Source: Children’s Health Defense

Story at a glance:

• Type 1 diabetes affects about four in 1,000 U.S. children and is linked to the disruption of the gut microbiome, particularly through early antibiotic exposure.
• A study from the University of Colorado Boulder found that there’s a 10-day window during early life when specific gut microbes are required for proper pancreatic beta cell development.
• When antibiotics are given during the 10-day window, they disrupt the growth of insulin-producing cells and contribute to the development of Type 1 diabetes later in life.
• Another study found that maternal use of certain antibiotics before and during pregnancy significantly increased children’s risk of developing Type 1 diabetes.
• To protect your child’s gut health and reduce their risk of diabetes, limit the use of antibiotics during pregnancy and infancy, encourage breastfeeding, use probiotics strategically and provide them a nutritious diet.

Type 1 diabetes is one of the most prevalent chronic conditions in children in the U.S., affecting around four out of every 1,000 youths.

This autoimmune disease causes the body’s immune system to mistakenly destroy the insulin-producing cells of the pancreas. This leads to lifelong dependence on insulin injections, frequent blood sugar monitoring and increased risk for severe complications.

While genetics is involved in its development, disruption of the gut microbiome has also been found to play a role. Particularly, early exposure to antibiotics in children has been shown to alter the composition and function of gut bacteria during vital developmental windows. These changes interfere with immune regulation and initiate the autoimmune cascade that leads to Type 1 diabetes.

A new study conducted by researchers at the University of Utah Health adds more evidence to support this link.

They found that antibiotic exposure during a specific 10-day window in early life disrupted the gut microbiota and prevented the normal development of insulin-producing beta cells in the pancreas, revealing how early antibiotic use reprograms metabolic health before symptoms ever appear.

How microbes influence pancreatic development and diabetes risk

Published in the journal Science, the featured study investigated how microbes affect the early development of pancreatic beta cells, which are specialized cells in your pancreas that produce insulin.

Using mice, researchers found a specific 10-day window right before weaning where the presence of beneficial microbes was required to stimulate the growth of these cells.

• Both bacteria and fungi promote beta cells — During the 10-day window, scientists used antibiotics (to remove bacteria) and antifungals (to remove fungi). In both cases, the mice failed to develop a normal population of beta cells. This means the presence of bacteria and fungi was necessary during this short period to properly support the pancreas’s ability to make insulin later in life.
• Specific microbes worked at a certain age — To see if this timing applied to humans too, researchers transplanted gut microbes from human infants into germ-free mice. Only samples from infants between 7 to 12 months old triggered beta cell development in the mice. Samples from younger or older infants had no effect. This suggests human babies also experience a brief window where the right mix of gut microbes supports pancreatic development.
• Three microbes were identified as key — Out of all the species tested, only three microbes consistently boosted beta cell development — E. coli (a common gut bacterium), Enterococcus gallinarum (a bacterial species commonly found in the intestines) and Candida dubliniensis (a type of yeast). When introduced during the 10-day window, these organisms increased the number of insulin-producing cells in the pancreas.
• C. dubliniensis had the strongest immune effect — Among the three microbes, C. dubliniensis had a significant impact. It increased the number of macrophages in the pancreas. Macrophages are part of the immune system and act like cellular “clean-up crews” that also help repair tissue. In this case, they appeared to support the growth of beta cells. When macrophages were blocked, the fungus no longer helped increase beta cell mass, confirming the effect was driven by immune involvement.
• The effect depended on the fungus’s cell wall structure — The structure of C. dubliniensis’s outer layer, specifically molecules called mannan and chitin, played a key role in triggering the immune response. These molecules are recognized by the immune system and act like biological “on switches,” alerting immune cells to support growth or repair. Without this structural signal, the fungus would likely have no effect.
• The fungus drastically reduced diabetes risk in vulnerable mice — In newborn male mice genetically predisposed to Type 1 diabetes, early colonization with C. dubliniensis reduced the likelihood of developing the disease.
• The health potential of beneficial microbes — Lead researcher Jennifer Hill, assistant professor at the BioFrontiers Institute at the University of Colorado, explained the broader significance of their findings: “Historically we have interpreted germs as something we want to avoid, but we probably have way more beneficial microbes than pathogens. By harnessing their power, we can do a lot to benefit human health.”

Timing and type of antibiotic exposure matter for diabetes risk

Providing more insights into the link between gut microbiome and diabetes risk, a large registry-based study published in January in The Journal of Pediatrics analyzed data from 2,869 Finnish children diagnosed with Type 1 diabetes and compared them to a reference group of 74,263 children without diabetes.

Researchers looked at the types of antibiotics used and the timing of exposure, from before pregnancy through the first two years of life.

• Macrolides given to mothers before pregnancy increased risk — The study found that children whose mothers took macrolide antibiotics, such as azithromycin or erythromycin, during the year before pregnancy had a 17% higher risk of developing Type 1 diabetes.
• Sulfonamides and trimethoprim significantly increased the risk — When mothers were prescribed sulfonamides and trimethoprim during pregnancy — often used to treat urinary tract infections (UTIs) — their children had a 91% higher risk of developing Type 1 diabetes. This was one of the strongest associations found in the study and points to the prenatal period as especially sensitive to microbial disruption.
• Trimethoprim may disrupt folate metabolism — One proposed mechanism for the increased risk during pregnancy is that trimethoprim interferes with folate metabolism, which is essential for fetal organ development, especially the pancreas. The researchers referenced this as a biologically plausible explanation for the elevated risk associated with prenatal exposure.
• Dual exposure to macrolides increased the risk further — Children who were exposed to macrolides both through maternal use (before or during pregnancy) and personal use during infancy had a 29% higher risk of Type 1 diabetes compared to those with no exposure in either period. This suggests a compounding effect when the same drug class is introduced at multiple stages of immune system development.
• Antibiotic effects were different between boys and girls — The study found that boys who received antibiotics during their first year had a higher risk of developing Type 1 diabetes, while girls did not show this increased risk. This indicates that the way antibiotics influence diabetes risk may vary based on the child’s sex.
• Total number of prescriptions didn’t impact risk — The overall number of antibiotic prescriptions, whether given to the mother before or during pregnancy or to the child after birth, did not correlate with increased or decreased diabetes risk. This means it’s not about how many times antibiotics are used, but which ones and when.
• Microbiome disruption remains a possible mechanism — The authors also discussed that early antibiotic use alters the gut microbiota in both mother and child. Since Type 1 diabetes is an autoimmune disease, disturbing the microbial environment during immune system programming could contribute to disease onset.

What are the other side effects of antibiotics in children?

While antibiotics are sometimes necessary to treat infections, they come with a range of potential side effects that affect your child’s health beyond Type 1 diabetes.

Early antibiotic exposure has been associated with several other risks, including:

• Allergic conditions and asthma — Studies consistently show that infants and toddlers who receive antibiotics are more likely to develop allergic conditions later in life, including eczema, asthma and hay fever. The altered gut microbiota appears to push the immune system toward an inflammatory, hypersensitive state.
• Recurrent infections and weakened immunity — By disrupting gut microbial training, antibiotics reduce your child’s ability to build a robust, adaptable immune system. Ironically, this makes them more prone to infections — the very thing antibiotics are supposed to treat.
• Increased risk for obesity and metabolic disorders — Several studies have connected early antibiotic use with higher rates of childhood obesity and metabolic issues. One explanation is that gut bacteria shape how the body creates energy from food and regulates fat storage hormones. When those bacteria are altered, metabolic balance shifts in the wrong direction.
• Behavioral and neurological changes — Disrupting the gut-brain axis early in life also appears to affect neurological development. Research has linked early antibiotic exposure with increased risks of attention-deficit/hyperactivity disorder  (ADHD) and behavioral disorders. Learn more about the neurodevelopmental effects of antibiotics in “Autism and ADHD Linked to Disturbed Gut Flora Very Early in Life.”
• Higher rates of antibiotic resistance in the child’s microbiome — Resistant strains persist in the gut for years, which reshapes your child’s microbial diversity and limits the effectiveness of future treatments against bacterial infections.

How to protect your child from antibiotics

If you’re a parent, soon-to-be parent, or even just planning ahead, the decisions you make before and during your pregnancy, as well as during your child’s earliest days, are important as they directly shape your child’s metabolism, immune strength and lifelong risk for chronic conditions.

While antibiotics are sometimes necessary, most of the time, they are overprescribed. You can start protecting your child’s gut microbiome during those key developmental windows as early as now.

Here’s how I recommend you approach it:

1. Avoid antibiotics during pregnancy unless absolutely necessary — Before filling a prescription, always pause and ask: Is this absolutely necessary right now? Or could there be a safer, lower-risk approach? Remember that the goal isn’t to avoid care — it’s to choose care that supports both you and your baby.I outlined some natural antimicrobials in “Natural Options to Try Before Taking Antibiotics,” but make sure to review each option with your healthcare provider to make sure they’re safe to use while pregnant.

2. Delay antibiotic use in your baby unless it’s urgent — If you’re told your baby needs antibiotics, ask about timing, dosage and diagnosis. If it’s something minor, like an earache or low-grade fever, consider monitoring or natural remedies first. Preserving your baby’s microbiome in the first few months is one of the most powerful long-term protective steps you can take.

3. Support your child’s microbiome from day one — If you’re able to breastfeed, continue doing so. Breast milk naturally delivers beneficial bacteria and prebiotics that help shape a healthy microbiome. If you’re using formula milk, look for one designed to support gut development through added prebiotics or microbiota-friendly ingredients.

Also, be mindful of your baby’s environment. Overusing sanitizers, antibacterial soaps or unnecessary medications disrupts the very microbial exposures your baby needs to build resilience. A little dirt and natural contact go a long way in training a strong immune system. Read “Dirt Don’t Hurt” to learn more about why dirt is good for children.

4. Use probiotics strategically, not generically — If your child has had antibiotics or was born via C-section, it’s worth replenishing their gut flora. Look for strains backed by research in early-life immune development, like Bifidobacterium infantis or Lactobacillus rhamnosus GG.

For mothers, improving gut health with beneficial microbes like Akkermansia muciniphila, which supports gut integrity and metabolic health, also benefits your child’s microbiome. Always time probiotics to follow, not compete with, antibiotic use, in case it’s required.

5. Build long-term metabolic resilience through food — As your child begins eating solids, use this as an opportunity to shape their microbiome for life. Offer fiber-rich plant foods (such as fruits, cooked vegetables and root vegetables) that nourish beneficial bacteria.

Include fermented foods like yogurt (unsweetened and ideally from raw or grass-fed dairy) or sauerkraut in small amounts. Avoid processed foods, especially those with vegetable oils, as these contribute to inflammation and disrupt gut health. Your child’s gut bacteria thrive on real food — not packaged snacks or sterile diets.

Frequently asked questions (FAQs) about antibiotics and Type 1 diabetes

Q: What is Type 1 diabetes and how does it affect children?

A: Type 1 diabetes is a chronic autoimmune disease where the body mistakenly destroys insulin-producing cells in the pancreas. This leads to lifelong dependence on insulin injections, blood sugar monitoring, and an increased risk of serious complications.

Q: How do antibiotics affect Type 1 diabetes risk?

A: Antibiotics, especially when used during crucial developmental windows in early life, disrupt the gut microbiome. This affects immune regulation and contributes to an increased risk of developing Type 1 diabetes.

Q: Can antibiotics given during pregnancy affect my child’s health?

A: Yes, antibiotics taken during pregnancy disrupt the development of your child’s gut microbiome, which increases the risk of autoimmune diseases like Type 1 diabetes.

Q: Which antibiotics are most linked to a higher risk of Type 1 diabetes?

A: The study found that macrolides (such as azithromycin and erythromycin) taken by mothers before pregnancy increased the risk of Type 1 diabetes in their children by 17%. Additionally, sulfonamides and trimethoprim, often used to treat UTIs during pregnancy, raised the risk by 91%.

Q: Can the effects of early antibiotic exposure be reversed?

A: Strategies like supporting the gut microbiome with probiotics or breastfeeding help mitigate some of the negative effects and support a healthier immune response in children.

Originally published by Mercola.