mid-15c., "bud, sprout;" 1640s, "rudiment of a new organism in an existing one," from Middle French germe "germ (of egg); bud, seed, fruit; offering," from Latin germen (genitive germinis) "spring, offshoot; sprout, bud," which is of uncertain origin, perhaps from PIE root *gene- "give birth, beget," with derivatives referring to procreation and familial and tribal groups.
The older sense is preserved in wheat germ and germ of an idea; sense of "seed of a disease" first recorded 1796 in English; that of "harmful micro-organism" dates from 1871. Germ warfare is recorded from 1919.