I personally get very nauseous with antibiotics, so I'm sure this isn't something to be very concerned about. I understand why you are, though. Nausea and vomiting seems to be a common side effect with this medication in dogs. I wonder if the pH is upsetting Sheldon's tummy and if your vet thinks Pepcid might help. It can't be used with antacids, but I wonder if Pepcid could help.
01 Doxycycline (Vibramycin) - VeterinaryPartner.com - a VIN company!
Nausea and vomiting are the most commonly reported side effects of doxycycline in dogs and cats. If this side effect occurs, it is most easily managed by giving the medication with food. (Other members of the tetracycline class should not be given with food as food binds the drug and prevents its absorption into the body. With doxycycline this is effect is not considered significant.)
Drugs of the tetracycline class have potential to permanently stain teeth if given to immature animals. (It binds to calcium, which is needed for growing bones and teeth.) Doxycycline has the least potential for doing this.
The tablets have a particularly irritating pH should they become stuck in the esophagus of a smaller patient (especially a cat). If the pill sits in the esophagus, it can cause enough irritation to eventually lead to a scar, causing difficulty swallowing. This can be prevented by following the pill with at least 6 cc of water or, better yet, using one of the liquid formulations.
Certain types of urine dipstick tests can erroneously test positive for glucose in patients on tetracycline-type medications.