Bilbo was of a different breed of hobbit. He had evolved from the old hobbits of the Anduin and moved ti the shire. Gollum was of the old race and therefore didn't recognize Bilbo's race. Look at the differences in the names: Bilbo of the shire and Meriodiac of the Brandywine. The differences in their body structure come from the place that they lived. Simple hobbit evolution.
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