Understanding Low Bifidobacterium Levels in Breastfed, Vaginally Born Babies

We often hear from parents who have taken all the recommended steps to support their baby’s gut health—vaginal birth, exclusive breastfeeding, minimizing toxin exposure at home—yet are shocked to see 0% or very low levels of Bifidobacterium on their baby’s gut test.

We understand how disappointing and concerning this can feel, especially when you’ve worked hard to do all the “right” things. First, it’s important to acknowledge that testing early is already a great step toward supporting your baby’s health. Early intervention can make a big difference. A young baby’s gut is still simple—and much easier to course correct!

Here are a few reasons why Bifidobacterium levels may be low, even when conditions seem ideal:

1. Your own gut may lack Bifidobacterium.

Research shows that about 30% of vaginally born, exclusively breastfed babies have 0% to very low levels of bifido. When moms are tested too, it turns out that in many of those cases, the mom's gut also has 0% bifido.
If the mother doesn’t have these beneficial bacteria in her gut, she can’t pass them on during birth or breastfeeding — no matter how ideal the delivery or feeding method is.

2. Other family members may not carry enough of it to help colonize baby’s gut.

Even if you're doing everything right, your baby’s gut environment is influenced by the microbiomes of other household members. If dad, siblings, or other close contacts also have low levels of bifido, there’s less chance of environmental exposure and seeding.

3. Not all probiotics work the same.

If you were taking probiotics during pregnancy or postpartum, it's important to know that not all strains effectively colonize the baby’s gut. Some babies do get the benefit from mom's supplementation, but in other cases, the transfer doesn’t happen — every baby is different.

If you're open to sharing the specific probiotic brand and strains you used, our microbiome specialists can help determine if they are likely to colonize your baby’s gut.

4. The gut test helps identify what’s missing so you can take action.

The purpose of gut testing isn’t to discourage — it’s to empower. With this information, you can now take steps to help introduce the right probiotics and support your baby’s microbiome development. It's completely possible to turn things around with the right support!

The bottom line:

Even with the best birth and feeding choices, some babies still need extra help seeding Bifidobacterium. You didn’t do anything wrong. Your efforts absolutely made a difference in your baby’s health — this is just one piece of the puzzle, and now you have valuable insight to guide the next step in your baby’s immune and gut health journey.