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Conclusion

The hypothesis that the amount of bacteria in shoes will be higher if they are worn without socks, is proven to be true.

The smell from our feet can be reduced by wearing cotton socks that are able to absorb sweat more effectively, and also by properly airing our shoes. The bacteria count can be lowered by frequently changing  socks and washing our feet with antibacterial soap.

Also consider

This science project can be repeated by wearing socks made from different materials like cotton or polyester.

Modify the science project by using shoes made from different materials like leather, PVC, etc.

References

Why do feet stink? - http://health.howstuffworks.com/skin-care/information/anatomy/question5141.htm

What causes smelly feet? - http://www.brighthub.com/science/genetics/articles/48373.aspx

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Complexity level:
8
Project cost ($):
20
Time required:
1 hour to prepare, 1 hour for science project experiment
Material availability:
Easily found
Safety concerns:

The bacteria should be destroyed before the swabs are discarded.  Pour some bleach into the petri dish to kill all the bacteria before disposing in the trash.