What to Do If You Need to Take Antibiotics When Pregnant or Nursing


Our intestinal ecology is made up of more than 100 trillion diverse microorganisms, collectively referred to as the microbiome. Over two pounds of bacteria, viruses and fungi comprise your gut microbiota; almost as much as the weight of the human brain!

The health of the adult microbiome begins at birth and can set the stage for lifelong health. During pregnancy, studies have shown that the maternal gut microbiota may be able to transfer to the baby and placenta through the blood stream. The unique ecosystem of bacteria in the placenta has been shown to originate from bacteria inside the mother’s mouth!

With the advanced studies taking place around human gut health, such as the NIH Human Microbiome Project, we are finding increasing evidence linking the health of the microbiome to diseases such as obesity, cancer, mental health disorders, asthma, and autism amongst many others.

From birth, the development of our microbiome influences the the way in which our immune system develops, and when it's disrupted our babies are susceptible to a whole host of inflammatory and allergic conditions. Ideally, women head into their pregnancy with a healthy microbiome and maintain this health throughout.

The Biggest Risk Factors That Can Disturb The Health Of The Microbiome Are:

  • Dysbiosis (the overgrowth of potentially harmful bacteria, yeasts, and other organisms, or lack of ample amounts of healthy microbes)
  • Antibiotic exposure of mother in pregnancy, labor or while breastfeeding
  • Cesarean birth
  • Lack of breastfeeding for at least the first 4 months of life, and ideally the first year
  • Antibiotics given to baby in the first 2 years of life

Unfortunately antibiotic treatment is widespread in our country and accounts for more than 80% of the medications prescribed during pregnancy.

Antibiotic treatment can often be life saving, but at other times their use is not really warranted, or should only be a last resort. Studies have shown that antibiotic use can have detrimental effects on both mother and baby's microbiome and overall immunity. It;s important that women are educated on these issues, and feel empowered to make the best decisions for themselves and their babies.

When becoming a mother, women are faced with so many decisions and have to tune into their center and their intuition to feel what is right for them in that moment. In these situations, we can give ourselves permission to pause, and fully consider all of the options, benefits and risks of antibiotic use, whether during pregnancy, labor or throughout breastfeeding. Sometimes taking antibiotics is the safest thing to do. Not to worry, if a mother decides that antibiotics are the best option for her there are many ways she can support her immunity, gut ecology and ultimately her baby. As Aviva Romm reminds us,

Do your best to not beat yourself up and remember, not every baby that has an antibiotic exposure develops consequences – many are just fine. And the consequence of not treating an infection can potentially be much worse! 

The key here is to be educated and empowered in your decision making, and having the tools to support yourself both metally and physically in whichever decision you make. Trust yourself.

What To Do If You Need To Take Antibiotics:

Take Probiotics 

Although it may seem counter intuitive to take probiotics while you are taking antibiotics, I assure you it is not. The antibiotics do not just "kill" off all the beneficial probiotics, and furthermore studies have shown that even transient probiotics, ones that do not colonize the gut can have powerful therapeutic effects. Lactobacillus and Bifidobacterium are two of the most common species used as probiotics and these supplements are readily available in most health food stores.

S. boulardii is actually a beneficial yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because the antibiotics can’t kill it.  S. boulardii is also preferable under these circumstances because there’s no risk of it harboring genes for antibiotic resistance and later transferring those genes to pathogenic bacteria. As with all things, finding the right probiotics will depend on each individuals circumstances and which antibiotics you are taking. Consult with your primary care provider or a qualified health professionalb to find the best fit for you. At least 3 months of consistent probiotic use is reccomended to help restore the gut mirobiome post antibiotic treatment.

Lactofermented vegetables (kraut and kimchee) are wonderful food sources of probiotics as well as kiefer, when dairy is tolorated. You can also make non-dairy kiefer with coconut milk which is delicious!

Klaire also has an infant probiotic that contains a variety of Lactobacillus and Bifidobacterium species designed for the infants microbiome.

Take Prebiotics 

Prebiotics are actually much more effective at promoting benificial bacteria in the gut than probiotics. They are food for all of the benifical bacteria that are already present in our gut. The more we feed these "good guys" the more they can thrive. Thus, prebiotics are a vital component to any gut restoration protocol. Inulin, a type of fructan oligofructose (FOS) carbohydrate, is a prebiotic that can be found in dandelion root, burdock root, chickory root, yacon, Jerusalem artichokes, garlic, asparagus, bananas (slightly green) and onions. Inulin is a non-digestible prebiotic, which allows it to pass through the small and large intestines unabsorbed. During this process, inulin naturally ferments and feeds the healthy intestinal microflora that populate our gut.

During and after antibiotic use, include plenty of soluble fiber in your diet, this is what feeds the beneficial bacteria. Soluble fiber can be found in starchy vegetables such as sweet potatoes and all root veggies, squash and peeled fruit. adding 1-2 tbs of ground flax to your food or smoothies every day can help make sure you are getting at least 35g of fiber a day. It may be helpful to avoid too much insoluble fiber during this time as it can be irritating to the gut lining. One exception to that is what is called resistant starches, which are plant based starches that come from legumes, whole grains, as well as sweet potatoes and white potatoes that have been cooled to room temperature. These resistant starches don't break down as well and therefore become excellent food for the gut flora.

Breastfeed if possible 

Breastmilk is basically superfood for babies! It provides a wide spectrum of biological factors that aid in the development of the gut, systemic metabolism, and the innate and acquired immune systems. It also develops a supportive and protective microbiome for the baby. Breastmilk contains so many substances that can benefit your baby’s immune system, including antibodies, immune factors, enzymes, and white blood cells. These important substances protect your baby against a wide variety of diseases and infections and strengthen their overall immunity not only while they are breastfeeding but in some cases long after weaning.

Avoid Stress  

Believe it or not, stress plays a major role in our gut health. Stress can affect our gastric secretions, gut motility, mucosal permeability and barrier function along with a host of other things. Chris Kresser has a great article on it here. So take a deep breath and work on re-framing your stress in ways that are not overwhelming or taxing on the body.

A funny little cartoon illustrating the importance on microbes on our babies devolving immune systems. #dirtisgoodforyou

A funny little cartoon illustrating the importance on microbes on our babies devolving immune systems. #dirtisgoodforyou

Women have many choices throughout pregnancy and birth, sometimes more than we are really even aware of. Luckily, so much is available now and we are able to share this knowledge in new and accessible ways. 

We live in a over-medicated world and antibiotics are prescribed for just about anything.  Though they can play an important role in health and safety, I encourage taking a deeper look into alternative care for you and your baby. Educate yourself. Trust yourself. And most of all love yourself; remember you are doing the best that you can.

I did then what I knew how to do. Now that I know better, I do better. ~ Maya Angelou


Koren, O & Kuperman, A. (2016, June 16). Antibiotic use during pregnancy: how bad is it?. Retrieved November 15, 2017, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911692/.

Kresser, C. (2014, Janurary 10). What To Do If You Need To Take Antibiotics. [blog post]. Retrieved November 15, 2017, from https://chriskresser.com/what-to-do-if-you-need-to-take-antibiotics/.

Reed, R. (2016, April 13). The Human Microbiome: Considerations for Pregnancy, Birth and Early Mothering.[blog post]. Retrieved November 15, 2017, from https://midwifethinking.com/2016/04/13/the-human-microbiome-considerations-for-pregnancy-birth-and-early-mothering/.

Romm, A. (2016, November 16). Protecting Your Baby’s Microbiome from the Start.[blog post]. Retrieved November 15, 2017, from https://avivaromm.com/protecting-babys-microbiome/.

Amanda Verdery Young