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Busting myths about your and your baby's various microbiomes

Dr Pamela Douglas18th of Aug 202311th of Oct 2025

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There's lots of misinformation out there about your and your baby's microbiomes

Because our microbiomes are astonishing complex ecosystems-within-ecosystems, vast microbial frontiers which are still in large part unexplored, some providers - who just want to help people - might accidentally interpret the emerging microbiome science in simplistic ways.

Here are examples of inaccurate beliefs about microbiomes which you might hear once you have a baby.

  1. A disrupted gut microbiome causes pain and unsettled infant behaviour.

  2. Taking antibiotics or having a caesarean section may cause baby gut discomfort or pain, unsettled behaviour, and an increased risk of health problems later in your baby’s life, due to disruption to your baby’s gut microbiome.

  3. Disruption to your baby’s gut microbiome results in green mucousy stools and unsettled behaviour.

  4. Biofilms in your milk cause painful white spots on your nipples.

  5. Bacteria from your nipples and areolas, especially when they are damaged, wash back into your milk when your baby feeds to cause breast inflammations like blocked ducts or mastitis.

  6. A thin biofilm lines all your milk ducts. When this thickens up, it causes breast inflammation like blocked ducts and mastitis.

Breast milk has by far the most powerful effect on your baby's gut microbiome

If you are breastfeeding your baby frequently and flexibly, your baby's gut is constantly washed through with immune superpower and potent microbiome enhancers. The impact of other environmental factors (like an initial caesarian section or a course of antibiotics or antifungals) fades into insignificance, is trivial, compared to the powerful waves of bioactive tissue flowing from your breast directly into your baby's gut and microbiome, hour after hour, day after night after day!

It's not true that you should stop breastfeeding your baby when you're taking antibiotics

In the clinic, I've seen women who've been led to believe, reading information on the internet, that they needed to stop breastfeeding and use formula while they were taking an antibiotic, because of the dysbiosis the antibiotics would cause in their own milk and their baby's gut. These hardworking women were devoted to their baby's needs, so they continued pumping and discarding their milk throughout the antibiotic treatment, to maintain milk production. It's painful, no matter how gently I communicate this information, for these women to hear that what they'd heard wasn't true, that it's much better for baby to continue with the breastfeeding despite the antibiotics and despite some transient disruptions to microbiomes. You can imagine how upset those women were when I told them this.

It's an example of how a simplistic lens, when applied to a complex situation, can result in unnecessary interventions and unnecessary stress and distress.

Recommended resources

What's in your milk's microbiome?

Misinformation about your and baby's microbiomes results in unnecessary treatments

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