No, cesarean does NOT affect the infant microbiome

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In the on going effort to demonize cesareans, the natural childbirth community seized on a tiny study and spun it into the claim that C-sections change the infant microbiome. A new, far larger study, shows that it does not.

As the Houston Chronicle explains:

[pullquote align=”right” cite=”” link=”” color=”” class=”” size=””]The infant gut microbiome is probably determined in utero.[/pullquote]

In a new study of 160 pregnant mothers and their babies published Monday, Aagaard and a team of Baylor researchers found that any differences in the microbiome of babies born via C-section are not the result of the birthing process …

“We do not see a lasting association between cesarean delivery and a distinct microbiome community or its function in infants beyond the neonatal period,” Aagaard said…

Where did the erroneous claim come from. It started with a 2010 paper by Dominguez-Bello that involved only 9 mothers (10 babies) that looked at swabs of the baby’s skin, mouth and nose and meconium within the first 24 hours after birth. You don’t have to be a scientist to understand that an observational study involving 10 babies for only 24 hours cannot be extrapolated to the population at large.

But Dominguez-Bello did just that anyway. Instead of undertaking a larger study to replicate her findings, she moved on the studying vaginal “seeding,” wiping C-section babies with their mother’s vaginal secretions. That study involved 18 mothers, 11 of whom delivered by C-section; only 4 babies were swabbed. The authors collected 6 sets of samples (oral, anal, skin) over 30 days. The authors claimed to find “partial restoration” of the infant microbiome.

In contrast, the new study by Aagaard et al. is far more robust. This study differed from the original studies in critical ways:

    • More participants: At 81 participants, this study is 9X larger than the original study.
    • More sample sites: Skin, mouth, nose and stool.
    • Longer follow up: The sampling was continued to 6 weeks of age.

What did they find?

1. The infant microbiome is not homogenous. As with the adult microbiome, it differs substantially depending on where in or on the body you take samples.

We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity.

2. Although there were some differences in microbiota between cesarean and vaginally born infants immediately after birth, these differences were restricted to the mouth, nose and skin. Gut bacteria did not differ based on mode of delivery.

Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R2 = 0.038), this was not true for neonatal stool (meconium; Mann–Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode.

3. The infant microbiome changes rapidly in the first 6 weeks. By 6 weeks of age there was no detectable difference between babies born by C-section and those born vaginally.

For infants at 6 weeks of age, the microbiota structure and function had expanded and diversified with demonstrable body site specificity (P < 0.001, R2 = 0.189) but without discernable differences in community structure or function between infants delivered vaginally or by cesarean surgery (P = 0.057, R2 = 0.007).

4. The environment in the uterus is probably not sterile as previously thought. Thus the composition of the infant microbiome may be determined in utero, not at the time of birth.

unlike the skin, oral cavity or nares microbiota, the neonatal gut microbiota at the time of delivery did not significantly vary by mode of delivery. The content of the first meconium is hypothesized to reflect the in utero environment (in which the infant is swallowing amniotic fluid continuously from mid to late gestation), and thus we speculate that these microbes were similarly transmitted from the mother to the fetus during gestation, suggesting that seeding of the early microbiota may occur earlier than was previously thought.

The authors conclude:

In summary, we undertook the largest study to date … to analyze both the composition and function of the neonatal and infant microbiota with paired maternal–infant subjects across multiple body sites. We observed that by 6 weeks of age, the microbial community structure and function had significantly expanded and diversified. We further demonstrated that there was no discernable effect of the cesarean mode of delivery on the early microbiota beyond the immediate neonatal period (and never inclusive of that in the meconium or stool) …

In other words, C-sections do not change the infant gut microbiome.

51 Responses to “No, cesarean does NOT affect the infant microbiome”

  1. Melaniexxxx
    January 28, 2017 at 10:51 pm #

    I feel so dirty whenever anyone mentions epigenetics now! Ugh!

  2. MaineJen
    January 25, 2017 at 10:53 am #

    Bless these researchers.

  3. Heidi_storage
    January 25, 2017 at 8:51 am #

    I screwed up my sons’ biomes in other ways–intrapartum antibiotics, prelacteal formula. I’m a baaaaad mother because I wanted to avoid trivial things like early-onset Group B strep sepsis and dehydration/jaundice.

  4. Are you nuts
    January 24, 2017 at 3:48 pm #

    I’m a finance person, not a science or medical person so excuse the dumb question. Isn’t 81 participants still a pretty small study? Obviously leaps and bounds better than 10… but still seems very small.

    • fiftyfifty1
      January 24, 2017 at 5:11 pm #

      Sample size really depends on what you are looking for. If it’s a study looking for a rare outcome (e.g. the development of a certain cancer) you may need thousands. But to ask a question like “do the sites grow the same bacteria”, 81 is very reasonable.

      • The Bofa on the Sofa
        January 24, 2017 at 6:46 pm #

        Yeah, if you need more than 80 subjects to find differences in the bacteria than either the difference is pretty small or there are lots of variety already.

      • LAWG
        May 3, 2017 at 7:47 pm #

        Au contraire. Sample size is extremely important and determines how likely the results will match the actual population.

        Sample size isn’t arbitrary.

        • fiftyfifty1
          May 4, 2017 at 5:31 pm #

          So what are you saying? You don’t agree with their P values? Ok then, tell us why they did their statistical analysis wrong and show us what they need to do different.

  5. New Mom
    January 24, 2017 at 2:23 pm #

    How to sell bullshit:

    1. Invent problem to create hysteria over said problem.

    2. Present product or industry as miracle solution.

    3. Make shit tons of money off of gullible people.

    This works for selling all kinds of bullshit. Ahem *WholeFoods*

    • The Bofa on the Sofa
      January 24, 2017 at 3:01 pm #

      Leonard: “You don’t go into science for the money.”
      Bernadette: “Speak for yourself. Last month my company both invented and cured restless eye syndrome. Ka-ching, ya blinky chumps!”

      (I can’t believe I can’t find a video clip of that0

  6. Helen
    January 24, 2017 at 2:06 pm #

    I would like to see — because I’m curious — a study comparing the gut biomes of babies adopted at birth to the gut biomes of babies with their biological mothers, with sampling taken at birth, six weeks, six months, one year, and two years. My hypothesis is that while the babies with their biological parents will have a closer match to their parents biomes at birth and six weeks, at two years both sets will be equally close to their parents biomes.

    • mabelcruet
      January 24, 2017 at 2:18 pm #

      Not quite an answer, but I think there is data to suggest that the children of a parent infected with Helicobacter pylori are more likely to test positive for it themselves. So that bug definitely gets transmitted (probably via faecal contamination)

  7. Erin
    January 24, 2017 at 1:42 pm #

    Slightly off topic

    One of my friends is now pregnant. She too had a previous section and has just had her first Consultant appointment. Apparently the form for discussing the pros/cons of a vbac cites:

    “Increased maternal satisfaction” as pro reason.

    Of course if your baby ends up with HiE or you get a 4th degree tear your satisfaction may vary as happened to at least 2 women I know during their “successful” vbacs.

    Seriously glad I refused to go over the form and cancelled my “birth options” clinic appointment.

    • CSN0116
      January 24, 2017 at 2:19 pm #

      My first VBAC recovery hurt worse and took longer than my two prior cesareans combined, hands down. Satisfaction, my ass. How truly fucked up its all become.

      • Allie
        January 25, 2017 at 1:34 am #

        My ass was definitely not satisfied after my vaginal delivery. I was incontinent for number 2, which I didn’t even know was a thing before having a baby, for 6 weeks after she was born. I desperately tried not to go and when it insisted on coming out anyway, I was in so much pain I had to poop in the shower with hot water running over my parts. Sorry for the TMI, but why on earth women are supposed to be okay with sacrificing their bodily function control to “achieve” vaginal birth is beyond me. Still incontinent for number 1 four years later, BTW – in case you were curious : )

        • Who?
          January 25, 2017 at 5:34 am #

          That’s just miserable, I’m sorry to hear it. I have a sneaking suspicion that there are a lot more women in your situation than we really know about.

          • January 25, 2017 at 6:11 am #

            I KNOW there are, after a 45+ year career seeing women who have been brainwashed into believing this is the “price” for having children. There are also a lot of women who experience pain, loss of sensation, and just become terrified of having sex.

          • guest
            January 25, 2017 at 10:04 am #

            I had 2 “easy, uncomplicated” vaginal deliveries both with tears so small it was my choice whether to stitch them or not. The 2nd delivery required 6 months of physical therapy to walk and sit without pain and both deliveries ruined our sex life. The stars must all align just so for intercourse to feel good and after the second, what used to feel good is now painful so my partner and I both had to relearn everything. I always recommend C-section to people who are on the fence. It’s been 3 years since my last delivery so I’m not expecting things to improve much more. My sex drive is totally gone which I attribute to there always being pain when we have sex. Hard to get in the mood when you know it’s not going to be fun. I am very vocal about this in real life, which usually garners me dirty looks, but I don’t care!

          • Erin
            January 25, 2017 at 12:27 pm #

            That’s what my MiL says. She had a fairly horrific time with her eldest (lots and lots of stitches) but she says the first thing she told my FiL after the birth was “get a mistress”.

        • Heidi_storage
          January 25, 2017 at 8:53 am #

          You know, this should be talked about more often. Sorry for your bad experience.

          • The Bofa on the Sofa
            January 25, 2017 at 12:39 pm #

            I have mentioned, I think the increase in the visibility of things like Poise pads shows that it IS being recognized more. I think this is a good start to that discussion of what causes it.

        • sdsures
          January 25, 2017 at 11:11 am #

          I’m so sorry.

          I have both #1 and #2 incontinence for non-childbirth reasons. My GP gave me some pills that helps calm down bladder spasms, but there’s nothing he could do for the #2. I begged him for incontinence pads, but they are only available in hospitals; GPs have no access to them; he was very sympathetic though. My husband cleans up the messes and we bought some of those surgical masks with earloops.

          • fiftyfifty1
            January 25, 2017 at 12:02 pm #

            Pro tip that probably does not apply to you, but may apply to other people you meet with #2 incontinence: If the incontinence started or worsened after having gallbladder surgery, the fix is daily low dose cholestyramine. Patients tell me it is life changing.

          • sdsures
            January 28, 2017 at 4:31 pm #

            Yeah, I still have my gall bladder, but thanks anyway!

          • Dr Kitty
            January 29, 2017 at 4:23 pm #

            I don’t prescribe or supply continence products but I refer to my local community continence team, who do.

            It’s a nurse led service and as well as supplying pads they teach intermittent self catheterisation for urinary incontinence and Peristeen anal irrigation for faecal incontinence if appropriate.

            Is there a service like that where you are?

          • sdsures
            February 4, 2017 at 1:36 pm #

            I can certainly ask! Thanks for the idea!

        • moto_librarian
          January 25, 2017 at 1:26 pm #

          I’m so sorry. I was able to fix urinary stress incontinence in physiotherapy, but the bowel issues require surgery. I am fortunate in that I have only had fecal incontinence a handful of times, but the urgency problem is extremely unpleasant. Often, I will make a trip to the restroom to urinate, sit down, and realize only then that I need to have a bowel movement. I cannot have one without splinting, which is also unpleasant. I’m hoping that an interstim device will help with the urgency and sensation, but the splinting will continue until I have a rectocele repair, which requires 8 weeks off of work.

    • Bugsy
      January 24, 2017 at 2:51 pm #

      One of my friends just had her first VBAC on January 1. It was unintended, as the baby came super fast a week earlier than the scheduled C-section.

      My friend has been in misery ever since. She tore badly, and said recovery from her c-section was a lot easier. I feel really bad for her; she has been struggling even to sit down since the VBAC.

      • Jen
        January 24, 2017 at 6:17 pm #

        That’s terrifying. It reminds me of the article on this site a week ago or so, about the woman who as scheduled for a section, but she went into labor a week early so the hospital forced her, against her wishes, to labor for twelve hours. Then they did an emergency section and, in their haste, left in part of the placenta, so she died.

        It’s horrifying to think that though I can schedule a maternal-request section for the first day of my thirty-ninth week, if I go into labor any earlier than that I could find myself in the hospital, in agonizing labor pain, begging “Baby Friendly” doctors and nurses to do the section, while they smirk and tell me I have to do it “the right way.”

        • January 25, 2017 at 6:05 am #

          I’ve got to note that my daughter’s ERCS went off like a dream, no arguments, no attempts to bully her into anything. It was, however, C/S #3, and even though the head was well-engaged, no one in their right mind would want to risk rupture. The baby nursery was most supportive, offering Similac until her milk came in (both previous children were fed with EBM in a bottle because she has badly inverted nipples). I had been fairly anxious that, since Hadassah has such close links with the US that they would have bought into all the lactivist, etc. woo. If the hospital was BFHI I was ready for all-out war.

        • sdsures
          January 25, 2017 at 11:03 am #

          That’s awful!

      • StephanieA
        January 26, 2017 at 11:45 am #

        I just had a friend who had her first section with her second baby. Her first delivery resulted in shoulder dystocia, bilateral clavicle fractures for baby, and a third degree tear for mom. She was traumatized and never wanted another vaginal birth. There were still people questioning why she didn’t want to try again.

    • The Bofa on the Sofa
      January 24, 2017 at 2:56 pm #

      Maternal satisfaction? My wife wanted nothing to do with a VBAC. She was far more satisfied in having the repeat CS.

      How can maternal satisfaction be anything other than “you got what you wanted”?

      • sdsures
        January 25, 2017 at 11:02 am #

        Oh. but it’s the EXPERIENCE!

        • The Bofa on the Sofa
          January 25, 2017 at 12:37 pm #

          My wife had absolutely NO interest in experiencing labor.

    • Dr Kitty
      January 24, 2017 at 3:20 pm #

      It doesn’t actually matter what the list of general reasons are.
      It is up to the patient to weigh them for herself and decide what she wants to do. What might be a pro for someone might be a con for someone else.

      They tried to pull that one on me.
      I said “a VBAC would be a completely unacceptable outcome to me and should I go into labour before my scheduled CS I will not consent to any intrapartum examinations or interventions designed to facilitate a VBAC”.

      If you think a CS is a “failure” and VB is a “success” then obviously, you’ll find VBAC to be a more satisfactory outcome.

      If you see VBAC as an undesirable outcome, in and of itself, then no, you won’t.

      • Erin
        January 25, 2017 at 7:29 am #

        I think it just annoyed me because it’s so subjective. Saying the chance of rupture is x is one thing but “satisfaction” is so personal. Plus it also links into the whole “normal” is best narrative which I don’t believe is true for everyone and I don’t think it’s an agenda the NHS should be pushing.

        However I’m hormonal, emotional and have spent the last hour reading the comments sections on Brexit on the Guardian and the Daily Mail. I could probably get annoyed by absolutely anything right about now. Also my plug went at the weekend and I’m terrified that this baby has read Ina May Gaskin and thinks he/she gets to decide when they arrive.

        • Empress of the Iguana People
          January 25, 2017 at 8:20 am #

          uh oh. Stay put, kid, until your mother says you can come out!

        • sdsures
          January 25, 2017 at 11:02 am #

          Spawn, please stay put!

        • Empress of the Iguana People
          January 29, 2017 at 7:57 pm #

          How’s it going E?

    • January 24, 2017 at 8:01 pm #

      Pshaw. When my OB and the resident OB each told me that due to the type of incision needed for Spawn’s CS I could never do VBAC, I reacted with visible happiness.

      My family has a history of needing fairly extensive pelvic floor repair in their 40’s and 50’s after having a few uncomplicated vaginal births so I was thrilled to get a “free CS” card.

    • Roadstergal
      January 25, 2017 at 12:40 pm #

      Um, isn’t ‘satisfaction’ the thing that the PATIENT DECIDES UPON HEARING THE LIST OF PROS AND CONS?

      Sorry, feeling shouty today.

    • Merrie
      January 25, 2017 at 1:03 pm #

      I guess if you want a VBAC and you manage to have one, you’ll be more satisfied than if you want a VBAC and either aren’t a good candidate and reluctantly get a RCS, or you try for VBAC and it doesn’t work out and you end up with a RCS. But if you don’t particularly care or don’t want a VBAC, that goes out the window. The assumption seems to be that most moms want VBACs which seems like an unwarranted generalization.

      I have two friends who had scheduled RCSs in the recent past. One didn’t want a VBAC (and she wasn’t a good candidate) and the other didn’t really have strong feelings. They both seem pretty satisfied.

  8. January 24, 2017 at 11:58 am #

    I feel like anyone who is worried about the hypothetical – and now imaginary – changes in an infant’s microbiome due to a C-section needs a firm dose of reality.

    Let me count the obvious ways choosing to try and vaginally deliver my son could have gone wrong:
    1) While waiting for labor to start, HELLP spirals out of control and I suffer a stroke or seizure which could kill one or both of us.
    2) I survive to the start of labor but labor stalls. My platelets have dropped during the lost time requiring general anesthesia instead of an epidural.
    a) Spawn is knocked out from the anesthesia and gets some mild hypoxia while intubation occurs.
    b) I need multiple blood transfusions.
    c) I bleed out and die.
    d) All of the above
    3) During the wait for labor with low platelet counts, the placenta abrupts.
    a) Spawn suffers major hypoxia and blood loss during delivery leading to death or disabilities.
    b) I need multiple blood transfusions.
    c) I bleed out and die.
    d) All of the above
    4) I manage to beat the odds and deliver Spawn vaginally. Too bad he’s breach and ruptures several blood vessels in his brain. That’s worth a grade 2-4 IVH.

    Can you see why caring about the hypothetical, imaginary problems to Spawn’s microbiome is absurd compared to a maimed or dead Mel and Spawn? Especially when an early CS gave me strong, healthy preemie instead of a dangerously compromised little guy.

    After all, the highlight of my day is feeling Spawn do his happy wiggle when he hears my voice or Nico’s voice. Watching him blow air back into his CPAP to set off alarms when he hears his preemie buddy Ace set off his CPAP alarms amazes me. Seeing him smile for the first time caused my heart to melt.

    I can’t see risking any of those simple joys for the theoretical fear of messing up his microbiome.

    • Montserrat Blanco
      January 24, 2017 at 5:42 pm #

      What? You prefer a perfect brain function to the gut microbiome?????? You preemie mums are crazy!!!!!

      I am really glad Spawn is doing great. He amazes me with the CPAP thing.

      Signed: a former preemie mom (just for those that do not know me).

    • PeggySue
      January 24, 2017 at 6:41 pm #

      LOVE the CPAP thing. Smart little Spawn!

      • sdsures
        January 25, 2017 at 11:18 am #

        Already showing his competitive nature.

        I like his spirit! #JurassicWorld

    • sdsures
      January 25, 2017 at 11:15 am #

      *hugs Spawn and preemie fistbumps* He didn’t have a brain bleed, did he? Or was that one of the hypotheticals? Asking because I was a 28-weeker and have hydrocephalus (have 2 shunts but both are disconnected because the hydrocephalus arrested in 2006). I don’t know what my brain bleed degree was. My first shunt was planed when I was five months old.

  9. fiftyfifty1
    January 24, 2017 at 11:58 am #

    Culture the sites directly?! But why? Couldn’t Dr. Aagaard have found a way to use the Add Health dataset to extrapolate back the results?

    • January 24, 2017 at 12:08 pm #


      You could re-contact every person in the data set and ask them how they feel about their microbiota by site is doing functionally. Ask them if they were born by CS or vaginally. You could then follow up with questions about how they think their microbiota by site has affected their life. Once you’ve gotten that far, ask them how they think their perceptions of their microbiota by site has affected their life.

      Throw out the data from the first three questions since they are completely useless and use the last one to do actual qualitative research on how people’s perceptions of new topics affects their view of past events.

      Yeah, I know that doesn’t answer the question about microbiome and delivery type, but that’s not a good question for an interview series. It’s a great question for someone who can swab babies over time. My question is better – although could use some refining – for an interview series.

  10. Taysha
    January 24, 2017 at 11:22 am #

    I love the smell of well-controlled science in the morning.

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