Big news in the world of the infant microbiome….

New research finds the colonisation of the baby’s gut microbiome STARTS DURING and AFTER birth, and NOT BEFORE.

In the study published in Nature Microbiology, scientists found bacteria was NOT detected in meconium PRIOR to birth.

The scientists only included babies born by breech C-section in healthy pregnant women — in this way they avoided the transmission of bacteria from mother to baby that occurs during a vaginal birth.

It was a relatively small study including 20 infants, but this research helps inform the hot scientific debate over whether a baby’s gut is colonised by bacteria whilst developing in the womb.

To make it clear — the research by Kennedy K.M. et al., (2021) has just been published in Nature Microbiology. Previously it was available as a pre-print (and needed to be peer-reviewed).

About meconium:

This research is about meconium. If you’re a midwife, you’ll probably know all about meconium.

Meconium is a thick, green tar-like substance that lines the baby’s gut during pregnancy.

Meconium is usually released as the baby’s first stool after birth. But sometimes the baby will have a bowel movement before birth — which means meconium is found in the amniotic fluid.

Unlike actual faeces, meconium is composed of materials ingested whilst in the mother’s womb; including intestinal epithelial cells, mucus and amniotic fluid.

The study:

The research was led by scientists from McMaster University and Charité — Universitätsmedizin Berlin in Germany.

20 samples of fetal meconimum were collected from rectal swabs during elective breech C-section — before labour and before antibiotics were administered. The samples were then sequenced.

The scientists then discounted likely skin contaminants found in many of the samples (most frequently Staphylococcus epidermidis).

The results:

The conclusion: bacteria were not found in the meconium prior to birth.

That means, according to this study, the fetal gut microbiome is not colonised before birth.

The abstract concludes: “We conclude that fetal gut colonization does not occur before birth, and that microbial profiles of neonatal meconium reflect populations acquired during and after birth.”

The meaning:

Previous studies found bacterial DNA in the meconium of a newborn — but the samples were collected hours to days after birth.

This study suggests the bacteria found in the meconium in previous studies were acquired during and after birth.

According to an article in Science Daily: “The key takeaway from our study is we are not colonized before birth. Rather, our relationship with our gut bacteria emerges after birth and during infancy,” said Katherine Kennedy, first author of the study and a PhD student.

Why this really matters:

This information needs to be widely known by all health professionals and parents.

This research shows the first exposures during and after birth really matter to the colonisation of the infant gut microbiome.

This research lends further evidence to the hypothesis that the infant gut microbiome is colonised by beneficial gut microbes acquired from the mother during and after vaginal birth.

These beneficial microbes are then fed by the special sugars (HMOs) in breast milk.

This helps ensure beneficial microbes quickly colonise the infant gut.

This ensures the right microbes are present for the optimal training of the infant immune system.

This helps protect a baby for life.


Science ref:

Katherine M. Kennedy, Max J. Gerlach, Thomas Adam, Markus M. Heimesaat, Laura Rossi, Michael G. Surette, Deborah M. Sloboda, Thorsten Braun, Fetal meconium does not have a detectable microbiota before birth. Nat Microbiol (2021).

Article in Science Daily:


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