Microbiome Seeding At Birth


  • Seeding refers to the transfer of microbes from mother to baby. It starts at birth, when microbes colonize the baby’s entire body.
  • Which microbes seed a baby in the first days of life is influenced by many factors, including route of birth, medical interventions during birth, and antibiotic and other drugs use.
  • Babies born by C-section don't inherit the rich blend of beneficial microbes that may help protect against disorders such as asthma and allergies.
  • There’s a lot you can do! Breastfeeding, vaginal seeding, and probiotics can help to restore a baby’s microbiome after C-section birth or antibiotic use.

How many times have you heard that you inherited your mother's eyes or her smile?

But did you know that you also inherited hundreds of thousands of tiny microbes? Like genes, our microbes pass from parent to child.

This transfer of microbes from mother to baby, or “seeding,” starts at birth when microbes colonize the baby’s entire body, from their mouth and skin to their digestive tract [1], [2].

A mom and her baby share a microbial bond

Moms are the most important source of microbes to their babies [3]–[5]. But unlike genes that we inherit at conception, the sharing of microbes between mom and baby continues after birth.

During birth, a mother passes on her gut, vaginal, and skin microbiomes to her baby. This sharing of the mother’s microbiome with her baby is essential for the establishment of a healthy microbiome.

After birth, a mom continues to pass along friendly and beneficial microbes by breastfeeding and skin-to-skin contact. A baby’s dad and any siblings also contribute to the baby’s microbial supply with kissing and close interaction.

Many of these shared microbes are invaluable partners in keeping your baby protected and well. The sooner they establish, the sooner they start their critical and time-sensitive work: teaching the newborn’s immune system how to develop. A baby’s first microbes may be crucial to future health.

Which microbes seed a baby in the first days of life is influenced by many factors, including:

  • Route of birth
  • Medical interventions during birth
  • Antibiotic and other drugs use

Regardless of the factors that come into play, we want to think about how to optimally seed a baby’s gut during their first 1,000 days. This means welcoming beneficial bacteria while reducing the risk of seeding with unfriendly microbes.

Why a vaginal birth matters

Birth mode is the driving factor shaping the composition of the gut microbiome in the first month of life and up to 1 year of age. The associations between birth mode ‒ vaginal or C-section ‒ and the baby’s gut microbiome are dramatic [3], [6], [7]. And we’ll explore these below.

In a vaginal delivery, the baby passes through the birth canal and emerges from the vagina.

During this passage, the baby comes in contact with the mother’s vaginal and fecal microbes because the vagina and rectum are so close to each other.

Babies that are born vaginally have more beneficial species of Bifidobacterium, Bacteroides, and Parabacteroides, than babies born by C-section [7].

Bifidobacteria are friendly bacteria associated with good health. This is because they:

  • Produce lactate and anti-inflammatory short-chain fatty acids (SCFAs) when they digest breastmilk sugars called HMOs (human milk oligosaccharides), which makes it hard for unfriendly gut bacteria to survive [8].
  • Play an important role in educating your baby’s immune system [9]–[12].
  • Promote the presence of a healthy microbiome by supporting the growth of other bifidobacteria [9], [13].
  • Provide nutrition, by synthesizing essential micronutrients, such as vitamins B6, B12, folate, and vitamin K [14].

Like Bifidobacterium, Bacteroides and Parabacteroides also play a major role in the early gut microbiome. These bacteria help to train the baby’s immune system and digest the starches when solids are introduced in your baby’s diet.

Having these friendly bacteria in the gut means having the best opportunity for the optimal development of your baby's microbiome.

The benefits of a homebirth

Homebirths are becoming increasingly popular in the United States, with an increase of over 77% between 2004 and 2017 [15]. The reasons for choosing homebirth are various and different from family to family. You might want to give birth without medical intervention or prefer to give birth in a comfortable, more relaxed environment in familiar surroundings.

Research has shown that giving birth at home is as safe as a hospital for low risk women having their second or subsequent birth. There is also a lower chance of having an assisted delivery, like a C-section or instrumental delivery [16]. You can discuss with your provider whether homebirth is the right option for you.

And what about the impact of homebirth in baby gut seeding?

The truth is, we don’t have much information about it yet. There are only two small studies that tried to depict differences between the microbiome of babies born at home and those born in the hospital. This research suggests that babies born at home may have more beneficial microbes for at least a month after birth, compared with those born in a hospital [17], [18].

We can speculate what are the reasons for these differences. Common hospital interventions, like antibiotic eye prophylaxis and early infant bathing, may contribute to why babies born in the hospital have fewer beneficial microbes in their gut.

Also, babies born in the hospital are more likely to be colonized with unfriendly microbes associated with interventions like C-section, antibiotic treatment, and formula feeding.

Hop over to our Tiny Health Gut-Friendly Birth Plan for suggestions to include in your birthing plan.

How a C-section birth affects microbial seeding

Even though the World Health Organization suggests that C-section birth is medically necessary in only 10-15% of pregnancies, they’re on the rise globally. In the United States, 34% of babies are born by C-section.

This is worth noting because babies born by C-section don't inherit the rich blend of beneficial microbes that come from a vaginal birth. And as it turns out, these microbes may help protect against disorders such as asthma and allergies [3], [19]–[22].

Instead, they pick up the mom’s skin bacteria [6], and unfriendly bacteria usually found in the hospital environment, such as Enterococcus, Klebsiella, and Clostridium species [3], [7], [23]. Many of these species often carry genes related to antibiotic resistance that allow them to survive exposure to antibiotics designed to kill bacteria [24], [25]. They are particularly dangerous in premature babies [26].

This C-section microbiome signature can persist in children up to 4 years of age [3], [27].

For example, we know that babies born by C-section have an increased risk of health problems such as:

  • Asthma, allergic rhinitis, and eczema [20], [28], [29]
  • Type 1 diabetes [30]
  • Obesity [31], [32]
  • Gut-related conditions (e.g. celiac disease, food allergies) [33], [34]

While more research is needed, the best available scientific evidence suggests that C-sections affect the microbial seeding of the baby’s gut. This means that it’s a procedure that should be used prudently and followed by measures to restore the natural composition of the microbiome.

Don’t forget to check our tips on how to restore the baby microbiome after a C-section birth below.

Medical interventions & antibiotics may impact seeding

During labor and birth, your doctor or midwife might suggest you take painkillers to cope or ask your permission to use special instruments to help deliver your baby (e.g. forceps or vacuum). It may be helpful to know before the birth which pain relief options and medical interventions will be available to you. We have compiled a list of hospital interventions that may be offered to you and their possible impact on your baby’s microbiome here.

Let’s be clear. The impact of interventions during labor on the mom and baby’s microbiome is not well understood.

But we know that almost any medication given during birth, including painkillers like epidural, has the potential to cross the placenta and reach the baby.

Epidurals are a popular choice for pain relief during labor. But epidurals may interfere with the baby’s spontaneous breast seeking and breastfeeding behaviors in the first 24 hours [35], [36]. This seems to be proportional to the amount of epidural received [37], [38], although studies on this topic are controversial.

We also know that common procedures to induce labor (e.g. pitocin) may increase the risk of C-section births compared to those who wait for it to begin spontaneously [39].

Other common interventions during birth are vaginal examinations along with external or internal fetal heart rate monitoring. But when not medically necessary, these interventions may be associated with poorer outcomes for mothers and/ or babies [40].

Because of this, opt for fewer labor and delivery interventions if possible. This will help to decrease the risk that mom and baby are exposed to unfriendly microbes.

A quick word on antibiotics

You may know by now that the use of antibiotics by mom before and during labor impacts the transfer of the mother’s own microbiome to her baby [7], [41].

Antibiotics have been associated with lower levels of seeding of beneficial bacterial species in babies - such as Bifidobacterium and Bacteroides - as well as the appearance of antibiotic-resistant bacteria in both mothers and babies [41].

C-section births require the use of antibiotics at the onset of the surgery to prevent infection. This is because women undergoing C-section have a 5 to 20 times greater chance of getting an infection from birth compared with women who give birth vaginally [42].

Prophylactic antibiotics may also be prescribed to all women that tested positive for Group B Streptococcus, independent of the type of birth.

If you had - or know you will have - to take antibiotics before or during labor, be sure to check on our tips below on how to restore your baby’s microbiome.

TLDR: breastfeeding!

How to restore your baby’s microbiome after a C-section birth

Babies born by C-section delivery are not exposed to their mother’s vaginal and fecal microbes the way vaginally-delivered babies are. Rather, they are exposed to skin microbes and microbes from the hospital environment [4].

This means that they tend to have lower levels of certain beneficial bacteria, including bifidobacteria [43], [44].

But as it turns out, there’s one way to ensure your baby has a healthy mix of gut microbes after a C-section birth: Breastfeed, if it’s available.

Within a couple weeks of breastfeeding, a baby born by C-section can have comparable levels of bifidobacteria as a baby born vaginally [45].

Breastmilk bacteria are early colonizers that can influence and help select the beneficial bacteria that follow, leaving a footprint that can be detected even in adulthood [46]. This means that if you had - or plan to have - a C-section birth, breastfeeding is one of the best things that you can do for your baby’s gut microbiome development.

What is vaginal seeding after C-section?

Vaginal seeding involves swabbing a baby with the mom’s vaginal fluids after a C-section birth [47]. The reason for this practice is that babies born by C-section pick up microbes from their environment and their mother's skin, which can increase the risk of developing health problems later in life [48].

During vaginal seeding, the mom’s vaginal fluids are collected before giving birth and then swabbed over her baby [47].

  • A sterile cotton gauze is folded and inserted into the vagina and left to soak up protective vaginal microbes.
  • At birth, the newborn baby is swabbed with the gauze, starting on the mouth, nose, and face, and moving to the rest of the body for about 15 minutes, before proceeding to standard newborn examination.

This early exposure is thought to give your baby a dose of healthy microbes that they would otherwise have gotten naturally during vaginal birth.

While research into the practice of vaginal seeding is new and in the early stages, it does hold great promise for the future health of our children.

In a landmark but very small pilot study, Maria Dominguez-Bello and her colleagues looked at the impact of vaginal seeding after C-section. They found that the skin and gut microbiome of babies in whom vaginal seeding was done resembled that of vaginally delivered babies [47]. A larger follow-up study with 177 babies, of which 30 were swabbed with a maternal vaginal gauze right after birth, confirmed these results. And it also showed that swabbed babies had more friendly Bacteroides [6], [49].

Importantly, no medical complications were detected in seeded infants during the follow-up period of both studies.

But because we don’t yet have solid data on possible risks associated with vaginal seeding, some caution is necessary. For example, it is not advisable for you to attempt a vaginal swab if you have:

  • Tested positive for Group B Streptococcus (GBS), HIV, Hepatitis B and C, or syphilis
  • Test positive for genital herpes (HSV)
  • Signs of bacterial vaginosis
  • A vaginal pH of more than 4.5

The main concern with vaginal seeding is the spread of undiagnosed infections, which could result in neonatal infection.

Please remember that vaginal seeding is not recommended as a DIY “self-help” practice. The American College of Obstetricians and Gynecologists (AGOG) does not currently recommend vaginal seeding outside the context of an institutional review board-approved research protocol. More research is necessary before accepting vaginal seeding as routine.

However, some moms who choose to do vaginal seeding may get the help of their midwife.

When considering vaginal seeding as a way to help restore your baby’s microbiome after a C-section birth, it’s a good idea to test your vaginal microbiome.

A vaginal microbiome test can help you make an informed decision and show what (good or bad) microbes may be passed along to your baby.

A tiny bit of mom’s poop can boost your baby’s immunity

Several lines of evidence show that the mother’s poop microbes transfer to, and persist in, the baby’s gut.

The first line of evidence is based on bacterial strains. A strain is a classification that pinpoints very closely related bacteria.

A significant number of bacterial strains from the mother’s gut can be found in the baby’s gut too. The proportions of bacterial strains are different. But the identity of many strains, including strains of Bifidobacterium and Bacteroides, match between mother and baby [2], [4], [50].

The second line of evidence comes from looking at babies who are born by attempted vaginal delivery that ends in C-section birth [51]. These babies are exposed to microbes in the birth canal, but because they don’t exit the mother’s vagina, they are not exposed to the mother’s rectum or feces.

Researchers found that they couldn’t tell the difference between the microbiome of C-section born babies, regardless of contact with the birth canal [51].

The third line of evidence comes from a small study of mother-baby fecal transplants [52]. This study looked at C-section babies who were fed a small amount of the mother’s feces with their first milk. Babies that received mom’s fecal transplant evolved to look like the gut microbes of vaginally born babies.

The microbiome of these babies was different from C-section born babies that did not receive the transplant [52].

But both beneficial Bifidobacterium and Bacteroides were found in the gut of C-section born babies that received the fecal transplant and vaginally delivered babies [52].

If you decide to try either a vaginal swab or fecal transplant after C-section, be sure to screen your fecal and vaginal microbiomes ahead of time for unfriendly bacteria. Doing so may help convince your provider to participate in your decision.

5 Tiny Health tips on how to restore your baby’s microbiome

  • Hold your baby closely. Placing your baby naked in your bare chest immediately after birth (if possible) has numerous benefits. Babies that get skin-to-skin contact interact more with their moms, stay warmer, cry less, and are more likely to be breastfed (and breastfeed longer). If you're not in a position to have your baby placed on your chest, your partner can hold your baby instead for immediate skin-to-skin contact.
  • Breastfeed as soon as possible. Breastfeed immediately after birth, even if you just had a C-section. Breastmilk nourishes the beneficial gut bacteria that help your baby thrive and have an endless of other benefits too.
  • Consider vaginal seeding. If appropriate, safe, and accessible.
  • Use a probiotic. If breastfeeding isn’t an option, you can consider supplementing with the right kind of probiotics for your baby and using a formula with HMO prebiotics.
  • Get dirty. Seeding doesn’t stop at birth. It continues throughout life, most intensely in the first 2 years of your baby’s life. Playing outdoors, having pets, and being exposed to natural environments have all been associated with reduced rates of allergies, asthma, and eczema in kids [53]–[55].

For more tips on how to give your baby the best microbiome start possible check our Tiny Health Gut-Friendly Birth Plan.


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