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Where is the line between good and bad microorganisms and why do we seem to know so much more about the bad ones?

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Sources:
Gross, A. G., & Harmon, J. E. (2007). The Scientific Literature: A Guided Tour. Chicago, IL: University of Chicago Press.
https://www.rcpe.ac.uk/heritage/history-germ-theory-college-collections
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https://www.cdc.gov/parasites/sth/index.html
https://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053866
http://edis.ifas.ufl.edu/ng047
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