When we think about inheritance, genes are often the first thing that come to mind. But there’s another powerful legacy passed from parent to child that’s gaining attention: the microbiome. This community of trillions of microbes—mostly bacteria—plays a vital role in immunity, digestion, and even mental health. While the mother’s role in shaping a baby’s microbiome is well recognised, emerging research shows that fathers also contribute meaningfully, both directly and indirectly.

I wanted to share some explorations on how both maternal and paternal influences shape a newborn’s microbiome, why this matters, and what expectant parents can do to support this critical part of their child’s development.

The Foundations of a Baby’s Microbiome

It was once believed that babies developed in a sterile environment, but recent evidence suggests otherwise. While there is still scientific debate, studies have detected microbial DNA in the placenta, amniotic fluid, and umbilical cord, hinting at possible prenatal microbial exposure (Collado et al., 2016; Perez-Muñoz et al., 2017).

However, the most substantial microbial colonisation begins at birth. During vaginal delivery, the baby is exposed to microbes from the mother’s vaginal and gut microbiomes—most notably Bifidobacterium and Bacteroides species, which help establish a resilient gut flora (Dominguez-Bello et al., 2010). In caesarean births, the microbial exposure skews toward skin- and hospital-associated species like Staphylococcus and Klebsiella (Azad et al., 2013), which may impact immune development in early life.

Breastfeeding: A Microbial Lifeline

Breastmilk is not just nutrition—it’s a living fluid packed with bacteria and prebiotics that feed beneficial gut microbes. Bifidobacterium longum subsp. infantis, for example, is specially adapted to digest human milk oligosaccharides (HMOs), key sugars that shape the infant gut ecosystem (Sela et al., 2008). The mother’s gut and skin microbiota influence what is transferred through breastfeeding (Pannaraj et al., 2017), reinforcing her critical role in microbiome development.

The Paternal Microbiome: More Influential Than Once Thought

Although the focus has historically been on the maternal microbiome, fathers are not passive bystanders. Paternal microbiota can shape a child’s microbial environment through shared living spaces, skin contact, and even seminal microbiota that may influence maternal microbial communities during conception and pregnancy (Weng et al., 2014; Donders et al., 2018).

Animal studies have demonstrated that paternal microbiome disruption (e.g. via antibiotics) can affect offspring development and immunity (Sarker et al., 2018), likely through epigenetic and germline signalling. While human evidence is still emerging, this suggests fathers' microbial health pre-conception may matter more than previously believed.

Shared Environment and Microbial Exchange

Beyond birth, a baby’s microbiome continues to evolve, shaped by contact with parents and the environment. Studies show that households share microbial communities, with family members developing similar microbial profiles over time (Song et al., 2013). Fathers who are highly involved in infant care—changing nappies, feeding, skin-to-skin contact—also play a direct role in microbial transfer.

The home setting also matters. Babies born in hospital environments are exposed to different microbial profiles than those born at home, with interventions like antibiotic use and early bathing influencing colonisation (Azad et al., 2013; Biasucci et al., 2008).

Why This Microbial Legacy Matters

The first 1,000 days of life, from conception to age two, are considered a “window of opportunity” for shaping long-term health. Microbial exposure during this period helps train the immune system and reduces the risk of allergies, asthma, autoimmune conditions, and metabolic diseases (Arrieta et al., 2015; Blaser, 2014).

Disruptions to this process—whether through antibiotics, stress, or poor diet—can have lasting consequences. That’s why it’s crucial for both parents to focus on gut health before and after birth.

Supporting a Healthy Microbiome as Parents

Here are evidence-based steps both parents can take:

• Prioritise Gut Health Pre-Conception: Include fermented foods, fibre-rich vegetables, and avoid unnecessary antibiotics (Koren et al., 2012).
• Consider Probiotic Supplementation: Certain strains such as Lactobacillus rhamnosus GG may reduce the risk of eczema and allergies (Kalliomäki et al., 2001).
• Vaginal Seeding? Proceed With Caution: Although popularised as a way to mimic vaginal birth for C-section babies, evidence is still inconclusive and should be discussed with a healthcare provider (Cunnington et al., 2016).
• Maximise Skin-to-Skin Contact: Especially for fathers, this can aid microbial transfer and bonding (Moore et al., 2016).
• Breastfeed If Possible: It provides unmatched microbial and immune support.

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The development of a baby’s microbiome is a collaborative legacy from both parents. While mothers play the more direct role through birth and breastfeeding, fathers also contribute significantly—through their own microbiome, shared environments, and active caregiving.

By understanding these influences, parents can take proactive steps to build a strong microbial foundation for their child, with benefits that last well beyond infancy.

References

1. Collado MC et al. (2016). "Microbial ecology and host-microbiota interactions during early life stages." Gut Microbes.
2. Perez-Muñoz ME et al. (2017). "A critical assessment of the sterile womb hypothesis." Nature Reviews Microbiology.
3. Dominguez-Bello MG et al. (2010). "Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns." PNAS.
4. Azad MB et al. (2013). "Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months." CMAJ.
5. Sela DA et al. (2008). "The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome." PNAS.
6. Pannaraj PS et al. (2017). "Shared and distinct features of human milk and infant stool microbiomes." Pediatrics.
7. Weng SL et al. (2014). "Bacterial communities in semen from healthy men differ from those in infertile men." Fertility and Sterility.
8. Donders GG et al. (2018). "Semen influences the vaginal microbiome and microenvironment." Clinical Infectious Diseases.
9. Sarker G et al. (2018). "Paternal programming of offspring behavior via sperm microbiota." Frontiers in Microbiology.
10. Song SJ et al. (2013). "Cohabiting family members share microbiota with one another and with their dogs." eLife.
11. Biasucci G et al. (2008). "Mode of delivery affects the bacterial community in the newborn gut." Early Human Development.
12. Arrieta MC et al. (2015). "The intestinal microbiome in early life: health and disease." Frontiers in Immunology.
13. Blaser MJ. (2014). Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt.
14. Cunnington AJ et al. (2016). "Vaginal seeding" of infants born by caesarean section. BMJ.
15. Moore ER et al. (2016). "Early skin-to-skin contact for mothers and their healthy newborn infants." Cochrane Database.

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Cute Clinic, founded by Simona Venckute, is a health and wellbeing practice focussed on naturopathic nutrition and functional medicine. Simona is BANT accredited and registered with the Complementary and Natural Healthcare Council, General Naturopathic Council, Association of Naturopathic Practitioners and is based in Chiswick, London with her family.