I would stick to conventional materials like paper based substrates and beddings. There are some good ones out there (Bedxcel substrate and PetLife safe bedding) are two of the best examples. Because they are paper based (not wood based) they won`t cause any problems to your mice. Some mice can even start having respiratory issues with other substrates like Megazorb, Carefresh and of course, shavings, so I would avoid those. Megazorb might not be so bad, but Carefresh and shavings are potential hazards to mice, even though manufacturers will tell you otherwise.
Using peat and soil is`nt a good idea because they retain moisture and because the mice are in a confined area (i.e, not outside) the substrate would build bacteria and cause problems. So until there is a soil based substrate made for rodents that is dry and safe, I would steer clear.