In the womb

Every one of us is a living, walking ecosystem of thousands of species; only one is mammal and the rest are microscopic single cell organisms (microbes for short).

But, when and how do we establish this partnership with our tiny life companions? At which point in our human life history do we come into contact with them? Is there a placental microbiome? Is the fetus sterile while developing in the womb?

Scientists have found that the fetus is exposed to microbes while developing in the womb, but the nature, degree and consequences of this exposure remains open and subject to future research.


The acquisition of our microbiota is called seeding. This is when we first meet, when our microbes introduce themselves (literally!) and we welcome them. It is known that seeding occurs at birth. However, contrary to what was believed until recently, the fetus developing in the womb does not live in a sterile environment. It is now clear from different studies that a baby is in contact with microbes well before birth, as they have found bacterial DNA in umbilical cord blood, placenta, amniotic fluid, meconium and fetal membranes. To clarify, we are talking about normal, healthy pregnancies and healthy babies, not to pathogenic infections that can lead to premature birth.

Whether we can call this antenatal encounter with microbes proper seeding is still unclear but it definitely seems to affect the microbial composition of the infant’s gut.

In fact, not much is known about this fetal microbiome yet. When does it happen? How? What is its function? Current research is limited but it gives us some clues worthy of further investigation.

Timing of fetal seeding

Results from one study suggest that it may happen in early pregnancy (first trimester) but for now it remains a big question mark.

Origin and routes for fetal seeding

Again, science has not got definitive answers but, unlike with the issue of timing, there are more studies on the matter and with good evidence for three probable origins of microbes seeding the fetus:

  • The maternal gut microbiota
  • The vaginal microbiota
  • The oral cavity microbiota

The evidence for exposure of the fetus to maternal gut microbes is strong. However, how these microbes travel from the mother’s gut to the fetus is unknown. One hypothesis is that they cross the gut lining, get into the blood and reach the placenta.

Microbes living in the vagina are close to the womb and, it is well known by science, that they can easily reach it and invade the amniotic fluid. The exact events in this process have not been described though. Either way, vaginal microbes in the amniotic fluid mean that they are going to be swallowed and breathed by the baby, and therefore they may be able to seed the fetus’ gut and respiratory tract.

Microbes coming from the mother’s mouth have also been proposed as potential colonizers of the fetus. Evidence for this is less clear than for the two previous sources of microbes, but one study showed that the placental microbiome was more similar to the oral microbiome than any other body site tested in healthy women.

Function of fetal exposure to microbes

One important and very likely hypothesis is that exposure of the fetus to the maternal microbes sets off the education of the immune system. In fact, there may be an active selection of protective bacteria to be transported to the fetus in order to begin this fetal immunological programming.