pathogen vs micro-organism

pathogen and micro-organism both are nouns.

Word	Noun	Adjective	Verb	Adverb
pathogen	Yes	No	No	No
micro-organism	Yes	No	No	No

As nouns, micro-organism is a hypernym of pathogen; that is, micro-organism is a word with a broader meaning than pathogen:

pathogen: any disease-producing agent (especially a virus or bacterium or other microorganism)
micro-organism: any organism of microscopic size

Other hypernyms of pathogen include microorganism, infectious agent, infective agent.

pathogen (noun)	micro-organism (noun)
any disease-producing agent (especially a virus or bacterium or other microorganism)	any organism of microscopic size