It is possible that your yeast is not a pure culture, but contaminated with fungi. If the yeast is a pure culture, there are a few other things you can test. Are you autoclaving the media for a sufficient length of time? Also, is the autoclave used in preparing the agar working properly? Does it reach the required temperature and pressure levels required to sterilize the medium? You can try running the autoclave (empty) through a cycle and see if you get the correct the temperature and pressure readings (i.e., 121C, 15 psi). It's possible you have a leak, or the temperature indicator is faulty. You can also test the autoclave using test vials w/spore strips to be sure the autoclave is working properly.
What kind of Petri plates are you using, e.g., glass or pre-sterilized plastic plates? The glass ones require autoclaving, but a faulty autoclave (above) could cause your problems. If you are using plastic plates, occasionally you can get contamination from plates taken from old (expired) plastic sleeves or plates taken from an old open sleeve that was not re-sealed properly after its last use.
Where do you do your transfers? Are you using a bio-safety cabinet w/ a UV light to sanitize the cabinet? If so, is the UV lamp working? Also, you might try swabbing the surface of the bench in the cabinet w/ ethanol before use. You can also check the age of the HEPA filters in the cabinet. If they are old, they should be replaced.
Is anyone in your lab working w/ filamentous fungi? Many fungi reproduce asexually using aerial hyphae that make millions of spores. These become airborne with only the slightest movement of air and can contaminate a lab.
If your university has a microbiology department, it might help to have someone from there visit your lab. He/she might spot some other source(s) of contamination and check your sterile technique.
I had contaminations with rhizopus and other fungi that I don't know.
However, I would like to clarify my question since we are not using Saccharomyces but we are making gut yeast cultivation it means that we are looking for yeasts from an insect gut. We would like to have only yeasts with that medium.
I also suspected the HEPA filter since other people are working with fungi
Yeast is a morphology - not a unique group of fungi. It's presumed any fungus can growth as a yeast - including Rhizopus Article Rhizopus stolonifer exhibits dimorphism
. Some fungi typically grow as yeasts in lab culture - others can be readily shifted back and forth yeast-mycelium in culture.
Normally we can use rose bengal agar for the selective isolation of yeast from any source, then it can be maintained on YPDA. Make sure that your isolate(s) is not dimorphic in nature. The dimorphism is seen under various conditions like : media composition, temperature, reproductive stage, stress conditions, etc.,
make sure the sterilization of media is carried out properly and even fumigation of LAF at regular intervals.
Back to your problem. Think you need classic approach to clone/purify your yeast culture. Streak for isolation, pick target colony, repeat until you've a clean culture.
You also need to address and resolve how contamination was established.