The Human Microbiome: considerations for pregnancy, birth and early mothering

This post was co-authored by Jessie Johnson-Cash and based on her presentation at the USC Midwifery Education Day.

The human microbiome is rather fashionable in the world of science at the moment. The NIH Human Microbiome Project has been set up to explore correlations between the microbiome and human health and disease. To date the human microbiome as been associated with, amongst other things obesity, cancer, mental health disorders, asthma, and autism. In this post I am not going to provide a comprehensive literature review – this has already been done, and the key reviews underpinning this discussion are: Matamoros et al. (2012) ‘development of intestinal microbiota in infants and its impact on health’and Collado et al. (2012) ‘microbial ecology and host-microbiota interactions during early life stages’. Instead I am going to focus on what this means for pregnancy, birth, mothering and midwifery.

What is the human microbiome?

Based on a chart by Matamoro et al. 2013. Adapted and extended by Jessie Johnson-Cash.

Based on a chart by Matamoro et al. 2013. Adapted and extended by Jessie Johnson-Cash.

Considerations for mothers and midwives

The following are not research based recommendations – the research is yet to be done. They are more considerations/questions arising from the developing knowledge around the human microbiome. There are quite a few health practitioners writing about gut health currently – one of my favourites is Chris Kresser because he includes references if you want to read the source of his information.

Pre-conception and Pregnancy

The commonly accepted belief that the the baby inside the uterus is sterile (whilst membranes are intact) is now being challenged. It seems that maternal gut microbiota may be able to translocate to the baby/placenta via the blood stream (Jiménez et al. 2008; Metamoros et al. 2013; Prince et al. 2014; Rautava et al. 2013Zimmer 2013). Women’s gut microbiota change during pregnancy and this impacts on metabolism (Koren et al. 2012Prince et al. 2014). So ideally women need to head into pregnancy with a healthy microbiome and then maintain it. Unfortunately our modern lifestyle is not very microbiome friendly, and many of us have dysbiosis (an imbalance in gut bacteria). Dysbiosis and too much of the ‘wrong’ bacteria has been linked to premature rupture of membranes and premature birth (Fortner et al. 2014; Mysorekar & Cao 2014; Prince et al. 2014).



There is a difference between the microbiome of a baby born vaginally compared to a baby born by c-section (Azad, et al. 2013; Penders et al. 2013Prince et al. 2014). During a vaginal birth the baby is colonised by maternal vaginal and faecal bacteria. The initial bacterial colonies resemble the maternal vaginal microbiota – predominately Lactobacillus, Prevotella and Sneathia. A baby born by c-section is colonised by the bacteria in the hospital environment and maternal skin – predominately Staphylocci and C difficile. They also have significantly lower levels of Bifidobacterium and lower bacterial diversity than vaginally born babies. These differences in the microbiome ‘seeding’ may be the reason for the long-term increased risk of particular diseases for babies born by c-section.

The environment in which the baby is born also influences their initial colonisation. A study by Penders et al. (2013) found that term infants born vaginally at home and then breastfed exclusively had the most ‘beneficial’ gut microbiota. It is likely that these babies only came into contact with the microbiota of their family during the key period for ‘seeding’ the microbiome. No one has researched waterbirth and the microbiome yet. Might it dilute the bacteria? The chance of colonisation and infection with group B streptococcus (GBS) is reduced with waterbirth (Cohain 2010Neugeborene et al. 2007). This may be due to dilution of the GBS or additional colonisation of the baby with beneficial bacteria. Another future research topic is caul birth and the microbiome. Does a baby born in the caul miss out on colonisation via the vagina?

What we do know is that antibiotic exposure alters the microbiome in adults (see above). When a woman is given antibiotics in labour her baby also gets a dose. In 2006 a medical expert review (Ledger 2006) raised concerns about prophylactic antibiotics in labour. A study in 2011 found that antibiotics given in labour increased the incidence of late-onset serious bacterial infections in infants (Ashkenazi-Hoffnung et al. 2011). I think more research needs to be carried out considering the number of women/babies given antibiotics in labour (eg. ‘prolonged’ rupture of membranes).


  • A vaginal birth in the mother’s own environment is optimal for ‘seeding’ a healthy microbiome for the baby (Penders et al. 2013).
  • Minimise physical contact by care providers on the mother’s vagina, perineum and the baby during birth.
  • Avoid unnecessary antibiotics during labour. If antibiotics are required consider probiotics for mother and baby following birth.
  • If the mother has a c-section… and I know it sounds weird but… she may want to consider swabbing her vagina and ‘wiping’ the baby with this swab. It is even more important to encourage and support breastfeeding for mothers who have had a c-section. Again, consider probiotic support.


After birth, colonisation of the baby by microbiota continues through contact with the environment and breastfeeding. There are significant differences in the microbiota of breastfed babies compared to formula fed babies (Azad, et al. 2013; Guaraldi & Salvatori 2012). Beneficial bacteria are directly transported to the baby’s gut by breastmilk and the oligosaccarides in breastmilk support the growth of these bacteria. The difference in the gut microbiome of a formula fed baby may underpin the health risks associated with formula feeding. In the short term, infant colic may be associated with high levels of proteobacteria in the baby’s gut.


  • Immediately following birth, and in the first days baby should spend a lot of time naked on his/her mother’s chest.
  • Avoid bathing baby for at least 24 hours after birth, and then only use plain water for at least 4 weeks (Tollin et al. 2005; RCM 2008).
  • If in hospital use your own linen from home for baby.
  • Minimise the handling of baby by non-family members during the first weeks – particularly skin to skin contact.
  • Exclusively breastfeed. If this is not possible consider probiotic support.
  • Avoid giving baby unnecessary antibiotics (Ajslev et al. 2011; Penders et al. 2013). Again, if antibiotics are required probiotics need to be considered.
  • Probiotics may also be beneficial for babies suffering from colic.


The more we understand about the human microbiome the more it seems fundamental to our health. Pregnancy, birth and breastfeeding seed our microbiome and therefore have a long-term effect on health. More research is needed to explore how best to support healthy seeding and maintenance of the microbiome during this key period. I have discussed a number of considerations and suggestions arising from what we already know. I welcome any comments, discussion and further suggestions from readers.

Further reading and resources

Watch the trailer for MicroBirth and support their project

5 ways gut bacteria affect your health

Gut feelings: the future of psychiatry may be inside your stomach

Gut bacteria might guide the workings of your minds

About midwifethinking

independent midwife, lecturer and student of all things birthy
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36 Responses to The Human Microbiome: considerations for pregnancy, birth and early mothering

  1. Babs says:

    A “Company” did a great presentation last year on their products surrounding gut flora and pregnancy and breast feeding support. It is absolutely crucial that mothers are given information and choices surrounding their birth. What evidence is there for automatic prophylactic antibiotic at the time of a caesarean? Yet it is standard practice. I have seen very irritable baby’s settle with probiotics.
    I got informed this week, by a medical officer, when women are admitted to ‘his’ hospital, they are under ‘medical’ care and that I was not ‘allowed’ to share information on ‘alternative’ cares or treatments. Shock horror- my crime was to inform the woman the best time to take iron supplements avoiding interactions with tea -tannins and dairy. Sorry I thought a midwife looks at the whole person and mother and baby not a disease.
    Thank you for this article. I hope practices will continue to improve.

  2. Denise Hynd says:

    Thank you for another enlightening share!
    It is crazy that when a woman’s membrane break before labour she is encouraged, nay told to come to the place that has bred multi-resistant bacteria and to have high doses of one of the things that helped grow those bacteria, prophylactic use of antibiotics. This is just one of the many illogical things the medical ‘scientists’ have us all support and coerce women to do with their vulnerable babies!!

  3. Rachel James says:

    Another suggestion would be to rub the vaginal swab in the closed palms of a baby born by Caesarian or across the mothers chest??

  4. Keeva Leighton says:

    Thank you Racheal, another very interesting article. I have been telling my co workers about positive vaginal/ anal flora for a while with varied reactions, I will now share this with them.

    Sent from my iPad

  5. ksk9764 says:

    Fabulous stuff as usual. I already share the benefits of vaginal birth with my NCT clients, but the prenatal and postnatal ideas are a terrific addition. Thank you.

  6. robynheud says:

    I sometimes think the medical industry fails to understand just how detrimental stress during pregnancy can be. The fact that it can affect the gut microbes is particularly telling. Unfortunately, my stress comes from seeing the doctor (white-coat hypertension, with a vengeance). Not only was I extremely stressed with my first pregnancy, I also had prophylactic antibiotics during labor, and my now-four-year-old has several allergies (food and otherwise), as well as eczema. My second, where I avoided the doctor unless absolutely necessary and had a homebirth was incredibly stress-free, and he has no allergies or eczema. I would love to see more research about the effects of stress in pregnancy, especially since so many other cultures encourage a very stress-free environment for the mom.

    • Valerie says:

      I would love to see pregnancy stress reduced as well. It can be terribly stressful for the mother considering all the testing and warnings, etc. she is subject to while expecting.

  7. Heidi says:

    Thank you for your article which just reconfirms my feelings on the importance of gut flora especially during childbearing. I too had a homebirth with my daughter, took probiotics, vitamin c powder and I was never ill during pregnancy and my daughter does not have any allergies. I also did not have GBS during pregnancy but I did a year after giving birth when probiotics were not taken as much due to simply just forgetting. I have since learnt my lesson and as a newly graduated midwife will encourage women to make informed decisions about what they put in their body to protect themselves and their children.

  8. altitudewellness says:

    What is your opinion regarding swabbing the vagina after a c-section of a woman who has tested positive for group B strep? Wouldn’t the GBS then have the opportunity to invade the infant and make him or her sick?

  9. This is fascinating. I have so much wondered how the micro biome affects the baby, and it’s curious to know that the sterile gut is being challenged. My second baby the waters broke when she was halfway out, and I have pondered if this affected her micro biome. Fascinating research.

  10. Reblogged this on Rootedforlife's Blog and commented:
    I have been reading up on the impotence of gut health and pregnancy .. this article is wonderful in explaining why a healthy gut is so important for pregnancy and baby !

  11. Kim says:

    Interesting stuff to consider. I found “The chance of colonisation and infection with group B streptococcus (GBS) is reduced with waterbirth” very intriguing since I was positive for my last two pregnancies and had one dose of antibiotics late in labour with each child. I would love to try a waterbirth this time and this just adds one more reason!

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  13. faerylandmom says:

    Reblogged this on Birth In Joy.

  14. Michaela K. says:

    Are you sure Dr. Odent said this? He is not pro water birth and when I studied with him he talked about it and said it is always better for the baby not to be born in water to get colonized properly.

    • I have just searched through all my Odent literature and can’t find where I got that idea from. So, I’ve removed it from the post. Thanks for pointing it out… and apologies to Michel for possibly misrepresenting him.

  15. April Hunter says:

    Forgive the question. As a doula (non medical) supporting a mother in a planned c-section, if the mother wanted to have the baby swabbed with her vaginal fluid, how would she technically go about this? Could we ask a midwife to do it? How would you suggest we state this in the birth preferences?

    • Good questions. You could put it in the birth preferences… but staff might freak out. The mother could do this herself, perhaps swabbing her vagina before c-section then wiping baby when she gets a moment after the birth (concentrating on face and hands)… or wiping the swab on her chest so that when baby goes skin-to-skin he will come into contact with the bacteria. Not sure… I haven’t seen it done yet! Hopefully someone who has will comment and give us some tips.

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  18. Denise Hynd says:

    Rachel do you know of any information, research based concerns around the impact of immunisation on the Microbiome?

    • No I don’t… definitely not my area of expertise. I’d want to know how the components of the vaccine (and they are all different) would act on gut bacteria. And they are not antibiotic components and they are given via the blood stream… so not sure!

      • Concerned says:

        Vaccinations are given into muscle, not intravenously( ie into the blood stream). It would seem you have upset The Sceptical OB. Interesting reading for a balanced view of a topic.

        • They are absorbed into the blood stream via intramuscular injection. The aim is to get them into the blood stream as this is where the immune response is triggered. Perhaps not clear enough in my comment…

  19. marijamiko says:

    Hi Rachel,
    Thank you for this article. Can you speak to the impact on a baby’s gut biome of vitamin d drops or other supplements which are given in small amounts, and whether there is a similar result as occasional supplementation with formula?

    • I don’t know about vitamin d drops or other supplements. But formula does disrupt gut flora and gut permeability. This is the reason that women with HIV are recommended not to ‘mixed feed’… the formula strips the gut protection = when HIV infected breastmilk enters the gut it can pass into the baby’s system.

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  22. Jenna Simons says:

    I have been thinking about the colonizaton in water birth issue….. is it possible that the vaginal flora sticks to the vernix? After my waterbirth, I didn’t wash the vernix off…wondering if this helped??

  23. Heather says:

    We are unable to have our own babies, so we are adopting. What would you suggest for our situation? Especially the post birth side of things. I don’t know how it will go in the hospital, so assuming we won’t be able to have the baby on the chest and without being able to nurse? I’ve done a lot of research and having never given birth and nursed I won’t be able to nurse the baby, so I’m avoiding that extra stress. I do plan to use the WAP formula. And who knows how the actual birth will go re vaginal or cesarean. What do you think?

    • Hi Heather. I guess the birth is out of your hands but the rest isn’t. Skin to skin with your baby and lots of body contact will colonise the baby with your bacteria – and there is no reason you cannot do this in hospital immediately after the birth. You may be surprised – it is likely hospital staff have come across adoptive parents wanting skin-to-skin before. If you are formula feeding then consider probiotic supplementation. You could consider donor breastmilk – depending on what is available locally to you. I was talking with a microbiologist recently and he pointed out that bacteria is transmitted to baby via the skin around the nipple so a supply line is preferable to bottles in terms of bacteria transfer – something to consider perhaps. Your baby will inherit their initial microbiome from the birth mother, but the environment you provide will add and build on that initial seeding. Perhaps some of my readers will have experience with this or further suggestions.

  24. Great article and love the NPR video…such a simple explanation for something I discuss every day in clinic! I have found great results in women with previously atopic kids, prevent this in subsequent offspring by doing pre and post natal probiotic supps. So many benefits for a healthy microbiome….
    Thanks Karen :)

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