The immune system is activated differently if the gut does not have a healthy microbiome - profile of "good bacteria" that inhabit your intestines. These Microbes in the small intestine help digest food, synthesize vitamins and regulate metabolism. What's more, the dominance of "good" bacteria helps to prevent the establishment of harmful bacteria, such as Clostridium difficile (C. diff.), which can cause a difficult-to-treat infection that can be life-threatening.

If someone is sick with a bacterial infection, they will absolutely take synthetic antibiotics. But it is important to remember that there may be collateral effects. You might be affecting your immune response to certain viral infections.

Antibiotics kill bacteria, not viruses. Nevertheless, some doctors prescribe antibiotics for viral infections such as colds and the flu as an extra precaution, perhaps to ease the concerns of patients who think they need medicine, or to prevent a subsequent bacterial infection from arising while the body is weak. But that practice — giving synthetic antibiotics as a preventive measure— may backfire. 

Taking antibiotics [by chance] could affect [the] responses of the immune system to a variety of viruses. It changes the balance of micro-organism in the gut (digestive system) that leads to “Obesity” and other diseases and Allergic reactions.