Users are suggested to migrate their queries over to Qiita.

Indeed, the previous link to now sends users to the new Qiita website.

Updated API for Qiita

The Qiita team has indicated they are planning to create a REST-like API. Upon stable release of this API, it should be possible for phyloseq to define an interface that will allow users to query this database and download data, converting it seemlessly into a phyloseq object. This is my current plan, anyway, but it is contingent on the Qiita API release, and also the extent to which the data is freely provided.