Exclusive breastfeeding for at least three months may lessen the effect of antibiotic use during labor and delivery on an infant’s microbiome.

Cesarean delivery and antibiotic use during vaginal or C-section childbirth decreases diversity of an infant’s microbiome [1, 2]. However, a study by Azad et al. suggests that exclusive breastfeeding for at least three months may lessen the effect of maternal use of antibiotics during labor and delivery on the microbiome [3]. Breastfeeding may repair the infant microbiome after antibiotic use. Birth is a key time for beneficial microbes to be transmitted from mother to infant, especially during vaginal birth [1, 4, 5]. However antibiotics that disrupt microbiome transmission may be used during both vaginal and Cesarean section (C-section) deliveries. During childbirth, especially in Canada and the United States, antibiotics may be used for several reasons. In vaginal deliveries, antibiotics are used to prevent transmission of Group B Streptococcus (GBS) transmission to the infant. However, the use of antibiotics for GBS is correlated with increased antibiotic-resistant Escherichia coli infections in infants [6]. Antibiotics may also be given to reduce opportunistic pathogen infections during long labors where the amniotic sac membrane has ruptured. Cesarean section surgeries use antibiotics as a prophylactic to prevent infections [7]. However, such widespread antibiotic use is not a common practice in Denmark, Norway, Australia, and the U.K.

Antibiotics vs Breast Milk

Recent findings on the bacterial microbiome calls into question some of these practices in childbirth [8-10]. Antibiotics are an important, essential tool in our collective “physician’s bag”, killing or inhibiting pathogenic bacteria. Yet they also damage helpful bacteria of our natural microbiome. The effects of antibiotic use may be especially problematic during early development when the baby’s immune system is learning to distinguish between helpful and harmful bacteria. Breast milk is often called “liquid gold” for its health and nutritional benefits to infants. For bacteria in the infant gut, breast milk is certainly a precious resource. Breast milk sugars enrich for species of beneficial Bifidobacteria bacteria in the infant gut and seem to limit the different types of bacteria that live in the breastfed infant’s gut. These bacteria and an overall lower bacterial diversity correlates with infants having fewer allergies, asthma, diabetes, and digestive system disorders both early and later on in life [4, 11-20]. Breast milk is a prebiotic – food for bacteria. It feeds certain beneficial bacteria, but can breast milk also be a form of probiotic? Does exclusive breastfeeding restore damage done to the infant’s microbiome when antibiotics are used during childbirth or when a C-section is performed?

CHILD study

Data from 198 healthy, full-term infants whose stool was collected at 3 months and 1 year and both birth mode and antibiotic use recorded. C-section delivery was classified as either elective or emergency (either with or without labor having initiated). The Canadian Healthy Infant Longitudinal Development Study (CHILD) study examines 3,500 children from 2nd trimester until 5 years old. Information is collected on the children’s genetic makeup and environmental exposures and compared to data from their biological samples to try to determine correlations between different conditions and allergies. For more information on the CHILD study in general see the video below:



Microbiome Differences between Delivery Mode

A significantly altered microbiome community that lacked Bacteroidetes and had increased Firmicutes was seen in 3 month old infants where antibiotics were used during delivery – no matter the birth mode. Similar results have been seen in other studies [21, 22]. Lowest diversity and numbers of bacteria were seen in emergency C-sections where multiple doses of antibiotics are frequently given. Fewer differences in the microbiome composition between vaginal and C-section births despite antibiotic use were seen when children were 1 year old.

Effect of 3 months of Exclusive Breastfeeding

As is found in other studies, infants born vaginally, breast fed and not exposed to antibiotics had a microbiome composed mostly of the family Actinobacteria (Genus – Bifidobacteria) and decreased levels of the family Firmicutes, such as the genera Clostridium and Enterococcus. The greatest effect for breastfeeding was seen with C-section delivered babies. At 3 months old, C-section infants that were breastfed, had a lower relative abundance of Firmicutes than those not breastfed. At one year, only babies born via emergency C-sections and not exclusively breastfed for 3 months, had higher Firmicutes levels. All other birth and feeding types had similar Firmicute/Bacteroidetes levels. The extensive microbiome disturbance in emergency C-section babies may be due to several doses of antibiotics being given. Additionally, antibiotics may have been present in the mother’s breast milk. While exclusive breastfeeding did restore the Firmicute/Bacteroidetes levels in elective and emergency c-sections. However, the microbiome community had higher levels of Verrucomicrobia, especially in elective C-section babies receiving antibiotics and breastfed. High levels of Verrucomicrobia also have been seen in adult gut microbiomes after receiving antibiotics [23].

Exclusive breastfeeding for 3 months seemed to restore the microbiome of infants where antibiotics were used during labor and delivery by 1 year of age.
Exclusive breastfeeding for 3 months seemed to restore the microbiome of infants where antibiotics were used during labor and delivery by 1 year of age.

Similar Microbes at 1 year, so is this a Problem?

After one year, no matter the birth mode, antibiotic use, or feeding, the baby’s microbiomes were much more similar than they were at 3 months. The microbiome seems to recover. Similar stabilizations of the microbiome at one year have been found in other studies [5, 24]. However, the end point may not be as important as the journey and the condition of the microbes after antibiotic exposure. Interactions between the beneficial microbiome and the infant’s immune system seems to “train” the human immune system [24-28]. Exposure to non-pathogenic bacteria allows the immune system to better distinguish between pathogens and non-pathogens. Inflammation is lower in these individuals. Additionally, although the specific bacterial taxa may have returned, metabolically they differ.  When these antibiotic-exposed bacteria were transferred to mice untreated with antibiotics, the mice grew fatter and became obese [29, 30].

Microbiome Repair

Exclusive breastfeeding for at least three months seems to modify changes to the infant microbiome when antibiotics are used. For infants, breast milk is a perfect combination of prebiotics and potentially probiotics, since bacteria are present in the breast milk. So for those mothers concerned about the damage antibiotics received during labor and delivery may have on their babies – consider exclusive breastfeeding for the first three months if possible.

Strengths of the study

  • Longitudinal, population level study
  • Multiple families across Canada
  • 198 infants followed through time
  • Data collected important to this question:
    • Maternal post-partum antibiotic use
    • Birth mode
    • Whether C-section was elective or emergency

Weaknesses of the study

  • Additional data that could provide more information
    • Infant’s meconium
    • Mom’s vagina
    • Mom’s milk microbiome
    • Mom’s milk nutrient profile (sugars, fats, etc..)
  • Limitations:
    • DNA extraction, primers, sequencing (under detect bifidobacteria)
    • Solid food introduction (timing of introduction or what introduced) was not considered when looking at 1 yo microbiome
    • Milk microbiome differs with both antibiotic use AND birth mode.

Other resources


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Would this information change your decisions concerning infant feeding if antibiotics were used during labor?

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3 thoughts on “Can Breastfeeding Help Antibiotic-Exposed Microbiomes Recover?

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  • December 13, 2017 at 11:46 pm

    Thank you for this. My baby was given antibiotics as a precaution due to a combination of factors. I was saddened by this as flora transfer was an impetus to be committed to a vaginal birth. I also didn’t have the chance to discuss it with the Drs, although I am not sure how “just in case” it was, or if they really thought it was necessary. I had wondered about the effects of breastfeeding on this, and really appreciate the article, especially with its good use of references.


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