Thank you for taking the time to comment. As far as I know, immunodeficiencies in children are often a result of genetic factors, which I think may be the case for your son given that his father had similar conditions. And environmental stressors are difficult to control as well. Sometimes I think it’s no wonder that medicine focuses on the cure (e.g., antibiotics) rather than prevention.
I did come across research trying to reconstitute the gut microbiota following depletion (e.g., from antibiotics or C-section). So far, if I’m not wrong, breastfeeding, exercising, and fecal microbiota transplant are the best ways to help the gut microbiota. Fiber-rich foods or probiotics seem to produce conflicting findings in some studies, which I can vouch for.
I was born with urinary reflux so I was on a 5-year antibiotic therapy to prevent infection. And so I always had gut issues. Fiber and probiotics did not help me, but rather eating a low-fiber diet did. So I think reconstituting the gut microbiota is very challenging as it is just so diverse, not to mention that the diversity further differs between each people.