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Engineering the Newborn Microbiome

Written by Clare Carrick ANutr BHSc (Nutrition and Health Promotion)

Scientifically reviewed by Dr Fathalla Ali, PHD Paediatrics


Your newborn’s gut microbiome helps shape their immune system, determining their overall health through toddler-dom, the teen years, and into adulthood (1). C-section deliveries, antibiotics during pregnancy and birth, formula feeding, and selective diets have all been shown to impact the development of baby’s gut microbiome, sometimes causing an imbalanced gut, which has been associated with a range of disease, from asthma to obesity (1, 2, 3, 4).


This information can feel like a heavy burden of responsibility. What happens if the birth doesn’t go to plan? What happens if antibiotics are necessary? What if breastfeeding doesn’t work?


The thing is, even with the best of intentions to do everything in your power to support your baby’s gut microbiome, only one thing is truly certain…parenthood shakes even the most carefully laid plans to the core.


You can have your ‘perfect’ birth plan laminated on the wall… a carefully curated, calming playlist, a home birth in water, no drugs or medical interventions…and you may still end up numb from the waist down, on a hospital bed, delivering your baby via c-section….

Perhaps you can’t breastfeed because of the medication you are on…or your doctor recommended antibiotics during the birth…


Whilst often these interventions are crucial and life-saving, and we are so lucky they exist, the unfortunate downside of gut imbalance and increased risk of later-life disease is, understandably, the subject of interest for many parents-to-be (1). Luckily, this topic has also piqued the interest of many scientists, who have been busy investigating new methods of ‘manipulating’ the newborn microbiome to help minimise these detrimental effects (1).


Microbiome Manipulation Methods

Microbiome manipulation is a lot like it sounds. Basically, it involves techniques to help guide and assist the development of the gut microbiome, and the idea is that, if used properly, it may be able to compensate for any detrimental impacts of events surrounding the birth (e.g. c-section or antibiotic use) on the gut microbiome (1). Four methods that have gained some traction recently are probiotic supplementation, vaginal seeding, faecal microbiota transplantation, and phage therapy (1). Some of these techniques are more accepted than others, and none of them should ever be attempted without a trained medical professional, but it is exciting to know that these developments are happening! Let’s take a brief look at each microbiome manipulation method and where it’s currently at…


Probiotic Supplementation

Probiotics can help populate the gut with specific bacterial species (1). Giving probiotics to preterm or low birthweight babies has been shown to help reduce infection, and the risk of necrotising enterocolitis (1). Bifidobacterium and Lactobacillus has even been shown to reduce the chance of death from necrotising enterocolitis in very low birthweight infants (1). Using probiotics at the same time as any prescribed antibiotics may also help to reduce the negative affect of the antibiotics on the gut (1). Best of all, the use of probiotics in preterm babies has been found to be safe and effective (1).


Vaginal Seeding

Vaginal seeding, where a baby born via c-section is exposed to a swab of the mum’s vaginal fluid (and therefore her vaginal microbes) has become a hot topic in recent years. Although it may seem like an easy way to help boost your baby’s gut microbiome development it can actually be incredibly dangerous, especially if it’s not performed by a trained professional (1). Whilst some small studies have shown that vaginal seeding alters a c-section baby’s microbiome to more closely resemble a vaginally-born baby’s gut microbiome, there is, as of yet, very limited evidence that this actually transfers to improved health outcomes (1)! At this point in time, vaginal seeding is still not widely used or encouraged (1).


Faecal Microbiota Transplantation

This involves some of the microbes from the mum’s poo being transferred to a C-section baby, to help introduce some of the bacteria they’d be exposed to if born vaginally (1). The idea behind this is that it would help restore the baby’s gut flora that may otherwise be lacking after a c-section delivery (1). Again, this idea needs more testing before widespread recommendations (1).


Phage Therapy

Phage therapy is still in the exploratory stage (1). This method uses bacteria-infecting viruses called bacteriophages, and, without getting too deep into the nitty-gritty, these bacteriophages are used to introduce genes into the microbiome and could potentially be used as alternatives to pre- and probiotics (1). A method to keep an eye out for in the future!


The Way of the Future

Pregnancy and child birth can throw a few curve balls that may impact the development of your baby’s gut microbiome. Although many aspects of this are out of our control, these four microbiome manipulation methods offer hope for the future, and give us some potential options to help compensate for any events that might negatively impact bub’s gut microbiome development.



  1. Wong E, Lui K, Day AS, Leach ST. Manipulating the neonatal gut microbiome: current understanding and future perspectives. Archives of Disease in Childhood-Fetal and Neonatal Edition. 2021 Aug 25.   
  2. Hesla HM, Stenius F, Jäderlund L, Nelson R, Engstrand L, Alm J, Dicksved J. Impact of lifestyle on the gut microbiota of healthy infants and their mothers–the ALADDIN birth cohort. FEMS microbiology ecology. 2014 Dec 1;90(3):791-801. 
  3. Keag OE, Norman JE, Stock SJ. Long-term risks and benefits associated with cesarean delivery for mother, baby, and subsequent pregnancies: Systematic review and meta-analysis. PLoS medicine. 2018 Jan 23;15(1):e1002494. 
  4. Horta BL, Loret de Mola C, Victora CG. Long‐term consequences of breastfeeding on cholesterol, obesity, systolic blood pressure and type 2 diabetes: a systematic review and meta‐analysis. Acta paediatrica. 2015 Dec;104:30-7.

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