difficult to keep bacteria from other particles apart, especially if one uses bright-field optics. Ideally you would like to have only bacteria, without many other things. I recommend the following:

  • Yogurt: You can make own yogurt and then put a sample under the microscope. It should be possible to see small circular cells (cocci), which may also occur in pairs or chains. There are also many clumps in the yogurt and you have to look between these. Watch the video here.
  • Cheese: It is also possible to scratch some bacterial cells off from certain kinds of cheese. Brevibacterium can be found on Limburger cheese, for example. One has to be aware that some cheeses use a combination of bacteria and fungi, however, and that the larger fungal cells may outweigh the bacteria. It is also possible to buy freeze-dried bacteria.
  • Freeze dried: It is possible to buy freeze-dried bacteria for the purpose of making yogurt. Take a small amount of it and put it into water to dissolve before putting it under the microscope.

What is the easiest solution to see bacteria?

Bacteria stained
Commercial slide showing stained spiral-shaped bacteria.

The easiest and least complicated solution to view bacteria using light microscopes is to buy a prepared permanent slide. The bacteria are then stained and in a sufficiently high concentration. The image above shows bacteria of such a slide. This is not only safe, but becasue they are stained they can be easily seen also with microscopes that do not have very good optics.


If you just want to look at microorganisms and do not mind so much if they are bacteria or not, then I recommend baker’s yeast (Saccharomyces cerevisiae). These are not bacteria but also interesting to watch. Add some water and sugar and watch them divide after a few hours. It is also possible to get some fungus from various cheeses. These fungi can be eaten and are safe.

In summary, there are easier (and maybe also more interesting) specimens to observe than bacteria. I you want to see individual cells, then I do recommend that you start out with yeast suspensions. These eukaryotic cells are much larger and can be more easily identified.

algae, bacteria
Large green algae (eukaryotes) and bacteria (prokaryotes) – the small dots.
Yoghurt bacteria grow in long chains.
Yoghurt bacteria grow in long chains.

Further Reading

72 thoughts on “Observing bacteria under the light microscope”

  1. Bacteria are difficult to observe. Try yoghurt bacteria. You can also buy dried bacterial cultures (Amazon.com) to make yoghurt.

  2. To observe bacteria try yoghurt. Bacteria are difficult to observe, because they are small and transparent. You can also by dried bacterial cultures (Amazon) to make yoghurt.

  3. Hi Oliver,
    I recently brought an bright field microscope, 1500x microscope. While showing my kids different pre made slides of different kinds of becterias, I was wondering if I could show them live collection of becterias from safe sources like curd etc, with regard to that can I use methlene blue as staining dye as gram stain was a little costlier.

    Also kindly guide me how can I can successfully stain( if I can). It is pertinant to mention that I have brought slide,coverslips, pasture pippete other prerequisites already…

    Thanking in anticipation.

  4. You were looking most likely at a mixture of bacteria and fungi. The fibers could have been the fungal cells, they grow in fibers. There were probably hundreds of different bacteria and fungi in it, if you drank out of it, it was contaminated with many different species plus those added from the air. And if you were looking at Streptococcus or any other species can not be said from microscopic observations alone. Microscopes help in saying IF there is something there, but not WHAT. Identifying bacteria is complicated stuff (DNA Analysis or biochemical Analysis) and in order to do this, you need to first bring them into a “pucre culture” and grow then in the lab, and this takes a lot of time. You can not identify bacteria from an original source directly.

  5. Sorry, no chance.
    1. You will have Problems even identifying bacteria from meat (too many other cells and debris around)
    2. You can not see under the microscope if a cell is alive or not. Movement is not an indicator, as not all bacteria move and if they seem to move, then this can be due to Brownian Motion.
    3. You have to put the herbs on an agar medium and then observe if bacteria are able to grow next to it or not. Use garlic as a reference, as this one definitively kills off bacteria. The substance diffuses into the agar and then blocks bacterial growth, even if away from the spices.

  6. My bio teacher used a chemical(like eye drops) to slow down microorganisms in the slide.
    Does any one know what that was, and where i can get it?

  7. Sir, im doing my undergraduate thesis, it was a meat herbal preservatives. Is it possible for me to see under the microscope the capability of oregano oil to kill a bacteria in a thin slice of meat using a compound microscope within a few no. of days, if not, sir can you give me some advice what kind of microscope to use to see that certain experimentation. Thank you sir!

  8. Hello sir,

    Being only a junior in high school, I am not very familiar with identifying microbes or the specific equipment needed for proper viewing/identification. I rediscovered a 6-week old bottle of tea, and noticed that it had large, mucus-like chunks of “stuff” floating in it. Since the bottle had been opened and drank out of, I assumed the material was some sort of bacteria. (I could be completely wrong here, and in that case, everything after this may be disregarded) I did some research on the most common types of bacteria which inhabit the mouth, and I found that Streptococcus was fairly common. (Whether it’s a type of Streptococcus A or not, I’m not sure) I filtered the material to obtain a more concentrated sample, and brought it to school this morning. Upon viewing it with a light microscope, I could not see any individual bacterium. (Obviously, as you explained, they are invisible and too small to be seen) What I did notice however, is that the material appeared fibrous. What was I seeing? Was I looking at some sort of bacterial colonies, or is the substance not even bacteria at all? Any answers or references would be extremely helpful!

  9. Hello, To see Brownian Motion, you can look at very diluted milk-water mixture. The milk fat droplets can then be seen vibrating. Would be an interesting school project to observe the Vibration as a function of temperature. If the milk is too concentrated, then the fat droplets can not move as freely as they bump into each other. Oliver

  10. Very interesting indeed. It seems unbelievable that a large particle could be moved by individual molecules, but then again, quantum mechanics is also unbelievable 😉 Thank you again for the pointer. It’s wonderfol to be able to point out an observable effect of molecules to my students. I sure will be looking for this effect in the future.

  11. Hello,
    Small particles moving about are nothing unusual. They do not even have to be alive, sometimes Brownian Motion is enough to make particles move. If you saw the particles inside the cells, then it is highly unlikely that they were bacteria. You were probably seeing some cell organelles, but even many of them are difficult to see sometimes using light microscopes. Plant cells do not rely on organic food, which is taken up.

  12. Thank you for this wonderful and instructive thread! I’m a science teacher (specialized in physics, not biology), and I’m wondering about an observation I did earlier this year. While observing plant cells in a leaf with my students, I noticed small black particles moving erratically about in some of the cells. This was at 400x magnification in a common light microscope. The particles were just large enough to be visible, and a lot smaller than yeast cells. Is it likely that we observed some kind of bacteria, or is there some other explanation? Do you know if this is common in leaves during the autumn?

  13. Culturing any kind of bacteria from humans requires increased safety (due to Staphylococcus aureus, etc). The bacterial concentrations of cultured bacteria can be extremely high. This is why proper safety and handling techniques are taught in university. Researchers found out, that there were more bacteria found on computer keyboards than on toilet seats. After all, toilet seats are cleaned and disinfected. When was the last time you disinfected your computer keyboard? The issue is not the toilet seat per se. It is rather objects that have come in contact with human skin (on which you can find possibly opportunistic pathogens.)

  14. hello l’m a university student and recently we had a practical on culturing bacteria and we cultured some from a public toilet seat after reading your article l actually think it wasn’t wise what we did

  15. hello,
    you can not tell by microscopy. Even cells that appear to move might be dead but move due to Brownian motion. You have to do cell plating in order to determine the viable count of bacteria.

  16. I performed the hanging drop mount technique of a culture and the culture showed no movement of the cells. How can i distinguish between whether the cells are truly non-motile or whether they may simply be dead?

  17. >identification thru the agar plate

    If you intend to observe the agar plate directly (put the agar plate under the microscope directly), then this is not possible. There are microscopes that are used in cell culture, which allow the petri dish to be directly placed on the microscope (inverting micrscope), but bacteria are far too small. It is also not possible to “identify” bacteria using microscopes alone, as the shape of the cells has too little information content.
    regards, Oliver

  18. Hi,
    I am a compounding pharmacist and we do sterile compounding (injectable and eye drops) in our sterile room. Part of our quality control is to do a finger tip test after we finish our work to prove that our hands are still “clean” at the end of the process. We use sterile agar plates for this purpose. Rarely, we will have a growth. We are now required to identify the growth. It has been a long time since I danced with a microscope in college! Is there a particular type microscope that would fit the bill for identification thru the agar plate so that we do not release anything into out lab? Any practical advice would be most appreciated! You are truly making a difference!

  19. DF and Phase contrast are both contrast enhancing techniques, both work for visualizing bacteria, but the principle is different and DF is very dust sensitive. For determining live bacterial count one generally has to do a growth test on agar plates. Some motile bacteria do not move, others are dead, yet others are simply not motile. Motility is not a good indicator. Decomposition is the breakdown of substances by bacteria. So dead bacteria will be consumed by other bacteria. Lactic acid bacteria live off the sauerkraut and form lactic acid as a waste product. If you want, you can say that these bacteria also “decompose” the sauerkraut, even though this term is often not used in that context.

  20. This type of microscope is not designed for this. bacteria are really small and in order to get the required resolution, the objective must be very close to the specimen. You need a compound microscope for this. The VHX-600E has a different application (epi-illumination).

  21. phase contrast for bacteria. Urine is generally free of bacteria, unless there is some infection. Microscopes can not be used to identify pathogens, however.

  22. Theoretically yes, especially if phase contrast microscopes are used, but bacteria are difficult to identify (small size).

  23. Hello, Is it possible to view bacteria from water sample taken from saltwater aquarium and any other organism with microscope up to 400x ?
    Thank you.

  24. Hi there!

    If I wanted to see any pathogens in a patient’s urine, would I be able to use a simple light microscope or would I need to use a phase-contrast microscope?

    Thanks in advance!

  25. I am counting bacteria and I do not know what to use can you help me please,


  26. Hello Mr. Oliver,

    I recently acquired a digital microscope Keyence VHX-600E. I want to use this to see bacteria. the lens has a magnification of 100x to 1000x. I used gram stain on the slide and I know it is of Bacillus sp. But I still can’t get a clear image of the individual bacterial cell. Is this kind of digital microscope capable of seeing this?

  27. Thank you for your generous time and comments on the subject of microscopy. I have found your comments very informative and even entertaining. I intend to purchase a microscope with some form of image capture in the near future. Your article on the different methods of doing just that was excellent. I have some experience in electronics and really liked the “web-cam” and “surveillance-cam” projects you built. This thread gave me valuable insight into what I will and won’t be able to see as well as a better idea on what I might purchase. So again thanks for your efforts, this is what makes the internet great !

  28. You might try to use Paramecia (cam be ordered, used for fish food), but beware that the public might not respond well to this. Paramecia have no nervous system, therefore can not feel anything, they are single celled but people might get emotional if you kill them.

    Alternatively you might want to treat a yoghurt bacteria culture (can be ordered in dry form) with acid and then demonstrate that it is not able to ferment yoghurt anymore.

  29. The charcoal filter is indeed a likely source. The filter lasts only for a certain quantity of water and then must be replaced. Microscopy will not be useful for identifying microorganisms in drinking water (no matter what type of technique you use), as the concentration of them is way too low. For determining bacteria in drinking water you have to collect bacteria from many liters of water by passing it through a micro-sieve, and then cultured on agar plates, which is done by laboratories, but not useful and feasibly at home.

  30. Is it possible to use darkfied/phase contrast to look for pathogens in distilled water?

    I home distill water, and have noticed that if the tank is not sterilised every few weeks can get (minor) symptoms. After sterilising the tank, the symptoms disappear.

    I would like to try and see what, if anything, might be causing this – and make it easier to know when to sterilise.

    There is a loose charcoal filter fitted above the tank, and I’ve sometimes thought that that could be a source of contamination.


  31. Could Darkfield be used as an alternative to phase contrast?

    I want to check fermented food for mould, also to get an approximate idea on the number of LABs in eg. sauerkraut.

    You say it is only possible to determine live from dead bacteria if they are motile – which I think some species of LAB are. But would the non-motile ones not decompose or something after death?

  32. I see your point: if bacteria do not move while alive, then we certainly can’t observe whether they are dead or not. Any suggestions on demonstrating the killing power of a strong acidic water (in a cost effective way)?

  33. Difficult to see, because microscopes are not reliable in telling you if bacteria live or not. Larger organisms stop moving, but many bacteria do not move on their own. How do you want to know if they got killed? To visualize bacteria you need a phase contrast microscope (expensive), otherwise they are too difficult to see. But even then it is not possible to see if they got killed or not.

  34. Hi Oliver,

    We are looking for a way to show a live culture (saliva or yoghurt starter culture), then to show them again after exposing them to a strong acidic water (2.5 pH) to see if the acidic water is effective in killing the culture. We want to do this as a live demonstration in front of an audience. Could we use a digital microscope? What would you suggest to be a way to do this?

    Thank you.

  35. Thanks Oliver for your suggestions.
    I will try to catch a good 400x biological microscope to go deep in my investigation on the subject.
    Happy Christmas

  36. Daniel,
    For viewing/counting bacteria 400x is sufficient (ideally phase contrast, expensive), the difficulties are somewhere else. There are often clumps and it is therefore difficult to see individual cells. For a reliable count, you have to do cell plating, but counting them out is theoretically possible. The cells might move around (evaporating liquid) and tracking them can be difficult. You need to dry the sample, but then the clumps might become worse.

  37. Dear Oliver,

    I would like to be able to distinguish between Streptococcus Thermophilus (round size 1um, often chains of cocci) and Lactobacillus Bulgaricus (rod size 3-10um, sometime making chains) in my homemade yogurt in order to characterize it regarding % of cocci respect % of rods in several yogurt coltures at different temperatures (35-45°C).

    So my dilemma is:
    – what biological microscope minimum magnification do I need to clearly see both bacterium in bright field? I mean, 400x is enough or not to distinguish between them?

    My fear is that a good 400x microscope (with 10x ocular) is not enough to accomplish my task and that I need 100x with oil immersion.

    I wouldn’t Gram stain them (for semplicity) hoping to find a trick to count them anyway.

    Any suggestion to obtain the best results with the lower cost as possible (100x microscopes are quite expensive)?

    Thanks a lot for you precious time

  38. Digital zoom alone is not enough to resolve bacteria. You need a microscope with a 40x or 100x objective to see them. Bacteria are generally difficult to see, due to their low contrast and small size. Regular bright field microscopes are not able to show bacteria well if they are not stained, so you need to get slides which are stained. Phase contrast microscopes (expensive) work best for bacteria (stained and unstained). If you just want to show cells (and if it does not matter if they are bacteria or not), then I would recommend that you use yeast (eukaryotic fungus), which are much larger and much easier to see.

  39. Hello,

    I am interested in being able to show prepared slides of bacterial on a monitor through a digital microscope for museum education purposes. Is this possible if I use prepared and stained slides? Do I need optical zoom or will digital zoom work with stained slides?



  40. Cold flu is not a bacterium, it is a virus and viruses can not be seen with light microscopes. You need an electron microscope of a magnification of about 100000x or more. Light microscopes only go up to 1000x.
    Bacteria can be seen starting 400x – 1000x but you need phase contrast equipment (expensive) to see them well.

  41. how much magnification do you need on a microscope to see cold of flu bacteria?

  42. I have no idea what this could be. Can you post a picture of this? It could be that the drying water droplets start to accumulate salts (etc) forming these lines.

  43. Hello,
    Of course it is possible to observe bacteria directly in e.g. a sample of saliva, but there is little scientific meaning to this. We already know what to expect. You will see different bacteria of different shape and size. There is no “higher” scientific point to this. This knowledge is already there. It only becomes more interesting when a variety of chemical tests are done on the bacteria in order to identify them (microscopy alone is not enough to identify bacteria), eg for diagnosis of illnesses, etc. And for this you must grow them in pure culture. There are other reasons as well.

    1. Saliva contains a mixture of different bacteria, sometimes it is more useful to observe bacteria of one kind. To get this “pure culture” you need to grow them on petridishes and then observe one single bacterial colony (which contain bacteria of one kind).
    2. the concentration of bacteria in saliva is lower than in pure culture grown on petridishes
    3. The growth medium used for petridishes can promote the growth of certain bacteria but not others. This way it is possible to selectively grow only those bacteria that one is interested in.

    I can think of one thing where it would make sense to observe bacteria directly in saliva would be in order to directly count the bacterial density, if this is what is needed.

    All the best, Oliver

  44. Hi Sir,

    Thanks for the helpful article.
    Im just interested in knowing why medtechs grow bacteria in a petridish and use the grown bacteria to put on the slide when they can just use the sample like saliva to see the bacteria?


  45. Sir, I am studying wet soil samples from my gardens. Some of the slides display white lines when they dry. What is the cause of this. I am using a light microscope at 400 power. The only thing I can think of is that the droplets are contracting causing division lines. They look like geomertric rice paddies as viewed from an airplane. Thank you! Richard

  46. Compound microscope with 400x magnification. Bright field is possible but phase contrast is preferred.

  47. Hello,
    In short: it is impossible to identify bacteria down to the species level just by Gram staining and microscopy alone. There are probably millions of different bacterial species and only a small number of them have been described so far. Shape and staining reactions are simply not able to give you this information (you can not identify several million different bacterial shapes, and even if, the shape says nothing about the species). Can you identify the type of animal by counting the legs? Or by looking at the color of the fur? Or by looking at the size? These characteristics too, are not species specific. If I give you a bird (2 legs) and a cat (4 legs) and then ask you to identify which one is which by counting the number of legs, then this is possible, because I have already reduced the options for you so that an identification is possible. But if the options are not reduced, you have no possibility.

    If you need to identify the bacteria for a university course, then your teacher probably gave you some species which were already identified before, and which you now have to identify. For example, if you are given a Bacillus subtilis culture and an E. coli culture and then asked which one is which, then of course you can find this out by doing a Gram stain (knowing the B. subtilis stainas Gram positive and E. coli Gram negative). But if you have absolutely no idea what the samples are, because they were taken from the wild, then there is no possibility to find this out by microscopy alone. There are simply too many possibilities and bacterial shape is too unspecific.

    There are some rare exceptions. For example, if you see aerobic, Gram positive endospore forming bacteria, then these belong probably to the genus Bacillus. But you won’t be able to go down to the species level. Gram positive cocci in chains could be Streptococci, but they do not have to be. You can also reduce the possible options by growing them on selective growth media and by observing the shape of the colonies. There is no single method. If you need to identify completely unknown bacteria, then I suggest that you use 16s rDNA sequencing and then search the database for the nearest relative, but the chances are good that the isolated bacteria have not been classified before and therefore are not in the database. So far only several thousand bacterial species have been classified, and there are many more in nature. Biochemical tests are possible but unless you use a commercial kit, it is very time consuming and these tests are often optimized for medically relevant bacteria (so if you have a new species, then the test won’t work, because the chemical reactions of this new species are not yet known and therefore not in the database).


  48. i am really sorry to trouble you again sir…but my doubt now is that will the shapes and gram staining results alone be enough to identify the bacteria or is bio-chemical test necessary to find out the species?i know that my questions are too basic but i am running out of time and have to identify my bacterial species as soon as possible sir..so can you please help me out of it sir?

  49. thank you so much sir for responding to my question…i will surely do further characterizations to identify the microbes present in the sample that i am considering…thank you once again sir for explaining me and clarifying my doubt.

  50. If i wish to examine saliva samples for bacteria and then show that on to a computer screen what would be the best microscope to buy?
    Thank you
    Also which microscope would you recommend to do this

  51. Hello, it depends much on the type of microorganism (but I assume that you refer to bacteria, having done the Gram test). Bacteria can generally not be identified using microscopy. Genetically very different species can look very similar, and genetically similar organisms can look very different. And: the shape of bacteria is not always consistent but depends on the stage of the growth. The information content of the shape is also not very high. It is like asking if it is possible to determine the brand of a car by looking at the color. Very different cars can have the same color and cars of the same brand can have different colors. So the problem is not microscopy per se, but rather that morphology is not a good criterion for identification. Microscopy is a good method to determine bacterial concentration of a sample and to determine if a certain sample has been contaminated. If you have a culture in which you grow round bacteria (cocci) and all of a sudden you see rods (long shape), then you know that the sample was contaminated.
    greetings, Oliver.

  52. hello sir…
    I have taken some pictures of microbes that i have isolated from distillery effluent sample sir.But my problem is that i could not do any other tests such as bio chemical tests etc to identify my microbes.the only test i did was gram staining and then captured the pictures using methylene blue stain…so will i be able to identify what microbes are actually present in my sample with the microscopic picture and gram stain results?

  53. Bacteria can vary in their size. Everything in the micrometer range is likely to be correct. bacteria have a size of about one micrometer (so 7 micrometers is in the correct range, but more towards the generous side), and eukaryotes have a diameter of about 10 micrometers. Filamentous bacteria can be even longer.

  54. Dear Sir,

    What is the usual size of a bacteria cell obtained from yogurt? I did my calculations and got 7 micrometres- does this sound reasonable?


  55. Dear Sir,

    Thank you so much for the answer. I’m sorry for making you write such a long answer, but it helped me a lot. I greatly appreciate your reply.

    Thanks again,

  56. Hello Daniel,

    There’s a good and a bad news:
    1. Yes, it is possible to collect bacteria using swabs and yes, this is the way how bacteria are usually collected from surfaces.
    2. But (unfortunately) you are not going to obtain useful data this way. Direct bacterial count under the microscope is not a suitable method. And I even do hope (!) that you are NOT going to find many bacteria this way – let me explain below.

    To point 1: The general method is, theoretically, quite easy.
    a. You use a marker to draw a defined area (eg. 5 square cm) on the fruit/vegetable from which you want to obtain the bacteria
    b. You use a moist cotton swab ans streak over the area, rotating the swab, doing this a defined number of times
    c. You then streak a clean slide (a defined area, defined number of times)
    d. Allow to dry completely first and then heat-fix (Google it) by pulling the slide through a gas flame or briefly putting it on a hot plate or over a lighter. This bakes the bacteria to the slide and prevents them from being washed off later. The slide should be hot, but you should still be able to hold it in the open palm without burning yourself.
    e. Observe defined area (maybe 5suqre mm) using oil immersion and count the bacteria. Observe several squares and then average.

    To point 2: Here we have several problems.
    a. You will not be able to see many bacteria, because there are too few on the vegetables. If you do find several of them, then the vegetable should not have been sold, or it is already rotting away. This is why I said that I hope that you won’t find too many bacteria.
    b. You will have real problems identifying the bacteria among the dust and debris that can be found on the slide. Individual bacteria are difficult to identify. You really have to know what you are looking for. There will be many soil and dust particles on the slide and these will be much more prominent than the few individual bacteria.
    c. Due to the generally low number of bacteria (some will still be on the swab), the sample size is too low and the collected data will not be significant.
    d. You will not be able to see a difference in bacterial count on the different vegetables. Why should there be more/less bacteria on the different fresh vegetables? Bacteria that feed on the vegetables are in the process of decomposing it and in this case it would not make much difference in comparing bacterial count anyway.
    e. There are several sources for error: you will not be able to collect all of the bacteria from the surface; not all of the bacteria will be transferred to the slide; some bacteria will not be recognized as such; other structures will mistakenly be considered bacteria; if bacteria are present, they might be in clumps and they might therefore not be counted as separate. All of these factors contribute to a statistical uncertainty. There is the possibility that the error (the standard deviation of the sample) is so high that the data is not relevant.

    The folks who do quality control of food do not use microscopes to determine bacterial count. They use swabs to collect the bacteria and then streak out agar plates to do a so-called plate-count. They then count the number of colonies formed on the agar plates. Now this is something that I do not recommend to be done in schools, due to safety. You are actively multiplying bacteria and the bacterial concentrations are really high and there is danger of infection. After all, you do not know which bacteria you are growing (and therefore you are already in a higher Biohazard category, which may not even be legal in some countries).

    The problem of directly making bacteria visible using the microscope is not a new problem. During the 19th century Hans Christian Gram developed a staining method to make bacteria visible in infected lung tissue. Otherwise he could not keep apart the bacteria from the human lung cells under the microscope. These bacteria could not be grown in petri dishes to do a plate-count. So it is an old problem. http://en.wikipedia.org/wiki/Gram_staining

    Now don’t believe me, but simply try it out to collect some bacteria from vegetables/fruits. It’s only a few minutes worth of time, but I think that you will quickly see the difficulties.

    If you are looking for a science project topic, then there are other things I would consider: Is this for a science fair, where people are looking at posters that you made? In this case I would recommend a project that involves photography (such as pictures of pond life under the microscope, different plant cross sections, etc), as this is more impressive for the audience. If you need to collect data (such as for the International Baccalaureate Extended Essay or other related research), then you must make sure that the collected data is sufficiently statistically significant – this means you need a lot of numerical data to talk about. I kind of doubt that direct collection of bacteria from different surfaces is suitable, in this case.

    In case you are wondering, why I’m giving you such a long answer: A few years ago, I had the task to supervise one of my students for a science project and she came up with exactly the same idea. She wanted to collect bacteria from different fruits and then count them under the microscope. I told her that this is not a good project, because of the low statistical significance of the data. But then again, if the collection of data is not of main importance, then it might well be worth a try. It is not a lot of work, and not too complicated.

    Last, if you want to see a lot of (safe) bacteria under the microscope, then I would buy freeze dried “yoghurt starter culture” and dissolve some of this powder in water to be microscoped. This also gives you a reference on how bacteria look like under the microscope.


  57. Hello Sir,

    I found this article very helpful. I am doing a science project in which I will be attempting to find the amounts of bacteria on different types of vegetables. I plan to use swabs to collect samples and then observe them under a light microscope, and then count them. Will I be able to count the bacteria I collect? Also, is this the correct process to do this experiment?


  58. Hello,

    The growth and cultivation of bacteria in a school environment does require a slightly more elaborate answer.

    First of all, it is not uncommon for teachers and students to cultivate bacteria in petri dishes (there are even instructions online on how to do this and it is not difficult), but I generally do not recommend this for several reasons. Even in our school teachers already considered doing these projects, but I generally advised against it. The reasons are:
    1. Legal aspects: The cultivation of unknown bacteria already belongs to Biohazard category 2 (out of 4), because the bacteria are unknown. Bacteria used for genetic engineering (such as E. coli) belong to the lower category 1, because they are known not to be dangerous. Depending on the legislation of the country, your school legally might have to have a license. Having said that, every rotting sandwich in the locker of a student is probably equally hazardous, but then again, these are not grown in a “controlled environment”.
    2. Safety issues: Bacteria grown on agar plates can reach incredibly high concentrations, densities which are rarely found elsewhere in nature. While there is no danger of the bacteria “escaping” from the plates (they stick to the colonies in which they grow), there is the possibility that students accidentally open the plates and touch the colonies. You then need to do elaborate disinfection. And the skin better be intact, otherwise there is the possibility of infection.
    3. When you collect samples from surfaces, then you will inevitably also collect spores of fungi. These have the unfortunate characteristics to grow fast and large, quickly covering the whole petri dish so that the bacterial colonies (much smaller) are overgrown and therefore not visible anymore.
    4. You need to know how to make sterile agar plates, otherwise there are contaminants on the plate, which form colonies. When you spread your sample from the surface, then you will also spread the contaminant over the plate, creating a so-called bacterial “lawn” and it will not be possible anymore to see the colonies of the surface. Alternatively, you must use very fresh plates, on which contaminants could not form colonies yet.
    5. Staphylococcus alert: Railings and other objects that came in contact with humans might contain Staphylococcus aureus, which can be (depending on the particular strain) quite pathogenic.
    6. microscopic observation of these colonies is therefore highly discouraged, because of safety reasons.

    In short, I would not do this, especially because other safer (and also interesting) alternatives are available.

  59. Hello,
    I am the editor-in-chief for a school magazine. Yesterday, we had an idea that we would swab different surfaces in the school (e.g. stair railings, elevator buttons, library computers, cafeteria tables, and so on), observe the bacteria cultures, and compile them in an article because it seems interesting.

    After some researching and reading this article, though, I’m not really sure whether this is a plausible idea. Would you have any advice regarding this? Thank you!

  60. Hello
    I think that you looked at some undissolved part of the probiotic pill. 400x-1000x magnification is enough to see bacteria. These pills are not pure bacteria but contain much filling material (sugar etc) so that it is possible to press them into a pill. The pill contains freeze dried bacteria, and these are not growing in colonies, but in compressed form. If you want to observe bacteria, then it is easier to observe some “yoghurt starter cultures” (search Amazon). These are bacteria in powdered form which can be dissolved in some water.

  61. Hi Mr. Oliver,

    Thanks for such a knowledgeable article. I have a question,
    I scratched off a bit of a probiotic pill and put under the microscope , even at 1600x all i was able to see was black sponge like structures. I wonder what i saw was colonies or something else? The bottle says “active organisms” though, and they are lactobacillus acidophilus.

    Thanks again

  62. sorry, but this is almost impossible. Unless the meat is totally spoiled (decomposing) the bacterial concentration is far too low. You would first have to isolate the bacteria and grow them before being able to analyze them. It is possible to do some staining to make the bacteria visible, but this is elaborate and the benefits are not clear. The question is, why you would like to do this. Is it for quality control? In this case microscopic analysis is not very helpful.

  63. I am trying to spot bacteria that is in meat under a microscope. I have a microscope that goes up to 1000x. I don’t quite know what to look for. Any sugestions?

  64. Pond water itself contains only few observable organisms. The interesting things can be found in the material which can be found growing on rocks an decaying wood and leaves. Scratch off some of this material and observe this.

  65. I found this article very helpful. I have an inexpensive microscope (Vivitar) that is supposed to magnify to 1200. I wish to use it to view what is in pond water and was unsuccessful the first time. If anyone has suggestions they would be welcome.

  66. John,

    Usually thrush is a fungus. Ie Candida Albicans.

    Just an FYI,


  67. Dear Sir,
    I was wondering if you could help I am trying to find somebody to identify the different strains of bacteria found on the bottom of horses feet,as part of a paper I would like to do on a farrier article.or even guided in the right direction on where to start. there is a verry common problem that horses suffer with called “THRUSH” a seamingly colective name for a load of bad bacteria!! this is why i would like try to identify them,there doesnt see to be anybody that has this for many,many years.I am not a student or scholar but a full time working farrier try to improve the welfare of horses!
    Thank you

  68. Hello, Do not observe bacteria which you do not know. Take bacteria from safe sources (yoghurt etc). You need to suspend some yoghurt in some water and then make a wet mount. Bacteria can be seen starting a magnification of 400x and more. athey are difficult to see, because they are quite small and transparent.

  69. i have a microscope and i would like to see bacteria and i know about colonies. i know that my microscope is not that strong. i was wondering if i stained the slide if with my weak microscope would be able to see the colonies a little bit.

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