This is the 14188th most frequent Russian word.
организмом
"Organism" - a living being, such as an animal, plant, or microorganism.
In this sentence, 'организмом' (organism) is used in the instrumental case to describe 'каждая бактерия' (every bacterium), specifying its nature as a living entity.
Живым организмом является каждая бактерия.
Every bacterium is a living organism.
Here, 'организмом' (organism) in the instrumental case indicates the entity affected by or related to the governing complex biological processes.
Организмом человека управляют сложные биологические процессы.
The human organism is governed by complex biological processes.
In this example, 'организмом' (organism) is in the instrumental case to show the object with which the medicines interact.