Best Substrate to use?

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polly, wire floors are well known to cause the abrasions that allow bacteria to enter the feet of our companion animals. Please refer to this which specifically lists wire floors as a cause of pododermatitis:

www.sciencedirect.com/science/article/pii/B9781416039693001803

Also

www.sciencedirect.com/science/article/pii/S1094919413000455?via%3Dihub

Substrate or Perches
For rabbits and rodents, the type of flooring or substrate can affect the distribution of weight between the metatarsus and claws.1 Wire flooring forces the animal to walk or rest entirely on the hock and metatarsus. Hard flooring, such as tile or cement, may lead to abnormal weight-bearing on the hock and metatarsus. Abrasive substrate, such as carpet, can also lead to pododermatitis from increased friction and irritation of the skin. It is best to provide deep soft substrate, such as hay, straw, or recycled paper, to prevent pododermatitis in these species.

[ntg]

Also, wire cages are not the most hygienic as its is much more difficult to sufficiently clean a wire floor than it is a flat surface such as wood or solid metal. Not to mention, pine wood has natural antibacterial properties.