Infant microbiome testing is becoming increasingly available — but is it always appropriate, and are we equipped to interpret the results? In this episode, I sit down with naturopath, herbalist, lactation consultant, and infant microbiome expert Dawn Whitten to take a close, balanced look at the new wave of paediatric microbiome tests. Dawn brings over 20 years of clinical experience in perinatal and early life health. In this conversation, she shares what these tests get right, where they fall short, and the very real risk of over-interpreting a rapidly changing ecosystem.
GUEST BIO
Dawn Whitten is a naturopath, herbalist, and lactation consultant with over 20 years of clinical experience in perinatal and early life health. She holds First Class Honours for her clinical research in herb-drug interactions, and was awarded a prestigious Fellowship by the National Herbalist Association of Australia for her contribution to herbal medicine in Australia. Dawn co-created the Postgraduate Evidence-Based Natural Medicine Program at the University of Tasmania and has been based at Goulds Natural Medicine in Hobart since 2006. She has worked closely alongside Dr Jason Hawrelak for over two decades, bringing his paradigm of restorative microbiome care into the perinatal and early life space.
🌐 Dawn’s website
EPISODE OVERVIEW
The infant microbiome is one of the most dynamic and rapidly changing ecosystems in the human body — and infant microbiome testing needs to be understood in that context. Since a landmark 2014 paper, our understanding of the gut-brain and gut-immune axis in early life has grown enormously. But commercial testing has moved fast, and not all practitioners or parents are equipped to interpret what these reports actually mean.
Dawn Whitten has been working in this space for over two decades. In this conversation, she draws on clinical experience, current research, and a deep respect for the biology of early life to explain when infant microbiome testing is useful, when it isn’t, and what clinicians need to know before ordering or acting on these tests.
WHAT YOU’LL LEARN ABOUT INFANT MICROBIOME TESTING
- What “normal” actually looks like in the infant microbiome across the first two to three years of life
- Why the infant microbiome can shift dramatically in just weeks — without any intervention
- The clinical risks of testing too early and acting too fast
- Why Bifidobacterium is the keystone genus of the infant gut and which species matter most
- The age grouping problem with current paediatric microbiome tests
- Why organisms like Blastocystis and Dientamoeba in a baby’s report may not be cause for alarm
- The problem with functional markers like faecal calprotectin and zonulin in infants
- What responsible infant microbiome test interpretation looks like in clinical practice
- What Dawn wishes these tests would do differently and what she’d love to see included
- Dawn’s Natural Early Life Health course for practitioners
IN THIS EPISODE, YOU’LL DISCOVER:
✅ Why the infant microbiome is a rapidly assembling ecosystem — not a miniature adult microbiome
✅ The story of a baby whose Klebsiella levels normalised spontaneously within weeks — without any treatment
✅ Why the BABY-Biome (0–3 years) and PAEDIATRIC-Biome (3–17 years) age groupings present clinical interpretation challenges
✅ Why faecal calprotectin reference ranges in infant reports are often based on adult cut-offs — and why that matters
✅ How Bifidobacterium breve, bifidum and longum subsp. infantis work collaboratively in the breastfed infant gut
✅ Why Blastocystis and Dientamoeba fragilis are increasingly recognised as commensal members of the paediatric gut
✅ The parental anxiety risk of reports that flag “imbalances” and “pathogens” in a developing ecosystem
✅ What Dawn would change about how these reports are designed and communicated
✅ How to think about infant microbiome testing using a first-do-no-harm framework
THE IMPORTANCE OF A MICROBIOME-FIRST APPROACH IN EARLY LIFE
When infant microbiome testing flags imbalances, pathogens or overgrowth, the instinct for both parents and clinicians is to intervene. But Dawn’s approach is guided by a principle that runs throughout her clinical work: first, do no harm.
The microbiome doesn’t always need to be corrected. Often, it needs to be supported while it grows. That means protecting breastfeeding where possible, nourishing the microbiome through diet, protecting beneficial microbes like Bifidobacterium, avoiding unnecessary antimicrobial disruption, and allowing time for the ecosystem to mature naturally.
Infant microbiome testing can be a valuable clinical tool in the right hands, at the right time, and for the right reasons. But it requires clinical education, interpretive skill, and a genuine understanding of early life microbiome ecology to use responsibly.
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SHOW NOTES
🎓 Love & Guts listeners receive 25% off Dawn’s Natural Early Life Health course — links below. Note: Jason Hawrelak’s Healthy Gut course is a prerequisite. Bundle options available. Offer available until 15 April 2026.
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This content is for educational purposes only and is not intended as medical advice. Please consult with your healthcare provider before making any changes to your health routine.