Gut microbiota and c-sections

Mounting evidence shows that the bacterial population of infants’ digestive system, known as gut microbiota, can be influenced by c-sections and formula use. It can no longer be disputed that c-section and formula feeding are both associated with changes to infant microbiota.

I had a c-section. I fed my daughter formula sometimes. So, this made me wonder: Does it matter? What are the consequences of having a different microbiome? This post will focus on c-sections, with one on formula to follow. This is not a formal review or meta-analysis, just my interpretation of a brief review of the literature.

Babies delivered by c-section have different microbiomes than babies delivered vaginally

A 1987 study (1) was the first to show that babies born by c-section have different microbiota than babies born vaginally, measured by the bacteria found in fecal samples shortly after birth. Importantly, there are millions, possibly billions, of different species of bacteria. This initial study found decreased numbers of Bacteroides fragilis (B. fragilis) in babies born by c-section. Follow-up studies found:

  • At 1 month of age, no differences in Bacteroides, but higher numbers of bifidobacteria in vaginally-delivered babies. The same study found no differences in microbiomes at 6 months. (5)
  • At 6 weeks of age, higher numbers of Bacteroides in vaginally-delivered babies (7)
  • At 4 months of age, higher numbers of Shigella and Bacteroides in vaginally-delivered babies (4).
  • At 6 months of age, higher numbers of Bacteroides in vaginally-delivered babies (2).
  • At 7 years of age, higher numbers of C. difficile in vaginally-delivered babies (3)
  • At 7 years age, lower numbers of C. difficile in vaginally-delivered babies (6)

Given that differences in C. difficile were not detected in the studies of younger children, and the existing findings are contradictory, I think it is safe to say that differences in C. difficile are better explained by data artifacts than by mode of delivery. However, the Bacteroides findings have been robustly replicated and seem to hold.

So that brings to mind two questions:

1. How long does this effect persist?

I can’t find any direct investigations of the effect of mode of delivery on microbiota after weaning(except the 2 studies I cited above that are contradictory and do not find differences in Bacteroides), let alone into adulthood. So, the best evidence has to come from a general understanding of the evolution of the microbiome across the lifetime. Is the microbiome stable, persistent, unchanging? Or does it evolve as we go through our lives?

In fact, the microbiome is flexible and adaptive, and changes dramatically over time. By adolescence (13 to 17), a child’s microbiome is no more similar to his/her mother’s than it is to his/her father’s:

“Although biological mothers are in a unique position to transmit an initial inoculum of microbes to their infants during and after birth, our analysis of mothers of teenage US twins showed that their fecal microbiota were no more similar to their children than were those of biological fathers…” (15)

Since, presumably, 0% of the fathers vaginally delivered their children, I think we can infer from this finding that by adolescence, mode of delivery no longer has a detectable effect on the microbiome.

2. Does it matter? What are the consequences of low Bacteroides numbers?

  • Obesity has been associated with a low ratio of Bacteroides to Firmicutes (11, 12)
  • Colon cancer has been associated with high Bacteroides numbers (8, 9), specifically B. fragilis (10)
  • Bacteroides can induce inflammatory bowel disease in susceptible animals (13)

(Credit to [14], review.)

So I would not be quick to say that c-sections cause obesity unless you are equally prepared to claim that vaginal delivery causes colon cancer and inflammatory bowel disease. In both cases, the data are preliminary, and that conclusion is an oversimplification of a complex, evolving system.

Additionally, consider that country of origin has a larger influence on microbiome population than does mode of delivery (7). Which country has the “best” biome? Who knows? What does that even mean? Then how can we say that a baby born by c-section has a worse biome than a vaginally-delivered baby?

Other important confounds:

As I was reading through these studies, I learned that antibiotics are given routinely before/during c-sections as preventive care. That’s what, as a reviewer, I would call a fatal confound. Are changes in Bacteroides populations due to c-sections, or due to antibiotic administration? Would we see similar microbiomes in babies delivered to mothers who had antibiotic administration for other reasons?


I don’t mean to suggest here that c-sections have no consequences for mother or baby, or even for the microbiome. I do think the preponderance of evidence shows that c-sections are associated with changes to the microbiome. I don’t think anyone can categorically say that the microbiome of a c-section baby is worse than the microbiome of anyone else. And if you’re really worried, there are always probiotics.



















Hospital records

I went to the hospital where I had Maya today and got a copy of my medical records. I remembered driving down the same road 5.5 months ago with a huge belly and intermittent contractions. So many things different, so many things the same.

The records are pretty consistent with my memory of events. 

11:51: Admitted to OB triage. Pain 4, BP 113/74, HR 67, FHR 120. Dilated to 4cm, 60% effaced, soft cervix, midposition.

12:11 to 13:43: Walking the halls. At 13:43, pain is a 7. Dilated to 4cm, 75% effaced, -2 station, soft cervix, midposition, bulging waters.

15:11: Vomiting present

15:16: Pain is a 10, BP 132/102, HR 94. Epidural requested. FHR 130.

15:30: IV placed

15:43: Epidural placed

15:53: Pain is a 0. BP 123/65, HR 83.

16:41: AROM ordered

16:50: Dilated to 7cm, 90% effaced, -2 station. Cervix is soft and midposition.

17:44: AROM performed. Dilated to 7cm, 80% effaced, -2 station. Cervix is soft and midposition.

18:18: Dilated to 8cm, 90% effaced, -2 station.

20:32: Dilated to 8.5cm, 90% effaced, 0 station

20:39: Declined pitocin.

22:10: Anterior lip. 100% effaced, 1 station.

23:11: Dilated to 10cm, 100% effaced, 1 station.

23:21: Coached on pushing, practice pushes.

00:36: Pushing

01:01: Oxygen face mask.

01:10: Allow patient to push for 1 hour, if little progress, prepare for c-section.

01:30 Pain scale 5, intermittent, epidural bolus given.

03:05: Transverse per practice push.

03:13: Pushing with little progress. Orders to prep for c-section. Will call MD after OR open.

04:22: Dr. at bedside to evaluate. Pushed with patient. Consents for c-section.

05:06: Delivery

05:08: Methergine IM

05:56: BP 149/74.

06:17: BP 153/72

Afterward my hematocrit levels were so low they ordered a blood transfusion. But I guess eventually they ruled against it.

Anyway, no real surprises. They counted 5 hours and 45 minutes of stage 2 labor and called the OB to do the section in the middle of the night. Pretty hard to argue that any of it was done for their convenience. 


In defense of unnecessary cesareans

I want to defend unnecessary cesareans.

I have a personal stake in this. I had a c-section. I didn’t want it. My baby’s head was turned sideways, facing my right hip (occiput transverse). I had been through 4 weeks of prodromal labor, with painful, productive contractions, followed by 24 hours of active labor. I had an epidural and artificial membrane rupture after about 15 hours labor, but no pitocin. I pushed for 5 hours, before the OB gently explained that I was doing everything right, but she didn’t think vaginal delivery was a possibility.

I held back tears until my husband left my side, and then I sobbed. I sobbed while the anesthesiologist reassured me and I sobbed while the medicine in my IV burned and stung me and I sobbed when my husband came back.

I had been told that I could avoid a c-section if I educated myself:

And if I believed in and trusted myself:

I was educated. I did trust myself. And somehow a c-section was still happening to me. I was terrified of what would happen to my relationship with my baby, and I was so scared of what I expected to be weeks or months of painful recovery:

You know why my c-section was traumatic? Because I felt like it was my fault. Because everything I read about c-sections treated them as something that happens to women who are uneducated and don’t advocate for themselves. Because I had bought into the idea that, if you don’t give birth vaginally, you did something wrong.

I don’t know if my c-section was necessary and I never will. Maybe if I had been somewhere without access to modern medicine, I would have been in labor for a few days, vomiting, in mind-warping pain, increasingly weaker and more exhausted, and eventually her head would have turned and I would have given birth vaginally.

Would that have been better?

Would that have been the way an educated person gives birth?

But I will never know if my c-section was necessary, and that gets to the crux of why I want to defend unnecessary cesareans: because of the gray area. C-sections are a great example of a signal detection problem.

There are some births where c-sections (and other interventions) are clearly unnecessary. There are other births where c-sections (and other interventions) are clearly necessary.
But an uncomfortable percentage of births fall in that gray area in between, where it is simply not possible to tell if the c-section is necessary or not. In that gray area, there are four possible outcomes:

1. True positive: A c-section is necessary and performed
2. True negative: A c-section is not necessary and not performed
3. False positive: A c-section is not necessary, but performed
4. False negative: A c-section is necessary, but not performed

Now, think about the consequences of 3 and 4:

So, obviously, we want to err on the side of more false positives than false negatives.
I worry a great deal that the natural childbirth movement will have the unintended consequence of shifting that signal detection criterion and increasing the false negatives — increasing preventable deaths and permanent injuries.
We need more research and better evidence so we can decrease the size of the gray area, not an arbitrary push to decrease c-sections.
And in the meantime, I wish we could cut c-sections a break. Stop treating c-sections like the worst case scenario and remember that there are a number of outcomes that are quite a bit worse. And until we have perfect signal detection, unnecessary cesareans are actually the better choice, compared to failing to perform a necessary one.