I'm deeply concerned with this issue and I fear its only getting worse. For all of the excessive use of Antibiotics in medicine this next issue just compounds the issue.
Functioning GM genes remain inside you
Unlike safety evaluations for drugs, there are no human clinical trials of GM foods. The only published human feeding experiment revealed that the genetic material inserted into GM soy transfers into bacteria living inside our intestines and continues to function.[39] This means that long after we stop eating GM foods, we may still have their GM proteins produced continuously inside us.(
http://www.responsibletechnology.org/health-risks)
Now imagine this scenario...A woman is prescribed a few rounds of antibiotics for good measure prior to giving birth, her child is born in a "sterile" environment with a mother that has a decreased biota. This childs immune system suffers and grows up with multiple allergies, eating conventionally processed foods that contain GMO's. Then when they become ill, are prescribed anti-biotics and continue to consume their conventional GMO laden foods. This antibiotic cycle in effect greatly reduces the quantities of beneficial biota and selects for the stronger anti-biotic resistant strains of the more pathogenic microbes. Then the continual exposure to GMO products allows for the transgenic markers (such as Bt-round up ready) to interact with these super strains of antibiotic resistant microbes producing super strains of anti-biotic resistant/pesticide producing (or other unpredictable traits) microbes...sounds like a recipe for serious (possibly irreversible) long term immunological disorders.
So even though your client may have cleaned up their diet and is taking massive doses of probiotics, the biota that they currently have could be making them sick from the transgenic materials that their gut biota have acquired in the past.
I'm not aware of any standardized testing for transgenic contamination of our native gut biota, but it may be worth looking into...
Don't panic, Go Organic!