How will you know if it is a pathogen? Infect another nem?
It is a guessing game aid by statistic.
Speaking hypothetically, if I get samples from 10 healthy anemones and culture them. If I recovered 5 species of bacterial (A, B, C, D, E) in these 10 anemones, and all five are in about 80% of the anemones. This is a clear cut case of normal flora.
Also if we quantity and do a colony count per ml, I would expect very sick anemone will have a much higher pathogen bacterial count per ml (say 50,000+ per ml), then a normal flora count (<20,000 per ml). These number just got throw out from my head as examples. I just have to collect a bunch of cultures, detail/pictures of the anemones when and from which the culture from. Details before, any treatment pre/post culture and out come. From these information, than I just have to try to draw accurate, meaningful conclusions from the data.
Knowing the information above, then if I culture a sick anemone and come up with A, B, C, E, F and colony count of all strain except F is 10,000 per ml. Colony count of F is 100,000 colonies per ml. This is a clear cut information that show F is a pathogen and A, B, C, and E are normal flora.
Analyze and come up with meaningful and accurate conclusions is a huge part of an experiment.