New research: Bacteria do not colonise the infant gut microbiome before birth — it happens during and after birth

Toni Harman
4 min readMay 13, 2021

Big news in the world of the infant microbiome….

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

In the study Kennedy K.M. et al., (10th May, 2021) published in Nature Microbiology, scientists found bacteria was NOT detected in meconium PRIOR to birth.

The scientists included 20 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, but this research helps inform the hot scientific debate over whether a baby’s gut is colonised by bacteria whilst developing in the womb.

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.



Toni Harman

I help parents and health professionals better understand the science of pregnancy, birth, breastfeeding and the microbiome.