Kidney stones.
For a long time doctors believed that kidney stones were caused purely by Western diet. However recent research suggests, that kidney stones ( calcium oxalate sones, which are the most common )  are caused by a lack of certain microbe in the gut – Oxalobacter formigenes (1). But what might kill this microbe in the gut? The answer is: antibiotics especially fluoroquinolones, like Cipro.  So what can be done?
1.  Increase intake of foods rich in fibers like flaxseeds, apples etc., as well as complex carbohydrates like potatoes and green leafy vegetables.
2.  Increase foods in your diet that are reach in magnesium and low calcium like buckwheat, brown rice, avocado, banana, coconut, cashew and potatoes ( 4,5).
3.  Drink enough water: 6 – 8 glasses of water everyday.
4.  Avoid oxalate containing foods like spinach, rhubarb, parsley, cranberry, nuts, black tea, cocoa, etc. (3).
5.  Avoid simple carbohydrates like candies, soft drinks.
6.  Stay away from dairy products.
7.  Consider vegetarian diet (2 ).

8.  Increase intake of products, that alkalize your urine like citrus.

Of course diet alone cannot fix the problem.  It cannot fix Neurotransmitter Imbalance, it may not be able to fix minerals and vitamins deficiency because of maldigestion or malabsorbtion. It cannot fix Hormonal Imbalances either. To figure out what is going on you need to see Functional Medicine Doctor to go to the root cause of the problem and elimiate it.

References:
1.  Stewart, Duncan, Cave. Oxalobacter formigenes and its role in oxalate metabolism in the human gut. FEMS microbiology letter 2004, 230:1–7.
2.  Robertson, Peacock, Marshall. Prevalence of urinary disease in vegetarians. European Urology 1982, 8:334–339.
3.  Rose, Westbury. The influence of calcium content of water, intake of vegetables and fruits and other food factors upon the incidence of renal calculi. Urologic research 1975, 3:61–66.
4.  Wunderlich. Aspects of the influence of magnesium ions on the formation of calcium oxalate. Urologic research 1981, 9:157–161.
5.  Hallson, Rose, Sulaiman. Magnesium reduces calcium oxalate crystal formation in human urine. Clinical science 1982, 62:17–19.