I have a project in mind, and I don't know if I can do it with Discourse

Kind of works… All posts of subdomain are published to same category so on the side of a site it looks like those two are connected.

But if there is need to hide those other categories ”connected” to a subdomain it will be more difficult — sure, when an user registerate an account on Discourse she/he can choose which subdomain, aka. category will be visible and all others are muted.

Using every subdomain as another SSO and via that could show one category and mute another.

Not work out-of-the-box or even easily. As @RGJ said having multiple installs is quite trivial so the right solution depends:

  • will category structure serve something, like need to build wider community, or
  • is there a real need to keep those separated
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