It is unwise to immediately and completely change ones medications or prescription habits just based on one study. These large observational multivariate studies are always hindered by bias, though trying hard to compensate for them.
On the other hand, these kind of findings should not be ignored.
Proton pump inhibitors are already known for a long time to cause trouble. The article already mentions several, like the bacteria get a change of growing in the changed environment of the stomach, a defensive barrier is removed, certain vitamins and drugs need the acidity to get absorbed etc etc. Kidney issues are also not news. Other weird side effects, like I'll never forget a patient with an extreme hypomagnesia, like 0.10 mmol/l or so. She did not feel well.
But not forget the number of patients who have gained significant quality of life and the reduction of severe gastric bleeding. Remember the time where Bilroth gastrectomies were as common as cholecystectomies. The two week maximum advise for the over the counter drugs is because of the risk of patients masking a serious condition like malignancies.
But there is no denying that most people at some point start their PPI for some discomfort, and continue to swallow them for the rest of their lives. (Ideal drug for pharmaceutical companies.) The majority should just quit them, change their food habits and posture and get on with their lives.
The use of these drugs should be reserved for those who really need them. Right now it is prescribed more or less as a luxury drug