Is Jesus truly present in the Eucharist?

This depends greatly on the belief structure which you are making reference to. For example, Protestant and Catholic denominations will have differing opinions to the details.

Some groups feel it is a metaphor, others that it is literal, and still others that it simply makes reference to God being part of all things.

In the true literal sense of transubstantiation, however, the answer is simply no. Though church based groups have claimed to have tested and shown the presence of blood/tissue following the ritual, it has never been demonstrated under scientific conditions.

For a more detailed and in depth explanation of the differing viewpoints in differing traditions, please see the full Wikipedia page on Transubstantiation;