The vast majority of the microbes in your body are in your large intestine (a large part of feces is dead and living bacteria); the rest live on body surfaces like skin and inside body cavities; your actual flesh very likely has no microbes in it, or very few (your immune system will kill any that do penetrate skin or intestinal walls), so it isn’t really accurate to say that your body is made up of x% microbes.
If you take the “sack of space a human occupies” bacteria cells outnumber human cells by an order of magnitude.
However, all of this bacteria is technically outside the epidermis. A human is a tube within a tube, and your GI tract is protected by tissue similar to your skin. It would be disastrous if all that bacteria were allowed free entry into our body.
Edit: Much of the mentioned bacteria live on your skin and in your digestive tract.
The relationship with our bacteria is fascinating, and there is lots of neat research on the topic; from fecal transplants, to behavior modification.