During Pregnancy: Antacids, Antibiotics, and Aspirin

mom snuggling noses with baby

This is the first installment in our series on reducing your baby's allergy risk. If you missed the introduction, read it here

In this lesson, we'll cover what you need to know about medication use during pregnancy and how it can affect your baby's chance of developing allergies. 


A baby uses her mother’s microbiome while in utero. Like everyone’s microbiome, Mom’s is constantly changing in response to what she eats, how well she sleeps, if she gets sick, what medicines she takes, and her changing hormones. 

It’s unrealistic to think that an expecting mother won’t use some form of medication for 9 months. So let’s talk about how some of the common medicines you take during pregnancy can affect your microbiome. Why? Because the strength of the microbiome your baby is born with (and thus their ability to avoid food allergies) is partly dependent on how strong your microbiome is at the time of labor.

A Quick Refresher: What is the Microbiome?

A Note About Medication Use in Pregnancy

There’s a LOT we don’t know about how drugs and treatments affect women and babies during pregnancy. That’s mostly because companies and doctors are (reasonably) scared to study drugs on pregnant women. However, without that information, doctors are basically guessing (see: Thalidomide used to treat morning sickness) and usually don’t know about the long term effects of drugs. 

Here’s what we do know about common medications you might need in pregnancy, and how they could affect the gut bacteria you pass on to your baby.


Your body creates stomach acid to break down food. During pregnancy, your baby grows and starts to squish your stomach, which can lead to acid can reflux. 

Doctors usually treat reflux with PPIs, or proton pump inhibitors. They can be prescribed, or your doctor might recommend an over-the-counter brand like Nexium or Prilosec.

However, a series of studies in the last 15 years have consistently shown that acid suppression drugs are linked to an increase in food allergy, food hypersensitivity, and asthma. 

PPIs reduce stomach acid, and in doing so may prevent proper digestion of proteins, disrupt the lining or barrier of the intestines, and also change the composition of your microbiome. 

If you want to limit use of medications, there are some natural ways you can try to limit and treat your acid reflux:

  • Eat smaller meals more frequently. Your squished stomach can only fit so much food now.
  • Eat foods that are easier to digest (toast, bananas, eggs) or smoothies that have been blended
  • Eat green leafy vegetables which help reduce stomach acid.
  • Try breathing and yoga poses that help your body create space for the baby
  • Try sleeping slightly elevated to reduce reflux

Reflux is terrible, and moms suffer enough during pregnancy. If you are having heartburn issues, talk to your doctor about both non-prescription and prescription ways to treat acid reflux, and don’t be afraid to use antacids when you need them. 


Let’s preface this discussion by first saying antibiotics are life-saving medicines that you should absolutely use if you need them, pregnant or not. Antibiotics work by killing off bad invader bacteria. Unfortunately, they can also kill of the healthy, helpful bacteria that make up your microbiome. 

Numerous studies have shown that heavy antibiotic use can severely reduce the number and diversity of bacteria throughout your body, and higher antibiotic use is linked to a higher risk of food allergies.

If you’re pregnant, don’t immediately jump to using antibiotics if you have a viral cold, or if your body will heal itself with rest and fluids. Reducing antibiotic use unless needed is the best studied way to maintain your healthy bacteria balance.

Important note: Antibiotics aren’t only in the medicine we take.  Antibiotics used in livestock can end up in the meat you eat. If you can, buy meat that is antibiotic free.

Aspirin / Ibuprofen 

Let’s be real — everyone, at some point in their pregnancy, ends up in pain. Having your core muscles and rib cage stretched out slowly almost always ends up pinching a nerve somewhere. And like most pregnant women desperate for sleep, many will turn to pain killers. 

There has not been extensive research on how aspirin and ibuprofen affect the microbiome or risk of food allergy. At least one study showed that frequent use of both types of painkillers does seem to reduce the diversity of the gut, but there isn’t strong evidence to suggest women avoid them altogether. 

As with all medications one way to deal with the lack of data on how painkillers affect you is to try to avoid them and use exercise, warm baths, and massage as the first way to treat pain.

Flu Shot and Other Vaccines

Straight up. Get your flu shot. Having the flu could put you and your baby at serious risk. Better news is that vaccines, like the flu vaccine, have been shown to have no effect on the gut microbiome or on the risk of food allergies. 

Instead, the relationship actually works the other way. It has been shown that a stronger gut biome can increase the effectiveness of some vaccines. 

Over-the-Counter Cold Remedies

Being sick when pregnant can be terrible. Your body is already overworked and tired. But there is no good data on the effects of over-the-counter cold remedies. When in doubt, avoid these medicines if possible. 

Try curing your common cold naturally with humidifiers, more fluids and rest instead of drugs. 

Remember that cold remedies don’t actually help your body fight off a virus, they simply mask the symptoms. It will take just as long to recover from a cold with or without OTC meds!