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.

Pre-conception and Pregnancy

The commonly accepted belief that the the baby inside the uterus is sterile (whilst membranes are intact) is 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). And the unique ecosystem of bacteria in the placenta may originate from bacteria in the mother’s mouth. 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). Gum disease (bacteria) has also been linked to pre-term birth. Suggestions:


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. 2006Prince et al. 2014). During a vaginal birth the baby is colonised by maternal vaginal and faecal bacteria. Initial human 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. (2006) 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 antibiotic resistance when treating late-onset serious bacterial infections in infants (Ashkenazi-Hoffnung et al. 2011). A more recent study found that antibiotics given during labour or a c-section are associated with infant gut microbiota dysbiosis (Azad et al. 2016). This is concerning considering the number of women/babies given antibiotics in labour (eg. for ‘prolonged’ rupture of membranes or for ‘epidural fever’). Add to that the use of prophylactic antibiotics for c-sections = a significant proportion of women and babies being exposed to antibiotics around the time of birth. Suggestions:

  • A vaginal birth in the mother’s own environment is optimal for ‘seeding’ a healthy microbiome for the baby (Penders et al. 2006).
  • 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 baby is born by c-section… Research is currently being undertaken into the use of vaginal swabs* to ‘seed’ c-section babies. The preliminary results are that the microbiome of swabbed babies are more similar to vaginally born babies. The protocol the researchers are using is:
    1. take a piece of gauze soaked in sterile normal saline
    2. fold it up like a tampon with lots of surface area and insert into the mother’s vagina
    3. leave for 1 hour, remove just prior to surgery and keep in a sterile container
    4. immediately after birth apply the swab to the baby’s mouth, face, then the rest of the body (you can see photos of this process here)
  • If a baby is born by c-section it is even more important to encourage and support their mother to breastfeed. It may also be worth considering additional probiotic intake.

*There has been a bit of hysteria about the safety of vaginal swab seeding in the media. I will leave it to Sara Wickham to address (rant about) this one.


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 (wish I’d know this 20 years ago!). Suggestions:

  • 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).
  • 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. 2006). 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

About Dr Rachel Reed

Doctor of (Birth) Philosophy • Author • Educator • Researcher
This entry was posted in baby, birth, midwifery practice, pregnancy and tagged , , , , , , , , , , . Bookmark the permalink.

119 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??

    • Jay says:

      Vaginal swabbing of cesarean-born babies does increase bacterial biodiversity, but not as much as being vaginally-born

  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.

      • You have to be pro-active with this. Most c-sections aren’t planned, and they all will get antibiotics in prep for surgery. So I tell all of my moms to swab their canal before they go in, put the swabs in a baggie, and bring them in their birthing bag. Moms can put the flora on them before the newborn nurses and that way the baby gets some exposure to canal flora and transmission to the gut. Both mom and baby need lactobacillus and bifidus; again baby can receive it if mom makes the probiotics in a paste with the breastmilk and puts it on prior to nursing.

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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 🙂

  25. Kelly Minehart says:

    My second baby was born “in the caul”. I am so curious as to how this may impact microbiomes. Any ideas? Thanks, Kelly

    • Hi Kelly
      Colonisation takes place by the baby’s face coming into direct contact with vaginal flora on the way through the vagina. If the caul is intact the baby’s face will not be in direct contact with this flora – the membranes will ‘protect’ it. So, in theory this may impact on colonisation. Of course, this is all just theory until someone does a study and finds out if there is a difference.

  26. amaturrahman says:


    I’m about 32 weeks of my first pregnancy, and I have to say, this article, and indeed this website, has been an absolute revelation. Thank you so much for such an enlightening read; I’m making my way through the related articles, and it’s been such a refreshing change to being barked at by an almost faceless team of midwives. Although I’ve not allowed myself to be overwhelmed by received wisdom and expectations, I was told at my last midwife’s appointment that I’ve tested positive for GBS, and I’m having a slight freak out because I was given literally no further information other than to be flatly told that I would be given antibiotics intravenously during childbirth. As this is my first pregnancy, I’m trying to resist the urge to trawl through the internet so as not to freak out more, but I do need to find out more. Is there any further reading you would suggest? I’m uneasy at the thought of being given antibiotics, especially after reading this article, but I simply don’t have a clue as to how I can best balance medical intervention with my own personal wishes. Help!

    Many thanks.

    • The UK NICE guidelines state that “Pregnant women should not be offered routine antenatal screening for group B streptococcus because evidence of its clinical and cost effectiveness remains uncertain” because so many women end up in your situation if routinely tested. Now that you have the information you need to make decisions about your care – and there are no risk free options. You can follow medical recommendations and risk the effects of antibiotics or you can wait and see if you or baby develop any symptoms of infection before treating it. Interestingly, a Cochrane review concluded that the effectiveness of giving prophylactic (just in case) antibiotics for GBS is inconclusive You will find information and debate on either side – you need to decide what is right for you and stick to it. By the way… no one can administer a medication to you without your consent. I am hoping to write a post about GBS in the future but unfortunately not in time for you.

      • Lenka says:

        I’m in the same boat tested positive for GBS being routinely tested in Victoria not realising the implications this would have on my birth. I have decided that I definitely don’t want any antibiotics during labour. What I’m unsure about and can’t seem to find any information on is what to do if I do run into the risk factor of my membranes being ruptured for longer than 18hrs or having a temperature higher than 38C. Ironically my hospital offers water births but not if you test positive for GBS and don’t take antibiotics. One thing I should definitely be doing to lower any risks!
        Do you have any advice or know where I can find more information on what to do if I run into this situation? It’s my first baby and I’m currently 40 weeks and 4 days.


        • Hi Lenka… you may have already had your baby. However, if you have GBS at the time of prolonged rupture of membranes it does increase you chance of the baby being in contact with the GBS. A high temperature is a sign of infection and should not be ignored. I think we need to be careful to distinguish between prophylactic i.e. just in case medication vs proactive in response to signs of complication/pathology. There is a new cochrane review re. GBS you might be interested in:
          Come back and let us know what happens 🙂

    • nora1 says:

      Hi amaturrahman,
      I was in your situation, ‘informed’ that I would have to labour with IV antibiotics, and wanted to share my experience. I did as much research as I could and basically found the information Rachel has given you and some other information about factors which increase the risk of infection in the baby. Based on my reading I decided to wait and see whether any of the risk factors were present when I started labouring and decide then. None were and I declined the antibiotics. We were kept in hospital for 48 hours for observation which I was happy to do, I was treated with a degree of contempt by one particular midwife who evidently disapproved of my decision. In the event, my daughter developed no infection. I know the outcome in our case can’t have any bearing on your decision but I just wanted to let you know you are not alone, do what feels right for you.

      • amaturrahman says:

        Thanks for sharing your own story. I’ve decided on doing pretty much as you had done, waiting to see if any risk factors might present themselves at the time of labour, otherwise declining the antibiotics. I’ve not had the most constructive of responses either, but I expected as much. From my own reading, the lack of consensus in dealing with this issue simply does not justify the medicalisation of birthing as a default response. One question that seems to stump any health official I ask is, if it is not a matter of routine to test for GBS, then surely there must be women who are going through labour unaware that they are GBS positive, and have no problem at all? I’ve not had any satisfactory answer as yet. Until then, I don’t suppose I can afford the stress! 🙂 We’ll just have to wait and see…

  27. I’m due to give birth to my first child in September. I plan on a natural, unmedicated birth at a birthing center with a midwife and doula (possibly water birth).
    My question is, what do I do if I suspect my gut bacteria is compromised? I understand my bacteria will be passed on to my baby but what if that’s not entirely a good thing? I suspect I have SIBO, a candida overgrowth, or perhaps some other fungal overgrowth.
    I’ve been eating paleo for almost 2 years now. I supplement with probiotics and eat fermented foods. I plan on giving my child an infant probiotic as I breastfeed.
    I had the privilege of asking Chris Kresser about this a few months ago. He suggested probiotics and fermented foods and if I believe I have a more severe overgrowth to work with someone one on one to treat it. Which was, well, exactly what I thought he would say but I was hoping for more. I haven’t worked with anyone on treating it or even tested for it (trying to save money). I’ve just been rotating probiotics and taking spoonfuls of coconut oil here and there.
    I’m just curious if anyone has any other suggestions or experience with this. Is there any way my kid will luck out and get more of the good than the bad bacteria? Or is she doomed to pick up my gut bacteria where I left it? Poor thing, I grew up in the 80s eating Twinkies and Ding Dongs! And had a mother that gave us a few antibiotic pills anytime we felt sick. Ugh.

    • Don’t beat yourself up… most of us grew up eating terrible food and taking antibiotics! All you can do is work to improve your own gut health (which you are) and give your child a better diet than you had growing up. In terms of your own gut health I would recommend seeing a naturopath and getting tested. It is expensive but from personal experience I can tell you that once you know what you are dealing with it is a lot more effective to ‘treat’ – and will probably save you money in the long term.

  28. sara r. says:

    I’ve been thinking about this lately and wondering how being born in the water might affect the baby’s but bacteria, or even being born immediately after water breaking or in the caul. My son was born at home in the tub, breastfed exclusively and had no vaccines, medications, organic diet, etc. Yet he still had some obvious gut imbalances that only resolved after adding a variety of fermented foods, most noticably water kefir. I wonder if water birth/precipitous birth makes it more likely that a baby wouldn’t get everything that they should have during the birth process. In talking to other mothers, it seems that this is not an uncommon experience. any thoughts?

    • The impact of waterbirth is currently unknown as mentioned in the post. I am currently working with some microbiologists to undertake some research in this area so watch this space 🙂
      Also bear in mind that the mother’s microbiome will influence the baby’s too. My second child had terrible gut imbalances probably due to my own poor gut health during pregnancy. She was born at home, not in water and breastfed. The co-factors are so complex and science is only just starting to understand it all.

    • motherofeleven says:

      Sara, all my births were quick. I had 2 born in a caul. No gut issues and no water birth. Even the ones that didn’t always have an organic diet. By far the healthiest, was the one born in a caul, who didn’t have a bath for weeks, breastfed the longest till she was over two, organic food, no medications, no vaccines, and natural, whole food vegetarian diet. She is on the 97th percentile for height and I am only of average height. All the others are healthy too. The only issues we had were with the first, who was vaccinated and had asthma until we stopped.

  29. motherofeleven says:

    The water used in a water birth would be from town water full of chemicals, and an ideal temperature to breed bacteria from human waste and when the baby is born, it is going to be exposed to everything that is in that water including the chemicals. Two high profile cases of homebirth deaths in Australia; one of a mother and another of a baby involved water births.

    While warm water helps increase blood flow, this can lead to more blood loss than if the mother had given birth out of water. There has also been reports of babies dying from drowning and becoming very sick from ingesting water, from the water birth. The benefits of pain relief do not warrant the risks.

    According to Chinese tradition both mothers and babies did not wash for a month after birth, and rested completely. Ancient wisdom, but makes perfect sense not only in terms of gut flora but bacteria on the skin which is so important to health and bonding. A water birth tampers with the process that nature provided. We wouldn’t think of diluting breast milk, why water down the vernix that covers the baby?

    There is nothing natural about a water birth.

    • Simone says:

      I would love to see your evidence for some of those claims please, did the mother and baby that died do so directly from the water birth or form issues unrelated to this, the evidence for increased bleeding as most I have read say no increase and the evidence for drowning babies in waterbirths as examples of what I would like more information on please?? As none of my personal peer reviewed readings have indicated any of these issues

  30. Bri says:

    I love the little movie and have shared it around!
    Also interesting to hear the importance of vaginal birth/breastfeeding for this area, another few things to add to a long list of reasons why you should try!
    I went over to the linked site for Chris Kressner and was a bit perturbed – I didn’t completely digest (pardon the pun) everything he was saying, but he seemed to be advocating giving up ALL grains, sugar (including fruit), dairy, coffee, and various other things. Is this something we should be encouraging pregnant women to consider? I do like the idea of a clean diet, eating whole, unprocessed foods etc but… his list didn’t seem to leave much on it! Maybe that’s the point. I’d be interested to hear your opinion on this.
    Thanks, great reading as usual. 🙂

    • Chris Kresser does not advocate such a strict approach long term. I’d recommend his book ‘your personal paleo code’ he provides the evidence for his recommendations and suggests cutting particular foods out for 30 days then reintroducing them one by one to work out which ones are OK for you. And fruit is not one of the restricted foods. It is also about what you do eat ie. introducing fermented foods and good quality un-processed foods. I’ve basically followed this approach to eating for nearly 3 years and it sorted many of my health issues – cleared my severe acne, fixed my gut issues… and better mental health too. I do eat rice, occasional dairy and coffee.
      As for pregnant women… yes I would suggest avoiding industrialised/processed foods, excess sugar, and caffeine. And including fermented foods and lots of veggies and healthy fats in the diet. 🙂

  31. Bri says:

    Thanks for this. It makes more sense that it is an elimination-type approach than a forever approach. Absolutely agree with avoiding processed foods, and antibiotics, all those ones that are more obviously “bad”. I’m definitely going to look more into fermenting foods, and as for the grains.. I’m intrigued… but I think I’m a born cynic/skeptic! Just need to keep an open mind. 🙂

  32. felicity says:

    Hi i aim to do my disertation for my midwifery degree on this subject and would really appreciate any research or details on the subject. Could you please recommend good reaearch papers for me to read? I really loved this article.
    Thank you in advance.

    • Hi Felicity
      This post was based on the available research… so click on the references to get the research articles. There is not a huge amount of research out there yet. I think this will change in the future as the microbiome and its relationship to birth/breastfeeding etc becomes increasingly understood.

  33. brodielien says:

    I am replying to a few posts in this stream! One regarding positive GBS and denial of antibiotics and the other regarding yeast overgrowth and colonisation concerns. My disclaimer: I’m a mother, a well educated mother but not in the fields of childbirth or science for that matter! However, I have a 4 year old that has severe food allergies, I tested positive for GBS in two pregnancies, I denied antibiotics in the second birth and opted for an alternative treatment…#2 is allergy free. I launched myself on a research journey that has been quite fruitful after the diagnosis of food allergy in #1. Here is what I know, after testing and experiencing success in my own home, about probiotic use:
    1. Vaginal flora in a “normal” environment is a complex mix of lactobacillus and bifidium bacteria.
    2. If you’re experiencing VYIs or BV you likely lack these bacteria.
    3. I often (once a month) mix a capsule of Ultimate Flora Vaginal Support (this contains several strains of both lactobacillus and bifidium) with a teaspoon of coconut oil (which by the way has antifungal properties) and insert it before bed. I did it weekly from 30 weeks until delivery with #2 at 41 weeks and 2 days.
    4. I’ve cured eczema with probiotic salve.
    5. I cured my IBS after a 12 month battle after baby #1 was born which I can only surmise was caused by 24 hours of penicillin.
    6. My measure of a quality probiotic: has counts in the billions, has at least 3 strains of lactobacillus and bidium, and is refridgerated.

    My success with an alternate treatment for GBS:
    The standard of treatment in many countries is a Hibiclens wash (a dilution of Hibiclens and water that is applied generously, by the doctor/nurse, from the rear to front and up the thighs every 2-4 hours of labor). I was very proactive with my wishes and brought tons of research to back up my plan! I was also “past due.” Prior to 40 weeks I’d be a little more wary. Premature babies and water that has been broken for more than 18-24 hours have a significatly increased risk of transmitting GBS to the baby. I was told a prenatal check up that if this Hibiclens idea was received wrong by the doctor on duty that CPS could get involved. Ridiculous!!! Sp, do your research. Know that there are risks either way and advocate for what you feel is best for your baby and you!

    • Steve Passage says:

      Would you tell me what probiotic salve you used to cure eczema? Or, did you make your own? Four of my grandchildren were c-section births and they all have eczema (to varying degrees) and some have food and pet allergies too. I want to get some of this salve to give to their Mother to try to help them. The only probiotic salves I can find on the internet are Cheeky Slave and Earth Mama Angel Baby Postpartum & C-Section C-Mama Healing Salve. One is $10 and ounce and the other is $30 an ounce. Please advise. Thanks

      • It might be a good idea to consult a naturopath… my understanding is that the issue is internal rather than external i.e. if the gut microbiota is good then it will reduce eczema symptoms. But, I am no expert on gut health and allergies 🙂

        • Steve Passage says:

          A little confused. You said you cured eczema with a probiotic salve. Which one?

          • Sorry… I did not write this. Is it in a comment by a reader?

          • Steve Passage says:

            Yes, brodielien says: August 16, 2014 at 11:48 pm. Her 4th point was that she cured eczema with a probiotic salve.

          • Hopefully she will come back and give you some further information!
            I do know people who have cured their eczema with reestablishing a healthy gut via probiotics and fermented foods. Again – a naturopath would be able to provide information and recommendations about this.

  34. Annie Craven says:

    What a great, interesting read! There are so many benefits of the vaginal birth and some people forget how important this step is for the well-being of the newborn. But of course, we are all different and not everyone has this option. Thank you for sharing your ways.

  35. Lauren says:

    In the event that I have a repeat csec with my upcoming birth (trying for a vbac), I have the vaginal swab in my birth plan. My midwives are fully supportive, but wanted me to research more if blood in the vaginal swab would mess up the benefits for baby and how and when they’d swab. I’d like to put the swab directly in his mouth too. Anyway we could do it before surgery and keep it sterile? Any ideas would be great, thank you!

    • Hi Lauren
      Check the other comments because I think there have been a few ‘tips’ included in some.
      You don’t need to put anything in baby’s mouth. If you put it on hands, face and your chest/breasts the baby will pick up the bacteria and colonise… putting his/her hands in and around their mouth and on your skin. You could do a swab just prior to surgery and put it in a zip lock bag. Or before surgery put some over your chest/breast and ask for baby to be placed skin-to-skin immediately. I’m not sure about lochia (blood after birth) – it may have a different microbiological make up. This is all still very new and it would be great if some ‘guidelines’ were developed. I’m hoping a reader who has experience with this will reply to you 🙂

      • Jessie says:

        I saw micro birth last night. There is some research being done on the use of vaginal swabs. The protocol the researchers are using is to take a piece of gauze soaked in sterile normal saline. Fold it up like a tampon with lots of surface area, insert into the mothers vagina and leave to incubate for 1 hour. It is removed just prior to surgery and kept in a sterile container. As soon as the baby is born the swab is first applied to the babies mouth, face then the rest of its body. The preliminary results show that the microbiome of the swabbed infants are more similar to vaginaly born infants than those born by caesarean.

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  38. Aly says:

    Thanks so much for this. I am currently 6 months pregnant but tested positive for GBS. It was really disappointing for me because I really wouldn’t have considered myself ‘at-risk’ with my hygiene practices and history, so I have been doing as much research on it as I can to see what I can do to get rid of it. I have been taking probiotics orally twice a day, pure cranberry juice (no sugar added) twice a day, apple cider vinegar once a week, increasing my intake of vitamin C… I’m hoping this will help, but if it doesn’t I just don’t know how to proceed. I have a midwife and was planning on a water birth, so theoretically I would think that I have a lower risk of passing this on to my baby. The midwife and I previously agreed to my treatment plan and I will be re-tested later; but if I am still positive is it worth getting the antibiotics? I’m really torn because I don’t want to kill of all the good bacteria as well, and I am not sure it is worth it… but I guess it is a risk either way.

    • I suggest you watch out for the booklet Sarah Wickham wrote for AIMS (Association for Improvements in Maternity Services – UK). It is available in November:
      I haven’t written about GBS because this booklet (I’ve had a sneak preview) covers absolutely everything.
      I’m guessing you are not in the UK as routine screening is not carried out there for this very reason. Many women are GBS positive (nothing to do with hygiene)… it comes and goes ie. next time you are tested it may have gone… and lots of women have it either side of being tested = ‘negative’ test. All routine screening does is stress women out and change their options.
      If you are still GBS positive when in labour you will be offered antibiotics ‘just in case’. I suggest you to some research around this ie. read the book… and check out this recent Cochrane review: that found the use of antibiotics was not supported by conclusive research.
      Ultimately you need to make your own decisions – only you know what is right for you and your baby.
      Good luck… come back and let us know what happens 🙂

      • Aly says:

        Thank you!!! I will definitely keep my eyes open for the booklet by Sarah Wickham, I want to get my hands on all the info I can. I’m actually in Canada, and I have a midwife – and the Ontario Association of Midwives recommends treatment with antibiotics. This is why I have found it difficult to make an informed decision, as it seems like most of the literature here supports the treatment.

        Although they recommend screening at 37 weeks, my midwife offered me early screening as I was going in for other routine blood tests anyways. I thought, why not? But now because I tested positive I have this cloud of worry over what is best for my baby. My midwife and I agreed on my natural treatment therapy of taking acidophilus, drinking cranberry juice 2x/day, bathing in apple cider vinegar, etc., and we decided I would be tested again prior to delivery to see if the bacteria still remained. I’m crossing my fingers – if I stick to this regimen quite diligently I’m hoping I can keep it at bay, naturally. And especially since the systematic review you suggested by the Cochrane collaboration indicates that treatment in labour does reduce mortality BUT has a high risk of bias, I don’t know if I can make a decision to treat based on such weak evidence. Since the overwhelming statement they provide is that antibiotics are not supported by conclusive evidence, I think my choice is clear. Thank you so much for providing the link to the Cochrane study, as I highly value their research methodology. I wish the health professionals here would provide this!

        I will see how it goes and check back after January – I am due then. And I sincerely appreciate your help.

        • It is really difficult to make a decision once you know. There are risks with either option. The risks of prophylactic antibiotics on the microbiome seeding and potential long-term health issues vs the risks of your baby being the rare ‘one’ that contracts a GBS infection.
          And remember that if your baby spends most of the labour with an intact amniotic sac GBS cannot get to baby until it breaks. In my experience more babies are born in the caul during waterbirth… so perhaps choosing to waterbirth might maximise the chance that the membranes will stay intact during labour? No guarantee – just based on my own anecdotal experience. The water also dilutes GBS as mentioned in the post.

          • Aly says:

            I had my baby boy on December 17, healthy and happy. I was re-tested for gbs 2 weeks prior to birth and was undortunately still infected despite sticking to my cranberry, garlic, and vitamin c pills. I did end up having a different birth experience than originally planned – I woke up in the night and thought my water broke, but when I turned on the light it was all blood so I ended up having to go to the hospital. I still had midwives but no water birth. Because of this, I worried about whether or not I should opt for the antibiotics. I only had 5 hours active labour, although a total of 16 hours. I had no other risk factors besides diagnosis with gbs and the midwife ended up breaking my water, and I ended up giving birth 1.5 hours after. We also left him without a full bath to preserve the vernix. So far he has been completely happy and healthy, so cross fingers that he has no issues.

          • Congratulations! Thanks for the update. Birth rarely goes as ‘originally planned’ 🙂 Enjoy your happy healthy baby boy!

  39. Angela says:

    Great article. I have shared this article with clients and one asked about seeding when the mother is GBS positive and will be treated with intrapartum antibiotics. Would the potential risks of colonisation be the same as those occurring during vaginal birth?

    • I’m not sure what you mean… can you explain your question a little more? The antibiotics would kill the GBS and other good bacteria too.

      • Angela says:

        In your article, you talk about research into the use of vaginal swabs to ‘seed’ c-section babies. If someone with GBS prepared a swab prior to the administration of antibiotics for the purpose of seeding the baby post birth, would the risks to baby be the same? Would an interval of time reduce the risk, or the effectiveness of the ‘material’ gathered on the swab for this purpose?

        • Oh, yes I see what you mean. That’s a really good question and I’m not sure anyone has a concrete answer, as there is currently no research. However, I would guess that the baby would have about the same chance of getting a GBS infection as a baby who had been colonised via a vaginal birth. It is the same bacteria just applied a different way – swab. The vast majority of babies born to GBS positive mothers do not get an infection. And the risk of infection would need to weighed against the risk of missing out on the beneficial bacteria.

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  41. Katie says:

    The article relating to the effects of intrapartum antibiotics on newborn infection may be slightly misquoted. It appears that the study actually reports a higher rate of *antibiotic resistance* among newborns who become infected, not an overall rate of higher infection amongst newborns who receive intrapartum antibiotics. Just a small detail 🙂

  42. Leah says:

    I am currently 33 weeks pregnant and it is likely I will have a c-section as the baby has been consistently breech due to my bicornuate uterus. Providing that we reach 36 weeks the baby will be born at a small regional hospital where our options are very limited. We have been told that immediate skin to skin is not routinely practiced post c-section but there is a small chance it may be possible providing that the maternity ward is not busy at the time. Their protocol is to wipe the baby down, place arm/leg bands, wrap the baby, bring it over to show mum and then take the baby to the nursery with dad to be weighed, measured, given vit K and hep B vaccinations and then bathed. Dad will then be allowed to have skin to skin until I am brought back from recovery.

    I am very keen to follow the swabbing protocol but understand it will probably be very difficult in this hospital. My current plan is to place the swab myself and then remove it just before I go to theater, apply it to my chest/breasts and then place it in a sterile container. Will the effectiveness be lost if I am not able to have skin to skin for perhaps an hour? Also, is there any danger in the swab being in the vagina for more than 1 hour?

    We plan to request that the baby is not bathed before he/she has skin to skin with dad. Hopefully at this time dad can apply the swab to the baby’s face, hands and chest. Would there be any benefit to applying the swab to dad’s chest before skin to skin or would it not help given that it is my bacteria not his?

    Thank you so much for writing this article.

    • Hi Leah. I am sorry that you find yourself in a challenging situation. I think in these circumstances it helps to be proactive. Contact the person ‘in charge’ e.g. the unit manager and state your decisions about the care of your baby after birth. What you are requesting is ‘best practice’ i.e. supported by research and many other hospitals provide this care. I’d be wanting a face-to-face meeting and then a written care plan. Ask if the hospital is a ‘Baby Friendly’ hospital… this is a WHO accreditation and would require the hospital to follow best practice ie. no separation of mother and baby and skin-to-skin and early breastfeeding.

      The weighing etc. can be done later – this is not urgent. Ask if the baby and your husband can remain with you in theatre and in recovery… and that you would like to initiate breastfeeding in recovery. If this is an absolute ‘no go’ then insist that the baby is not bathed. Most hospital do not do this until 24 hours – it is a safety issue re. temperature never mind everything else!

      Regarding the swabbing. There wouldn’t be a danger of the swab being in for longer than an hour. Prior to surgery you could remove it and put it in a clean/sterile container and give it to your husband. If he ends up with the baby in the nursery he can swab the baby’s face and mouth with the swab. I don’t think he would need to swab his own skin… the baby would go from vagina to your skin – so your baby would go from ‘vaginal bacteria’ to his skin. It is likely that you share lots of bacteria. And baby would get your bacteria with your first breastfeed – hopefully soon after birth.

      I hope that helps. It would be great if you could come back and let us know how it all goes 🙂

      • Leah says:

        Thank you so much for your advice. You have definitely given me some great direction in order to be proactive. I looked up the list of “Baby Friendly Hospitals” and our local hospital is unfortunately not on the list. From what I understand they are very proactive with immediate skin to skin, early breastfeeding and rooming in post vaginal birth but sadly not so post c-section.

        I am currently under a private obstetrician. Do you think it would be best to speak to her about my decisions for care of our baby after birth or should I also speak to someone in charge at the birthing unit?

        • Speak to your obstetrician and find out who is in charge of midwifery at the hospital. There may be issues about what theatre staff will ‘allow’ in theatre (ie. not skin-to-skin… which is a shame because many theatres support it). However, it will be midwives responsible for your postnatal care and baby’s care.
          I had a client who went into her planned private hospital to meet with the staff who would be responsible for her baby on the postnatal ward and showed them her written plan and discussed her requirements (about no separation and breastmilk, etc.). They were fine with it and she got what she wanted even though it was not necessarily policy. Sometimes consumers forget how powerful they are 🙂

  43. Bronwyn says:

    Love this. Thank you for amassing the research. One question: the hyperlink labeled Penders et al 2013 leads to a study published in 2006. The study seems to be the right one, but the date is off. Is that what you meant? 2006 wasn’t THAT long ago, and yet I don’t remember hearing much about the microbiome back then.

  44. darcylcraig says:

    I am curious what type of probiotics you recommend for Mama or Baby if they have been exposed to antibiotics during labor and birth. Thank you!

    • The aim is to replace the ‘good’ microbiota that has been reduced or eradicated by the antibiotics. If you look at the flowchart in the post it will give you some idea about what needs to be replaced (the microbiota listed next to a green arrow). Generally a broad range probiotic, at least to begin with. I’d also suggest including fermented foods in the diet.

  45. Fiona says:

    Sorry to come to this so late, but just wondered if the vaginal swab might still be beneficial longer after birth? Os it something that has to be done immediately?

    • My understanding is that the initial seeding is done at the time of birth. If a vaginal microbes are not in contact with the baby’s skin at this point the seeding will take place via the other available microbes… they will colonise the baby and become established. So, I think swabbing later would have a limited effect. Not sure though, and there is no research looking at this.

  46. Olivia says:

    I have read this and now worried about the healthiness of my babe’s gut and whether I can rectify any damage!?? :-/
    She’s now 14wks old and was born via emergency c section due to the midwives causing my adrenalin to kick in and baby deciding to turn round back to back and not wanting to be born anymore after being nice and calm in the water at home (planned home birth). She’s exclusively breastfed apart from one night on day 3 when I was made to agree to formula being given as she had lost 10.8% of her birth weight when weighed that day. I don’t know whether having taken placenta encapsulation pills will have helped in any way?? Is the damage done now she’s more than 3 months or can I rectify in some way to try and make her less susceptible to any health issues later on….? She has had her injections as usual (I am UK based)
    Hope to hear soon

    • Hi Olivia
      The problem with new information is that we can look back and regret what we did when we didn’t know. However, seeding the microbiome is only the first step. You can improve your babies microbiome by breastfeeding and doing all the things mentioned in the post for pre-conception and pregnancy. I’m not sure about placenta encapsulation pills… there has been nor research in this area. Your daughter is not damaged and there is still plenty of time to help her build and sustain a healthy microbiome 🙂

  47. Thank you for this informative and thorough post! I have shared it on my Madhupa Maypop and Sweet Gum Springs Apothecary (and personal) pages on FB. As an herbalist and microbiome geek, I can’t tell you how many health conditions I see arise in those precious little ones due to the lack of understanding of this important inoculation of beneficial bacteria!

    • Thank you. It is good that there is a growing awareness about the importance of the microbiome for health. It think in the future this will be commonly understood (fingers crossed 😉 )

  48. L says:

    is it too late to seed a baby at four months?

    • Yes – seeding takes place during the birth process and the first hours/days afterwards. However, anyone can help to balance their microbiome – even adults. For your baby look at the suggestions list in the post and apply what you can now ie. don’t use harsh cleaning products, breastfeed, and when your baby is eating solids offer him/her a range of foods that support healthy gut bacteria. We can significantly shape our microbiome through diet and lifestyle, despite missing that seeding period.

  49. Christine says:

    I don’t know if you’re still answering questions from this post, but I’ve been really curious lately about my third birth. I had a vaginal breech birth that began at home with my waters breaking and ended in the hospital 2 hours later with a successful drug-free vaginal delivery of my frank breech almost 10 lb boy. Here’s my question – He came through the canal so fast, and backwards. There was meconium everywhere. Did he get the same exposure to the vaginal flora as he would have had he come out face first? Thanks!

    • Good question! And this is a purely hypothetical answer as no research has been done (not surprisingly). His head and face still moved through your vagina collecting the vaginal bacteria. The baby doesn’t need to marinade in the bacteria (although some do)… they just need to collect it. A bit like wiping up something up – you can do it quickly. The colonisation happens as that collected bacteria spreads and replicates. I hope that kind of answers your question 😉 And congratulations on your amazing birth! 🙂

  50. Izzy Gawin says:

    Thank you for your article 🙂
    I have a question; my baby was born via vaginal birth but then taken in and put on really strong antibiotics (we had a really fast birth and he developed transient trachypnea which they mistook for an infection and after a long long battle with the stupid “specialists” and being referred to child services, we took our baby home). How damaged would his gut be because of this? He had 3 different types of broad spectrum intravenous antibiotics over 3 or 4 days. He is currently 5 weeks old, would he benefit from a reseeding done now? I should have done it as soon as we got home..

    • Your baby will benefit from breastfeeding and contact with you. Newborns are very resistant and so many lifestyle factors influence their health other than just exposure to antibiotics. Thankfully because so many newborns are subjected to ABs unnecessarily.

  51. Abbey says:

    I wish I had known this when I gave birth. I had an emergency c-section. We were both given antibiotics due to a few complications. 10 days after birth my baby had chronically bad gut health, windy, bloated, stomach cramps, waking every 40 mins in pain, anxious, couldn’t settle and then when we introduced solids he had allergic reactions, and got worse! Why don’t hospitals say “hey, I’m really sorry we had to give you and your baby antibiotics. As a precaution we advice that you do x,y and z (skin to skin, probiotics, bring your sheets from home etc) to help counteract the damage this may cause …” . Instead I was told nothing, was handed a baby and left to get on with it… All of my friends thought I was being dramatic when I said my baby was unsettled, including the Doctor!!! Thank fully a naturopath saved us and we are working on restoring my babies gut health. Why is this not comm practice / knowledge??!

    • Unfortunately medicine is generally resistant to new knowledge that challenges mainstream/standard practice. It is frustrating – especially when you have had to deal with the consequences.

  52. Paula Gallion says:

    My 2nd son was born vaginally en caul and I believe he missed out on the healthy benefits of the vaginal canal bacteria. Although he exclusively breast fed and weaned at 2.5 years, he constantly gets infections and has battled eczema. Interesting article, thank you!

  53. Cath says:

    If you are GSB positive (whether you know it or not), the membranes rupture, and you want to wait for labour to start naturally, even if it’s past the 24 hours mark: Are there any signs to watch for at home in case *the baby* gets infected in utero? Is there a way of detection if you are at the hospital?
    I apologise since these are things I should ask my care-provider, and I will at the next appointment, but I don’t trust them, since they’re not in favour of waiting more than 24 hours after MR.

  54. Cath says:

    Thank you so much (also for your responses in the other articles). I had already read that wonderful article regarding ROM, but I was wondering if there were more signs of a possible baby-infection than “if the amniotic fluid changes colour or smell, any reduction in the baby’s movements”. Kind of afraid of a possible undetected infection while you can’t observe the baby as well as when it’s already born. But now, thinking about it again, I see it was an excess question. Fetal distress could tell us as much as seeing a born baby having aslypiratory probably you have a good chance of catching the signs while waiting with ROM. Right?
    Sorry, my brain works really slow during pregnancy 🙂
    Thank you again for your time, for all the resources and for presenting the information so helpfully in the articles.

    • Yes – the suggestions were for women waiting at home without a care provider.

      However, a rising heart rate (baby and/or mother) can indicate infection. A care provider can determine this if they know what is a normal heart rate for that particular baby and then identify a rising baseline. I don’t advocate women do this themselves because understanding the nuances of fetal heart rate patterns is complicated. For example heart rate accelerations are a healthy sign whereas a gentle rise in baseline is not. I’d rather women connected in with their baby and paid attention to their movements and to their own intuition. If they are worried enough to want fetal heart rate monitoring – they should probably be in hospital.

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