Treatment with antibiotics found to reduce effectiveness of flu vaccines by impairing immune response to flagellin (bacterial tail whip protein)

This was not true of all vaccines, however. FTA:

Antibody responses to vaccines containing immune stimulating substances called adjuvants were not affected by a lack of gut bacteria. For example, bacteria were not critical for responses to the Tdap (Tetanus-Diphtheria-Pertussis) vaccine.