The Collaborative International Dictionary of English v.0.48:

Germ \Germ\ (j[~e]rm), n. [F. germe, fr. L. germen, germinis,
   sprout, but, germ. Cf. Germen, Germane.]
   1. (Biol.) That which is to develop a new individual; as, the
      germ of a fetus, of a plant or flower, and the like; the
      earliest form under which an organism appears.
      [1913 Webster]

            In the entire process in which a new being
            originates . . . two distinct classes of action
            participate; namely, the act of generation by which
            the germ is produced; and the act of development, by
            which that germ is evolved into the complete
            organism.                             --Carpenter.
      [1913 Webster]

   2. That from which anything springs; origin; first principle;
      as, the germ of civil liberty.
      [1913 Webster]

   3. (Biol.) The germ cells, collectively, as distinguished
      from the somatic cells, or soma. Germ is often used in
      place of germinal to form phrases; as, germ area, germ
      disc, germ membrane, germ nucleus, germ sac, etc.
      [Webster 1913 Suppl.]

   4. A microorganism, especially a disease-causing bacterium or
      virus; -- used informally, as, the don't eat food that
      falls on the floor, it may have germs on it.
      [PJC]

   Disease germ (Biol.), a name applied to certain tiny
      bacterial organisms or their spores, such as Anthrax
      bacillus and the Micrococcus of fowl cholera, which
      have been demonstrated to be the cause of certain
      diseases; same as germ[4]. See Germ theory (below).

   Germ cell (Biol.), the germ, egg, spore, or cell from which
      the plant or animal arises. At one time a part of the body
      of the parent, it finally becomes detached, and by a
      process of multiplication and growth gives rise to a mass
      of cells, which ultimately form a new individual like the
      parent. See Ovum.

   Germ gland. (Anat.) See Gonad.

   Germ stock (Zool.), a special process on which buds are
      developed in certain animals. See Doliolum.

   Germ theory (Biol.), the theory that living organisms can
      be produced only by the evolution or development of living
      germs or seeds. See Biogenesis, and Abiogenesis. As
      applied to the origin of disease, the theory claims that
      the zymotic diseases are due to the rapid development and
      multiplication of various bacteria, the germs or spores of
      which are either contained in the organism itself, or
      transferred through the air or water. See Fermentation
      theory.
      [1913 Webster]

The Collaborative International Dictionary of English v.0.48:

Germ theory \Germ theory\
   1. (Biol.) The theory that living organisms can be produced
      only by the development of living germs. Cf. Biogenesis,
      Abiogenesis.
      [Webster 1913 Suppl.]

   2. (Med.) The theory which attributes contagious and
      infectious diseases, suppurative lesions, etc., to the
      agency of germs, i.e. pathogenic microorganisms. The
      science of bacteriology was developed after this theory
      had been established.
      [Webster 1913 Suppl. +PJC]

WordNet (r) 3.0 (2006):

germ theory
    n 1: (medicine) the theory that all contagious diseases are
         caused by microorganisms