Like every human, you have trillions of microorganisms teeming on and in your body. This complex ecosystem of bacteria, fungi, viruses, and other bugs, along with their genetic material, is called the microbiome. And, like other parts of your body, your microbiome can be robustly healthy or decidedly unwell.

The microbiome is the sum of its parts: localized communities of microbes (microbiota) that live in the gut, on the skin, and in the mouth.

Together, these communities support your body's immune function and help regulate mood, cognitive function, and digestion. When you’re pregnant, your microbiome forms the basis for the microbiome your baby will develop.

The decisions you make during your pregnancy – about what you eat, which medications you take, how you give birth – will influence the development of your baby's microbiome. So it's important to know how to keep your microbiome healthy to ensure your baby's microbiome will have the best possible start.

How much does diet affect my microbiome?

The adage, “You are what you eat” applies to your microbiome. Truly, the healthier your diet, the healthier your gut.1 During pregnancy, a microbiome-healthy diet should include:1,2

  • Skinless chicken
  • Lean meats
  • Beans
  • Organic fruits and vegetables
  • Whole grains
  • Olive oil
  • 2-3 servings weekly of wild-caught salmon or other low-mercury fish (see lists online)2
  • Fermented foods with natural probiotics – like yogurt, kefir, sauerkraut, and miso

The typical Western diet – high in fat, sugar, and processed foods – can have a negative impact on the microbiome and lead to health problems for both mother and child.1

Conversely, the high-fiber and plant-based foods in a microbiome-healthy diet will increase the levels of beneficial microorganisms in the gut microbiota that promote anti-inflammatory, anti-carcinogenic, and immune-regulatory functions.3

Will being overweight affect my microbiome?

If you are significantly overweight prior to pregnancy or you gain too much weight during pregnancy, then your risk of having a large baby increases – which increases your risk of a C-section.4

Being overweight before pregnancy results in a gut microbiota with less diversity in the third trimester.5 Passing along a less than optimal gut microbiota to the baby might result in the baby having a higher risk of diseases like diabetes and obesity later in life.5 

Will delivery affect my baby's microbiome?

When you give birth, you help establish your baby's microbiome by transferring some of your microbes to your baby. These microbes begin colonizing their tiny new host, quickly multiplying and developing into microbiotas entirely unique to your baby.6 But how the baby is delivered makes a difference.

In general, babies born by cesarean delivery have a less diverse gut microbiota – the largest microbial community in the body – than babies delivered vaginally.6 

That’s not ideal, because lower microbial diversity at birth can lead to problems later in life, including allergies, asthma, celiac disease, and obesity.6 Despite this, microbiome diversity is not a reason to avoid a necessary cesarean delivery for a baby who is not doing well in labor or can’t be safely delivered vaginally.

Why do babies born via C-section have less diverse gut microbiotas? Because these babies don’t come into contact with the rich diversity of microbial life in the vaginal canal during delivery.6 Instead, they acquire microbes found through skin-to-skin contact and from the delivery room environment.4,7 

Researchers are exploring something called “vaginal seeding” as a possible intervention to pass along more of the mother’s microbes to babies born via cesarean delivery.8 They swab the vaginal fluids from the mom, then wipe the swab on the baby's mouth, nose, and skin soon after birth.8

In one very limited study, vaginal seeding did help C-section babies develop a more diverse gut microbiota – similar to the microbes of babies born vaginally.8 But doctors caution that much more study is needed to determine the benefits and risks of vaginal seeding, and it is not recommended at this time unless it’s part of a research study.8

What happens to my baby's microbiome when my baby arrives early?

Your microbiome health will have an impact on whether or not your baby is born prematurely. For example, a healthy vaginal microbiota can protect against sexually transmitted infections, which are a risk factor in premature births.4 Likewise, a robust mouth microbiota helps protect against periodontal disease, another risk factor in pre-term deliveries.9 

Babies born before 37 weeks miss two types of protective gut bacteria typically found in healthy, full-term infants: Bifidobacterium and Lactobacillus.4 

Remember: in a healthy microbiome, diversity is key.

Pre-term infants also have marked differences in their fecal, skin, and mouth microbiotas compared to healthy full-term babies.9

With less diverse microbial communities and fewer common microbes – which are necessary for developing a healthy immune system – premature infants can be susceptible to serious conditions such as chronic lung disease, sepsis, and necrotizing enterocolitis. Lower diversity might also affect the baby’s growth and development.9

What if I or my baby need an antibiotic before or right after birth?

While antibiotics given at this time can disrupt the microbiome, doctors emphasize it is not a reason to decline an antibiotic.7

When a woman takes an antibiotic just before or after birth, she passes along her altered microbiome to her baby, which affects the baby's microbiome too. Some infants exposed to antibiotics at or near delivery have been found to have fewer protective microbes in their gut microbiotas.7

As antibiotic use during pregnancy and delivery has increased, there has also been an increase in drug-resistant infections, such as MRSA, in mothers and babies.7

Babies exposed to antibiotics immediately after birth also have higher risks of health problems later in life, including asthma, allergies, obesity, and inflammatory bowel disease.8

Although antibiotics can change the maternal and neonatal microbiome, breast feeding and normal life exposure help restore a healthy balance of microbial life. Supplements also may be helpful during nursing.

Is breast-feeding better for my baby's microbiome?

Both breast milk and formula help seed a baby's budding gut microbiota, and scientists have detected differences in the gut microbiotas of breast-fed and formula-fed infants.10 

When you breast-feed, you directly pass along your microbiome to your baby.10 And there does seem to be an advantage to breast milk. By studying infant stool samples, scientists have determined that breast milk helps babies develop protection against respiratory and gastrointestinal infections and reduces the risk of later developing diabetes, allergies, obesity, and inflammatory bowel disease.11

Because of the many protections breast milk offers the baby, the American Academy of Pediatrics recommends that infants be fed breast milk exclusively for six months and continue with breast milk until age one.11

What if you can’t breast-feed? Some evidence suggests that giving your baby an infant formula supplemented with probiotics and prebiotics promotes development of a gut microbiota similar to breast-fed babies.12 Probiotics are live microorganisms, like bacteria and yeast, and prebiotics are compounds, like fiber, that feed those microorganisms.

Can I prevent or treat microbiome problems?

Before and during pregnancy, an excellent way to ensure your gut microbiota is as healthy as possible before giving birth is to eat a low-fat, low-processed-sugar diet, rich in fiber and omega-3 fatty acids.1

But even when something happens that interferes with ideal development of your baby’s microbiome, there are things you can do. Research has shown, for instance, that giving premature infants probiotic supplements to support their microbiome will reduce serious infections and even death.13

In fact, a growing body of evidence, including more than 30 randomized trials involving more than 8,000 premature infants, shows that giving preterm infants probiotic supplements is both safe and feasible.13

Taking a probiotic supplement during pregnancy can also improve many other conditions you might have. For instance, taking a daily probiotic supplement that includes Lactobacillus rhamnosus GG and Lactobacillus acidophilus helps improve glucose metabolism during pregnancy and while you’re breast-feeding.1 

Eating yogurt every day that contains L. rhamnosus GG can protect pregnant women from mercury and arsenic toxicity.1 And daily consumption of milk-based probiotics helps lower blood pressure and the risk of preeclampsia during pregnancy.1

Although no research currently shows that taking a probiotic changes your baby’s microbiome, scientists have found that giving probiotics to pregnant and breast-feeding women can help their babies in other ways.

In one study, a probiotic supplement containing L. rhamnosus given to nursing mothers significantly reduced the baby's risk of developing eczema.14 Additional studies found similar positive results when they gave breast-feeding moms probiotic supplements that included combinations of either L. rhamnosus LPR and Bifidobacterium longum BL999, or L. paracasei ST11 and B. longum BL999.14


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