As the microbiome field has matured over the past decade, some questions have been answered easily, while others have remained more difficult. One of the most complicated and challenging biological questions has been whether the method that a baby is delivered (vaginally or by cesarean section) affects their microbiome. Research papers have been published that support both sides of the hypothesis. Although some researchers suggest that there is no difference, others have adopted the practice of manually applying the missing microbiome (sampled from the mother) to their newborn babies.

But now, new research suggests that cesarean-born babies may not be missing out on essential microbes. The team of scientists found that, whether born vaginally or via cesarean section, babies receive essential microbes from their mothers. The reduction in transfer of their mother’s gut microbiome through fecal microbes, when babies are born via C-section, may be compensated for by other niches—for example, breastmilk.

This research is published in Cell Host & Microbe in the paper, “Mother-infant microbiota transmission and infant microbiota development across multiple body sites.”

“We wanted to have a better idea of how the infant microbiome develops in different parts of their bodies and how it’s influenced by factors such as birth mode, antibiotic use, and lack of breastfeeding,” said Wouter de Steenhuijsen Piters, MD, PhD, a postdoc in the Bogaert lab at the University Medical Center Utrecht, Netherlands.

To do this, the team recruited and repeatedly sampled 120 Dutch mothers and soon-to-be-born babies. From the babies, they collected skin, nose, saliva, and gut microbiome samples two hours after they were born and when they were one day old, one week old, two weeks old, and one month old.

The team also collected six different microbiome samples from the mothers—skin, breastmilk, nose, throat, fecal, and vaginal—to determine which of these sources were “seeding” the babies’ various microbiomes. Then, they analyzed these results in the context of several factors that are thought to impact microbiome transfer, including mode of delivery, antibiotic use, and breastfeeding.

“We saw that many niches of the mother are important for the transmission of microbes, and if some of these pathways are blocked for one reason or another—in this case, we saw that happening with the cesarean section—then these microbes can still reach the infant through other paths,” said de Steenhuijsen Piters.

Regardless of birth route, the researchers found that approximately 58.5% of a baby’s microbiome is derived from its mother. However, different maternal microbial communities contributed to different infant microbiomes. Cesarean-born babies received fewer microbes from their mother’s vaginal and fecal microbiomes, and acquired more microbes from breastmilk.

“Microbiome transfer and development are so important that evolution has ensured that those microbes are transferred one or another way from mother to child,” said Debby Bogaert, PhD, physician scientist at the University of Edinburgh. “Breastfeeding becomes even more important for children born by cesarean section who do not receive gut and vaginal microbes from their mom.”

“It’s a smart system, and it makes sense from an evolutionary perspective that these types of pathways are redundant to ensure that the child can begin life with the appropriate ‘starter kit,’” said de Steenhuijsen Piters.

Now, the team plans to investigate non-maternal influences on infant microbiome development. “We could see that the maternal microbiome explains almost 60% of the infant’s total microbiome, but there’s still 40% that we don’t know about,” said de Steenhuijsen Piters. “It would be interesting to stratify that unknown fraction to see where all the microbes come from; whether fathers contribute, for example, or siblings, or the environment.”

Ultimately, the researchers want to understand how microbiome development in infants relates to long-term health. “Next, we want to explore whether this early life process, influenced by mom, is affecting not only short-term infection risk in the first year of life but also longer-term health in terms of things like allergies and asthma,” said Bogaert. “In the future, we might be able to utilize this knowledge to help prevent, diagnose, or treat health problems.”