Paternal and maternal transplants boost infant gut health after cesarean delivery

The gut microbiome is integral to health throughout life. A recent study published in the journal Cell Host & Microbe explores the paternal role in infant gut seeding and the impact of induced seeding by maternal fecal microbiota transplant (FMT).

Study: Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Image Credit: Natalia Deriabina / Study: Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Image Credit: Natalia Deriabina /

How cesarean delivery shapes early health

The fetal gut is sterile, as seeding begins after birth. Materno-fetal transmission of microorganisms occurs intrapartum and afterward, contributing to about 50% of microbial taxa in the infant's gut by one year. This process may be disrupted by cesarean delivery, as vaginal delivery also facilitates the colonization of microorganisms in the infant's gut.

Antibiotics are often administered to mothers who undergo cesarean delivery to reduce the risk of post-operative infections. Antibiotic treatment may also alter the composition of the maternal microbiome, thereby reducing the amount of maternal bacteria available for colonizing the infant's gut.

Cesarean delivery currently accounts for over 25% of births worldwide. Breastfeeding, skin-to-skin contact, and antibiotic stewardship can be utilized to mitigate the effects of cesarean delivery on infant gut colonization.

Currently, researchers estimate that about half of the strains found within the fetal microbiome are not acquired from maternal transmission. Therefore, in addition to the maternal influence on the development of the infant gut microbiome, individuals in the infant's proximity may also be sources of health-associated microorganisms. However, a limited understanding remains of which species are acquired from these individuals and their functional role within the infant gut microbiome.

What did the study show?

The current study aimed to investigate microbiota sharing between both parents and the infant's gut, as well as how its composition changes throughout the first year of life in infants born by vaginal and cesarean delivery.

The researchers examined two metagenomic data sets from 81 infants and 433 samples. A total of 285 and 113 samples were obtained from 53 vaginal and 21 cesarean deliveries, respectively. An additional 35 samples obtained from seven caesarean-born infants in the Finnish SECFLOR study who subsequently received maternal FMT were also included in the analysis.

Changes in infant gut microbiota

Despite initial significant differences from the adult gut, the infant gut became more similar to that of the parents over time. The infant's age and intrapartum antibiotic prophylaxis (IAP) were the strongest predictors of differences in the gut microbiota composition compared to the delivery mode.

The infant received significant microbial seeding from the mother by three weeks of age, with seeding decreasing over time from 61% to 30% at three weeks and 12 months, respectively. For the father, microorganism sharing was lower by three weeks at 25% but remained at 20-22% thereafter until 12 months. Therefore, maternal and paternal contributions were very similar, irrespective of the mode of delivery.

Each of the parents provides a distinct fraction of microbiota diversity to the infants.”

The mother appears to contribute Bacteroides species. Five of out six species more commonly shared with the mother had higher relative abundances with infants born vaginally as compared to those born by cesarean delivery.

FMT and infant gut microbiota richness

In infants who received FMT, the gut microbiota exhibited markedly from both infants born through cesarean delivery who did not receive FMT babies and those born vaginally.

The reception of FMT from the mother increased the growth rate of bacteria in the infant gut. Maternal FMT also increased strain sharing with the mother; however, FMT may introduce species not typically found in young infants.

Babies born by caesarean delivery exhibited differences in relative abundance for 16 species, eight of which were restored by FMT to levels comparable to vaginally delivered infants. Other species reached higher levels in the FMT group as compared to vaginally delivered infants. 

FMT produced stable seeding that was observable throughout the study period. Nevertheless, FMT-derived species exhibited reduced growth rates over time compared to those obtained by natural seeding.

Strict anaerobes and some fiber-degrading species survive poorly when introduced through FMT. In contrast, the ability to break down human milk oligosaccharides (HMOs) appears to provide a growth advantage, as babies will often consume breastmilk during the first few months of life.

Further research is needed to compare the results of induced and natural seeding, which will shape the formulation and administration of FMT in the future.

FMT and pathogen colonization

FMT reduced the likelihood of gut colonization by pathogenic bacteria to levels comparable to that in vaginally born infants not exposed to IAP. This type of microbial colonization is higher among cesarean-delivered infants and is comparable to vaginally born infants exposed to IAP.   

IAP and infant gut microbiota

IAP affects both maternal and infant gut microbiota composition and increases pathogen colonization.

Taxa like Clostridium perfringens, Enterococcus fecalis, two Klebsiella species, and Staphylococcus aureus were more common in infants than in adults. However, Staphylococcus aureus was more common in cesarean-delivered infants than vaginally-delivered infants. Among infants born vaginally, E. fecalis and K. pneumoniae were more common if the mothers received IAP.


Irrespective of the mode of delivery, fathers contribute a stable and growing percentage of gut microorganisms throughout the first year of life that ultimately reaches parity with the mother's contribution by that point. The contribution of household members to microbiota development in infants is a vital area that deserves more study.

The study findings also indicate that antibiotics given after birth negatively affect bacterial growth rates and microbiota maturation. Furthermore, FMT is a promising approach to induce seeding when the natural process is disrupted for various reasons.

Journal reference:
  • Dubois, L., Valles-Colomer, M., Ponsero, A., et al. (2024). Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Cell Host & Microbe. doi:10.1016/j.chom.2024.05.004.
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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