They are the substances which are unfit for offering in yajna. Some specific examples are given below.
Medhatithi’s commentary on verse 5.5 mentions 2 impure substances which meat comes from:
As regards meat, even though it grows out of semen and blood (both impure substances), yet the present prohibition does not apply to it; because it has been dealt with in a totally different context.—(5)
Semen and blood are both impure substances, but garlic, leeks and onions, and mushrooms can probably proceed from these two. Medhatithi basically says that the prohibition on meat has been explained elsewhere in Manu Smriti as shown in this answer.
amedhyair avamṛṣṭam || 25 ||
25. [Nor must that food be eaten] which has been touched with an unclean substance [a substance which can not be offered in a yajña].
Apastamba Sutra 1.5.16
Food originating from unclean substances (impure things) must have touched these things at some point.
m ūṣakalāṅgaṃ vā || 27 ||
27. Nor [that in which] excrements or limbs of a mouse [are found],
Apastamba Sutra 1.5.16
These impure substances include excrements and limbs of a mouse. Food originating from these contain some of these, so the food must not be eaten.
4.56. Let him not throw urine or faeces into the water, nor saliva, nor (clothes) defiled by impure substances, nor any other (impurity), nor blood, nor poisonous things
Manu Smriti
This verse explicitly mentions examples of impure substances. These same examples appear in Vishnu Smriti and Yajnavalkya Smriti.