Keeping Mama and Baba Healthy - Building a Healthy Microbiome When Having Having A Caesarian Birth


by Lucinda Miller

Microbiome Caesarean Birth Gutsy Advice

A healthy gut microbiome during pregnancy and breastfeeding is even more critical when you have a caesarian section birth. Learn some easy tips to help build healthy digestion and immunity for you and your baby during pregnancy.

There are many reasons why a mother chooses to, or is advised to have, a caesarian-section birth – sometimes this is a planned decision, and very often it is a very unexpected last-minute intervention put in place for the safety of baby and mum.

One of the reasons why mamas-to-be are increasingly keen to have a natural birth is because it is now known that a mum passes on very special microflora from the vaginal birthing canal to their baby in a natural birth. These magical microbes help to populate the little one’s gut flora, which is critical for building their immune system, neurotransmitters (brain happy hormones) as well as a healthy digestion. Unfortunately, this unique microflora is not passed on nearly as easily to a baby when that is born via c-section, and so it takes a bit more work to help your baby acquire these important microbes.

There are very important links between a healthy gut microbiome and preventing all sorts of things from allergies, asthma, eczema to childhood cancers, and supporting child development, learning, motor skills as well as mood and temperament. Use of antibiotics in early childhood may also pose a greater risk for child obesity, especially if the child has also been on reflux medications because they are both very disruptive to the baby’s gut microbiome.

Probiotic strains may also be important in preventing premature or stillborn births, and new research has found that lots of lovely lactobacillus strains in the gut may help mums-to-be reach a full-term pregnancy.  

Often antibiotics are prescribed for maternal infections in pregnancy and during the birth. Antibiotics are also routinely given to new mother’s who have a post-birth infection including breastfeeding complications like mastitis. They are one of the main interventions a doctor will prescribe if a baby or toddler becomes unwell in the early years such as an ear infection or tonsillitis. Even though these medicines can be life savers, then can also disturb a healthy microbiome quite dramatically. This is where gut microbiome boosting is even more critical, and should be a high priority for at least 6 weeks (and ideally for 3 months) after a course of antibiotics. 


It is thought that close to the time of the birth, special “dendritic cells” which are rich in the mother’s microbiome, travel from the mother’s gut to form the lymph nodes in the breast tissue.


So, as you can imagine optimising mother and baby’s microbiome is something that new mums are usually keen to get right! So, if you are likely to need a caesarian section, or you or your baby have taken a course of antibiotics then here are some things you can do to help you and your baby thrive: 

Probiotic-rich foods:

During pregnancy and breastfeeding, it is a good idea to bolster your diet with probiotic-rich foods. These can be simple things like including live yoghurt, or more exotic (but now very easy to buy in supermarkets) are probiotic foods like kefir, miso, sauerkraut, kimchi and kombucha.

Plants breed a healthy microbiome:

A wide variety or fresh fruit, veggies, salad, nuts, seeds, cacao, olive oil and pulses all contain clever plant pigments and antioxidants called polyphenols that build a healthy microbiome. The greater the variety of plants you eat, the greater the diversity and the healthier the microbiome. Aim to eat 7-10 different plant-based foods per day (think big mixed salads or assorted veggie soups) to help bolster you and your baby’s gut flora. 

Probiotics to the rescue:

Even with great intentions, a healthy diet when pregnant or breastfeeding may not be achievable due to sickness, fatigue or simply being too busy looking after other children or working prior to maternity leave. This is where probiotic food supplements can be an easy solution to help build the key strains of beneficial bacteria needed to keep mum and baby healthy. We stock a hand-picked collection of probiotics suitable during pregnancy and breastfeeding for mum and baby at our online shop

Breast is best when possible:

When it comes to populating your baby’s microbiome, breast is best, as breast milk passes beneficial bacteria from mum to baby. It is thought that close to the time of the birth, special “dendritic cells” which are rich in the mother’s microbiome, travel from the mother’s gut to form the lymph nodes in the breast tissue. These dendritic cells are clever as they signal the mum’s gut microbiome directly to the breast milk. This means a mum-to-be needs to nurture her own gut microbiome during pregnancy and whilst breastfeeding to ensure there is a healthy balance of microbes passed onto her baby.

If you have any concerns, please do make contact with the practitioners at Nature Doc for further Nutritional Advice - Nature Doc Practitioners.

Nature Doc practitioners work closely with two specialist Doctors : Dr Richard Fry - Consultant Child, Family and Adult Psychiatrist & Dr Tim Ubhi - CEO and Clinical Director at the Children's e-Hospital.


Pregnancy & Childhood : Gutsy Science Pages

Vaginal Seeding After Caesarean Section by Gynae Geek
This topic has not been mentioned in this blog, but I will be sharing my own blog on the topic of pregnancy and vaginal seeding too.

Nature Doc : “The Good Stuff” Book

Nature Doc Website



 1 - The Maternal Infant Microbiome: Considerations for Labor and Birth. Alexis B. Dunn et al.

2 - Intervention strategies for cesarean section–induced alterations in the microbiota-gut-brain axis. Angela Moya-Pérez et al.

3 - Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention? Lieke W. J. van den Elsen et al.

 4 - Microbiome in the Gut-Skin Axis in Atopic Dermatitis. So-Yeon Lee et al.

5 - Cesarean Section and Risk of Childhood Acute Lymphoblastic Leukemia in a Population-Based, Record-Linkage Study in California. Rong Wang et al.

 6 - Association of the Infant Gut Microbiome With Early Childhood Neurodevelopmental Outcomes. Joanne E. Sordillo et al.

 7 - Gut microbiome composition is associated with temperament during early childhood. Lisa M.Christian et al.

 8 - Antibiotic and acid-suppression medications during early childhood are associated with obesity. Christopher M Stark et al.

9  - The vaginal microbiome and preterm birth. Jennifer M. Fettweis et al.

 10 - Influence of own mother's milk and different proportions of formula on intestinal microbiota of very preterm newborns. Zanella A

 11 - Role of the Human Breast Milk-Associated Microbiota on the Newborns’ Immune System: A Mini Review. Marco Toscano et al.   

 12 - Mother’s Milk: A Purposeful Contribution to the Development of the Infant Microbiota and Immunity. Kirsty Le Doare et al.


© Millie Pilkington

© Millie Pilkington

 Lucinda Miller MH MRNI MGNI

Lucinda Miller is The NatureDoc. She runs a team of UK-wide Nutritional Therapists specialising in fertility, pregnancy and child health. She runs www.NatureDoc.Shop online which stocks pregnancy and breastfeeding friendly supplements, as well as a hand-picked selection of natural pregnancy and newborn essentials. She is also author of bestselling family cookbook ‘The Good Stuff’.

Written by © Lucinda Miller. All rights reserved.

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