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I manage a real estate portal w.example.com where we have to target specific areas. Now my question is whether should I go with the directory structure i.e. w.example.com/chicago.html or chicago.example.com considering50 such areas. Also tell me is it harmful to have so many sub-domains? Please help.
You can have as may sub-domains as you want. This will never harm you but sub-domains won't give you any SEO benefit from your main domain. I would suggest you to consider a sub-domain if you are dealing with different products/services rather than for different regions.
For different regions it is advisable to use subfolders if you really want to get the benefit of your main domain.
If you have different languages then you can use sub-domains. For example en for english, de for german, ae for arabic etc.
1. Each sub-directory is treated as saperate website by the algorithm, so if you put your contents in saperate sub-domains, it will not share any SEO benefits with each other and as a whole the main site will suffer the erosion of SEO metrics. But incase of sub-folder these advantages are passed on to the main site an as a whole the entire site benefits from the efforts you do for each page/section.
2. No, It is not harmful to have many subdirectories