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How Mom’s Gut Microbiome Impacts Her Baby

Published June 10, 2023

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How do babies acquire their microbiomes? Are babies born without them? And do babies’ gut microbiomes resemble that of their mother’s? Since the gut microbiome is crucial for baby’s health and well-being, it’s important to examine how a mother’s gut microbiome can affect her baby before, during and after birth.

What is the maternal microbiome?

First let’s understand that the microbiome is defined as the genetic material of all microorganisms- including bacteria, parasites, and viruses- colonized in an environment [1]. The human microbiome consists of trillions of microbial cells [2], and these microorganisms live in gut, stomach, oral cavity, vagina, mammary glands, skin, and respiratory tract [3]. When we consider the potential interactions between mom and baby before, during and after birth, the maternal microbiome in the gut, vagina, on the skin, and in mammary glands can be transferred to her baby.

In our body, most of our bacteria are located in the gut, and colonized in the colon [4]. A disrupted maternal gut microbiome is associated with prenatual issues like shorter gestational age, lower birth weight, and poor psychological development for an infant. Aside from prenatal effects of maternal gut microbiome, the maternal microbiome can be shared with infants during the birth based on how baby is delivered along with maternal vaginal and skin microbiome [5]. After birth, the human milk microbiome and skin microbiome are passed to infants via breastfeeding. Thus, the maternal microbiome colonized in the gut, on the skin, in the reproductive tract, and the mammary glands can influence the pregnancy outcomes, the fetus’ development, and establishing the infant’s microbiome.

The factors we know influence the maternal microbiome, and indirectly infants' health.

The maternal microbiome may influence the development of the baby's microbiome via the transfer of bacteria through childbirth. The seeding of an infant’s microbiome may even start before the birth. Originally it was believed that the womb is sterile, and a fetus was not exposed to any microbes during pregnancy until time of delivery. However, recently researchers have found particles that are produced by bacteria in the placenta [6]. To support these findings, a recent study showed that more than half of the microbial families identified in meconium, baby’s first poop, were also detected in the placenta and amniotic fluid. Specifically, bacteria from the same genera like Escherichia/Shigella, Lactobacillus and Propionibacterium were found in meconium, placenta and amniotic fluid [7]. Although still we do not know enough about the microbiome transmission of the gut microbiome during pregnancy [3], these findings can imply that a baby’s gut microbiome begins shaping before birth. Thus, the maternal gut microbiome before and during pregnancy is a critical factor in baby’s development.

Lifestyle and environmental factors of the mother, like diet, physical activity, tobacco exposure, antibiotic usage, and pet exposure, all play a role in the characteristics of the maternal microbiome. For example, infants of a mom who consumed high fruits and vegetable during pregnancy had a higher abundance of Cutibacterium, Parabacteroides, and Lactococcus in their stool when compared to moms with low fruits and vegetable intake. These types of bacteria have several benefits like immune system regulation, improving intestine health, and increased protection from infection [8]. This implies that maternal lifestyle can have both short and long-term impacts on her infant’s health.

How prenatal antibiotic exposure impacts baby’s health

Research shows that prenatal antibiotic usage disturbs the microbiome for both mom and baby. A recent study found a significant difference in abundance of bacteria when they compared the gut microbiome of infants prenatally exposed to antibiotics with infants without antibiotic exposure during pregnancy. For example, the abundance of Lachnospiraceae family was greater in prenatally antibiotics exposed infants compared to infants not exposed at 12 months. We know that the higher Lachnospiraceae abundance is related with higher body weight in children [9]. The alteration in microbiome due to antibiotic usage during pregnancy can have long-term effects on babies’ health including childhood obesity [10, 11], asthma [12], atopic dermatitis, and food allergies [13].

How delivery type can influence the development of a baby’s microbiome.

Delivery is a crucial experience for the microbiome transmission. Researchers have found a significant difference in the microbiome of naturally delivered babies and those delivered via cesarean.

The gut microbiome of babies delivered vaginally is similar to the gut microbiome of their mother. In comparison, babies born by cesarean section have bacteria that more closely resembles the hospital environment where they were born and their mom’s skin [14].

Specifically, abundance of Bacteroides species in the gut microbiome is lower in infants delivered via cesarean section when compared to naturally delivered babies. Note that a Bacteroides dominant microbiome is associated with better cognitive functions in infants [15]. A recent study from Boston showed that Bacteroides species were detected in the gut microbiome of infants born by both cesarean section and vaginal delivery in the first days of infant life. However, babies delivered via cesarean section lost the Bacteroides species at week two, while it was still abundant in vaginally delivered infants.

Transfer of maternal microbiome to babies after birth: Does breastfeeding influence babies’ microbiome?

Over 800 bacterial species live in the human milk microbiome, and these microorganisms seed a baby’s gut and oral microbiome via breastfeeding.

A breastfed baby consumes from 1×105 to 1×107 bacteria through breastfeeding each day, which represent one third of the baby’s gut bacteria. The microbiota acquired via breastfeeding is sourced from the maternal gut, maternal skin, environment, and infant’s mouth. We know that mom’s diet before or after birth, physical activity, tobacco exposure, body weight, geographical location, socioeconomic status, lactation stage, delivery type, parity1, and prenatal antibiotics exposure can affect her breast milk microbiota [16, 17]. Given the role of human milk microbiome on early microbiome seeding of infants, maternal lifestyle factors require more attention for improving short- and long-term health of infants.

Aside from bacteria present in milk, human milk oligosaccharides, the 3rd most abundant component of human milk, serves as the food or “nourishment” for friendly bacteria. Human milk oligosaccharides promote the growth of the Bifidobacterium genus [17,18], which is related to improved infant development and immunity [20].

There are different types of human milk oligosaccharides, and their presence in human milk is influenced by maternal factors like genetics, delivery method, parity, geography, diet, and age. This show the importance of how bacteria and human milk oligosaccharides passed via breastfeeding is an important way to seed an infant’s gut microbiome [19, 21].

Summary The maternal microbiome is critical for shaping the infant microbiome via transferring microorganisms during the pregnancy, delivery, and the postpartum period via breastfeeding. Ideally, a mom can share rectal, vaginal, skin, and mammary microbiome with infants through vaginal delivery and breastfeeding her baby.

Healthy lifestyle habits like a balanced diet, physical activity, eliminating unnecessary antibiotic usage, and avoiding tobacco exposure during pregnancy and postpartum should be emphasized to ensure a more balanced microbiome for both mom and baby.


1 Parity is the number of times a woman has given birth to a live neonate (any gestation) or at 24 weeks or more, regardless of whether the child was viable or non-viable (i.e. stillbirths).


1. Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges [published correction appears in Microbiome. 2020 Aug 20;8(1):119]. Microbiome. 2020;8(1):103. Published 2020 Jun 30. doi:10.1186/s40168-020-00875-0

2. Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the human microbiome. Nutr Rev. 2012;70 Suppl 1(Suppl 1):S38-S44. doi:10.1111/j.1753-4887.2012.00493.x

3. Ogunrinola GA, Oyewale JO, Oshamika OO, Olasehinde GI. The Human Microbiome and Its Impacts on Health. Int J Microbiol. 2020;2020:8045646. Published 2020 Jun 12. doi:10.1155/2020/8045646

4. Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016;14(8):e1002533. Published 2016 Aug 19. doi:10.1371/journal.pbio.1002533

5. EBioMedicine. The maternal microbiome: another bridge linking mothers and infants. EBioMedicine. 2021;71:103602. doi:10.1016/j.ebiom.2021.103602

6. Walker RW, Clemente JC, Peter I, Loos RJF. The prenatal gut microbiome: are we colonized with bacteria in utero? Pediatr Obes. 2017 Aug;12 Suppl 1(Suppl 1):3-17. doi: 10.1111/ijpo.12217. Epub 2017 Apr 26. PMID: 28447406; PMCID: PMC5583026.

7. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S. Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep. 2016;6:23129. Published 2016 Mar 22. doi:10.1038/srep23129

8. Fan HY, Tung YT, Yang YSH, et al. Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome. Nutrients. 2021;13(5):1559. Published 2021 May 5. doi:10.3390/nu13051559

9. Zhang, M., Differding, M.K., Benjamin-Neelon, S.E. et al. Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome. Ann Clin Microbiol Antimicrob 18, 18 (2019). //

10. Mueller NT, Whyatt R, Hoepner L, et al. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond). 2015;39(4):665-670. doi:10.1038/ijo.2014.180

11. Mor A, Antonsen S, Kahlert J, et al. Prenatal exposure to systemic antibacterials and overweight and obesity in Danish schoolchildren: a prevalence study. Int J Obes (Lond). 2015;39(10):1450-1455. doi:10.1038/ijo.2015.129

12. Rantala AK, Tapia G, Magnus MC, et al. Maternal antibiotic use and infections during pregnancy and offspring asthma: the Norwegian Mother, Father and Child Cohort Study and a nationwide register cohort. Eur J Epidemiol. 2022;37(9):983-992. doi:10.1007/s10654-022-00897-y

13. Metzler S, Frei R, Schmaußer-Hechfellner E, et al. Association between antibiotic treatment during pregnancy and infancy and the development of allergic diseases. Pediatr Allergy Immunol. 2019;30(4):423-433. doi:10.1111/pai.13039

14. Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. The infant microbiome development: mom matters. Trends Mol Med. 2015;21(2):109-117. doi:10.1016/j.molmed.2014.12.002

15. Tamana SK, Tun HM, Konya T, et al. Bacteroides-dominant gut microbiome of late infancy is associated with enhanced neurodevelopment. Gut Microbes. 2021;13(1):1-17. doi:10.1080/19490976.2021.1930875

16. Notarbartolo V, Giuffrè M, Montante C, Corsello G, Carta M. Composition of Human Breast Milk Microbiota and Its Role in Children's Health. Pediatr Gastroenterol Hepatol Nutr. 2022;25(3):194-210. doi:10.5223/pghn.2022.25.3.194

17. Sánchez C, Fente C, Regal P, Lamas A, Lorenzo MP. Human Milk Oligosaccharides (HMOs) and Infant Microbiota: A Scoping Review. Foods. 2021;10(6):1429. Published 2021 Jun 20. doi:10.3390/foods10061429

18. Arzamasov AA, Nakajima A, Sakanaka M, et al. Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR. mSystems. 2022;7(5):e0034322. doi:10.1128/msystems.00343-22

19. Carr LE, Virmani MD, Rosa F, et al. Role of Human Milk Bioactives on Infants' Gut and Immune Health. Front Immunol. 2021;12:604080. Published 2021 Feb 12. doi:10.3389/fimmu.2021.604080


Hatice Cetinkaya, MSc

Hatice Cetinkaya is a research associate and adjunct instructor at the University of Cincinnati, Ohio. Hatice is interested in maternal and infant health with emphasis on nutrition.