Antibiotics During Labor And Their Effects On Baby’s Health

Newborn baby being introduced to its mother after a hospital c-section


  • Intrapartum antibiotics (given during labor and birth) -like those given for Group B Strep (GBS), chorioamnionitis (also called intrauterine inflammation or infection), or C-section- may disrupt your baby’s gut microbiome. Side effects of antibiotics during labor may vary depending on length and dosage.
  • No association has been found for intrapartum antibiotics and allergic disease in children. There may be a mild association with weight gain, but the evidence is contradictory.
  • Breastfeeding, probiotics, and safe exposure to pets, soil, and farm animals can help minimize gut microbiome disruption.

There are different situations in which you might need to use antibiotics during labor:

  • A positive test for Group B Strep (GBS)
  • C-section
  • Chorioamnionitis

Let’s go over each one of these conditions, and then explore how these antibiotics, also known as intrapartum antibiotics, may affect your baby’s gut microbiome and overall health.

Click here to read about antibiotics during pregnancy and how these may affect mom’s and baby’s health.

Group B Strep (GBS)

Group B Strep (GBS) is not an infection. Having GBS means you have Streptococcus agalactiae bacteria in your gut or vagina, which is not a problem for you but may be for your newborn baby if you have a vaginal birth. GBS has been linked with potentially life-threatening infections in newborns [1].

According to the American College of Obstetricians and Gynecologists (ACOG), all pregnant women in the US should be screened for S. agalactiae at 36-37 weeks of gestation independently of the planned mode of birth [2]. The GBS test is not routine in other countries; instead, whether it’s performed or not is based on a risk assessment.

For a positive detection, standard GBS treatment is to receive antibiotics to prevent passing GBS to the baby. For a mom with a positive GBS test that doesn’t receive group B strep antibiotics during labor, a baby’s mortality risk from GBS is 0.001% when born at term or 0.01% when born preterm [2]–[4].

Antibiotic treatment for GBS is administered a few hours before birth [2], [3]. The standard treatment is intravenous penicillin or ampicillin, usually administered every 4 hours during labor until birth. Other antibiotics like clindamycin or vancomycin may be used in cases of penicillin allergy or antibiotic resistance.

C-section: antibiotics before or after cord clamping?

Antibiotics are given during C-section to reduce mom’s risk of developing wound infection or endometritis. Different healthcare institutions recommend that these are administered before C-section incision [5], [6]. But they could also be administered after cord clamping to minimize antibiotics during labor effects on the baby. Which timing is better when it comes to mom’s risk of infections and baby’s microbiome?

Four clinical trials found that antibiotics before incision were better for the mom because they significantly reduced the risk of wound infection, endometritis, or hospital stay [7]–[10]. However, five clinical trials found that antibiotics after cord clamping didn’t increase the risk of infection when compared to antibiotics before incision [11]–[15].

On the other hand, only two very small studies have looked at the effects of C-section antibiotics on the baby’s gut microbiome. They didn’t find any difference when comparing antibiotics before incision with after cord clamping [16], [17].

In conclusion, antibiotics effectively reduce the risk of infection for mom, but clinical trials vary in their recommendations for the optimal timing of antibiotic administration. Given that some clinical trials found that the risk was reduced when antibiotics were administered before incision, this is what healthcare institutions recommend. But ultimately, the decision should be yours. With only two small studies looking at changes in the baby’s gut microbiome, we can’t strongly say that there are no effects.


Chorioamnionitis, also known as intrauterine inflammation or infection, is an infection that can affect the amniotic fluid, placenta, fetus, fetal membranes, and/or decidua. It’s often caused by vaginal bacteria that go up through the cervix and into the amniotic sac [18]. Approximately 3-5% of term births are complicated by this infection [19].

Some common complications of chorioamnionitis for the baby include pneumonia, meningitis, and blood infection. For mom, chorioamnionitis increases the chances of a C-section birth and may lead to postpartum hemorrhage, endometritis, and blood infection [20].

To reduce the risk of such complications, the ACOG recommends antibiotics during labor for all cases of suspected and confirmed chorioamnionitis [20].

Intrapartum antibiotics may alter your baby’s gut microbiome

Scientists have explored how intrapartum antibiotics impact the baby’s gut microbiome. Here are some of the findings:

  • Babies born by vaginal birth or C-section, whose moms received intrapartum antibiotics, had lower levels of Bacteroides at one year of age [21], [22]. Bacteroides are generally friendly gut bacteria [23] and are typically more prevalent in the gut of babies born vaginally than in babies born by C-section. This decrease was mainly seen in those babies that were not exclusively breastfed at three months of age, pointing out that breastfeeding may protect against these disturbances and even help to restore your baby’s microbiome after C-section birth
  • At three months of age, vaginally born babies whose moms received intrapartum antibiotics had significantly lower abundance of beneficial Bifidobacterium than unexposed babies [24].
  • Babies whose moms received intrapartum antibiotics had higher levels of Firmicutes at 10 and 90 days of age and lower levels of Actinobacteria at 10 days of age [25]. An example of Firmicutes are Enterococcus bacteria, which ideally are not present in high levels in babies. An example of Actinobacteria are Bifidobacterium species, which provide many benefits for babies.

Do antibiotics during labor affect your baby’s health beyond the gut microbiome?

A few studies have looked at the association between intrapartum antibiotics and the risk of developing disease during childhood:

  • Allergic disease. No association has been found for intrapartum antibiotics and higher risk of developing eczema, asthma, allergic rhinitis, or food allergy [26]–[28]. One of these studies did find an association when exposure to intrapartum antibiotics lasted more than 24 hours, but this analysis only considered 11 women and so results are not very strong [28].
  • Weight gain. A big study reported a mild association between intrapartum antibiotics and increased weight gain at 5 years of age, which was more pronounced for C-section babies [29]. But a medium-size study did not find an association in vaginally-born children at 2-5 years of age [30].

Things you can do to restore your baby’s gut microbiome and decrease the risk of long-term health issues

There is not enough evidence to strongly say that antibiotics during labor pose a huge risk for your baby’s health, but we don’t know for sure (yeah, that’s annoying). 

Given the uncertainty, if you had to receive intrapartum antibiotics, we would recommend the following actions to provide extra support to your baby’s gut microbiome:


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