In a new study, researchers found that repeated treatments with antibiotics increased the risk of Type 1 diabetes in the rodents. 
The finding is harrowing, considering that approximately half of all prescriptions written for antibiotics in the United States are inappropriate and that a recent study found that antibiotics are prescribed to children about twice as often as they should be. 
For the study, Martin Blaser, M.D., a professor of translational medicine and microbiology at the NYU Langone Medical Center in New York City, and colleagues looked at the effects of antibiotics on non-obese mice that were susceptible to type 1 diabetes. The mice were very young – about the equivalent of a 6-months-old or 1-year-old child.
The mice were given either three doses of antibiotics at different times (pulsed therapy) or a steady but very low dose of antibiotics. Mice given no antibiotics served as controls.
The researchers found that the mice who received the pulsed therapy were twice as likely to develop type 1 diabetes as the mice that received no antibiotics.
Other findings included alterations to the microbiome in the gut, which led to changes in T cells. The T cell changes, in turn, led to increased inflammation in the insulin-producing islet cells of the pancreas.
When Blaser and his team transferred some of the altered gut microbiota from the antibiotic-exposed mice to the other two groups of mice, the risk of type 1 diabetes increased in one group but not the other.
Read: Have Antibiotics “Shut Down” Your Immune System?
The researchers wrote in the journal Nature Microbiology:
“These findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating type 1 diabetes onset in non-obese diabetic mice.”
What is Type 1 Diabetes?
Type 1 diabetes is an autoimmune disorder, usually diagnosed during childhood. It’s at least partly genetic, but cases of the disease have risen rapidly since World War II, and it’s now being found in increasingly younger children. 
“That means there’s some strong environmental aspect.”
He believes that the “environmental aspect” is the widespread use of antibiotics.
Antibiotics can decimate “good” bacteria and shift the makeup of the microbiome, which greatly affects people’s metabolism and immunity, making them more susceptible to diabetes and other diseases, Blaser explained.
In recent years, evidence has emerged that the loss of this good bacteria may even cause mental illness.
One particularly strong class of drugs, called fluoroquinolones, can cause disabling side effects involving the tendons, muscles, joints, nerves, and central nervous system. In July 2016, the Food and Drug Administration (FDA) warned that fluoroquinolones are too strong for simple bronchitis, sinus infections, and urinary tract infections.
Read: We now Know HOW Antibiotics Kill Off Good Bacteria in the Gut
In the mice, the antibiotics negatively affected all the genes involved in cholesterol metabolism. Said Blaser:
“We found that cholesterol metabolism in the intestinal wall was very deranged. This was a big surprise to us, and we hope to test it further.”
There’s no way to know whether antibiotics would have the same effect on children, although past research seems to suggest it might. And when it comes to giving kids antibiotics, the fewer, the better. Blaser said:
“I think we need more careful exams by doctors, and for both doctors and parents to understand that antibiotics aren’t free. They carry not only the risk of resistance, which is a cost to the whole community, but possibly health risks to their child.”