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After my January 9, 2015 post I was asked more about the microbial differences in babies who had been born by cesarean vs vaginal deliveries. What could be done about this? Should this be of concern when c-section rates in some places are approaching 50% of all births? Well,some researchers are concerned, including Dr. Dominguez-Bello, who is doing ground-breaking research in this area. She is doing a long-term study in which babies born by cesarean section are immediately swabbed with a gauze cloth laced with the mother's vaginal fluids and resident microbes. Several (but not all) articles that I looked at said that the gauze is a "saline-soaked gauze". Summary of the method:1) Incubate gauze in mother's vagina for 1 hour 2) Extract gauze before C-section  3) Expose newborn to the vaginal gauze (Mouth first, then face, then rest of body). If for some medical reason they don’t (and there is a C-section), then this is a restoring intervention. Note that Dr. Dominguez-Bello always first checks to make sure the mother is HIV-negative and strep-B negative, and showing no signs of a STD. The basic premise is that babies should have crossed the mother's birth canal to be "seeded" with the mother's microbes, but if for some medical reason they don’t (and there is a C-section), then this is a (somewhat) restoring intervention. From Feb. 2014 New York Academy of Sciences:

Hats Off to Bacteria!

Why are bacteria in the body? What do we, and the bacteria, gain from this arrangement? And who's in charge? "There is a dialogue," Dominguez-Bello said, "sometimes a fight, sometimes a good dialogue. We have evolved with them. The first form of life on Earth was bacteria. Whatever came after had to deal with bacteria, cope with bacteria, associate with bacteria ... 

Human microbiota perform many essential functions, such as producing vitamin B12, digesting plant fibers, helping to train our immune system to distinguish self-molecules from nonself-molecules, and helping to fight off pathogens. It is increasingly clear that we cannot accomplish these functions alone, and in exchange the bacteria receive food and a warm, safe home. [Martin]Blaser noted that some species are "obligate symbionts," meaning that our bodies are the only environment in which they can survive. If these strains are killed with antibiotics before they are transmitted to other people, especially to the next generation, the bacteria could disappear forever.

One of the hallmarks of mammals is birth through a birth canal. The birth canal is rife with bacteria; as babies travel down it, they are inoculated with lactic acid bacteria that accumulate during the last trimester of pregnancy. These bacteria are the initial educators of the baby's naïve immune system, which must learn to "tolerate our microbiota and attack microbes." Babies born by cesarean section—approximately 50% of babies in New York City—miss out on this natural initial exposure and instead are first inoculated with bacteria floating around the operating room. These bacteria are comprised predominantly of human skin bacteria not from the mother but from the doctors, nurses, and previous patients in the room. We do not yet know the health consequences of this alternate initial exposure. "[Cesarean sections] are breaking a natural law," Dominguez-Bello said, "and there are consequences."... Importantly, only babies born via elective C-section miss out on the inoculum; those born by emergency C-section, after their mother's water has broken, are exposed to the bacteria in the birth canal.

"What antibiotics have in common with C-sections is ... abuse," Dominguez-Bello said. Both are medically necessary in some cases, but overused..." While both C-sections and antibiotics are valuable tools, we can no longer pretend that they do not have some detrimental outcomes. Research has found the colon microbiome of Americans is half as diverse as that of hunter-gatherer populations, such as Amerindians in the Amazon jungle and African populations living a traditional lifestyle. There is also less diversity in Americans' skin and mouth microbiomes. Thus antibiotics, while necessary in emergencies, should not be used in every infection. Some species of bacteria never recover after an antibiotic exposure, and others can only colonize us during a specific time in our lives; if we miss this chance, we can never recover it. Current antibiotics are "like atomic bombs," Dominguez-Bello said, obliterating every bug they encounter. 

Dominguez-Bello is conducting a study in Puerto Rico in which babies born via C-section are immediately swabbed with their mother's vaginal secretions; these babies will be followed for years, and compared to those born vaginally and those born via C-section without swabbing. If significant differences between the babies are detected, she hopes that swabbing will one day become mainstream practice, or that more women will learn about the importance of the human microbiome and opt for vaginal birth when possible.

Excerpts from an interview with Dr. Domingues-Bello.Her study is now going on in Puerto Rico, Chile, Bolivia, and soon in Ecuador, Stockholm, and USA. From the June 2014 Common Health:

Research: Could Birth-Canal Bacteria Help C-Section Babies?

The usual drill is to wipe the effluvia of birth off of newborn babies, cleaning them up and readying them for snuggling. But in a fascinating departure, researchers have begun to experiment with the opposite: collecting birth-canal bacteria and wiping them onto babies after birth. Why in the world? For good reason: to explore whether it might help babies delivered by C-section to restore some of the vaginal bacteria that they would have been exposed to if they’d gone through the birth canal.Why do that? On the theory that altered bacterial populations could help explain why C-section babies tend to have higher odds of asthma, allergies, obesity and other health risks.

Dr. Maria Gloria Dominguez-Bello, an associate professor in the Human Microbiome Program at the NYU School of Medicine, presented some preliminary results on that research at a recent conference of the American Society for Microbiology here in Boston. Those initial findings suggest that indeed, using gauze to gather a mother’s birth-canal bacteria and then impart them to babies born by C-section does make those babies’ bacterial populations more closely resemble vaginally born babies — though only partially.

Many questions remain. But the research sounded so intriguing — and the intervention so simple, if it gains medical approval — that I asked Dr. Dominguez-Bello to discuss it. Our conversation, edited: Your poster reports that there were six vaginal births, seven C-sections and four C-sections in which the babies also received the ‘inoculum’ of vaginal bacteria. But it wasn’t clear to me: To what extent did the mothers’ bacteria restore a more normal balance of bacteria in the C-section babies? A little or a lot?

When we analyzed the sharing — how many microbes any site of the baby’s body share with their mom’s vagina — we doubled the number of bacteria that the C-section babies were exposed to. But the vaginal process was six times as much. So the vaginal delivery still exposes the baby to a lot more... So those C-section babies still don’t have the full exposure of the vaginal babies.

That’s logical because during labor, the baby is rubbing against the mucosa of the birth canal for a long time and bacteria start growing even before the baby is out — growing and colonizing the baby during birth. In half an hour, you get multiplication of bacteria. If the baby gets one cell, an hour later the baby has probably four of those cells and five hours later, it’s exponential. Also, C-sections involve antibiotics. There is no C-section without antibiotics, and we don’t know what the effect is of that gram of penicillin. If it’s good enough to kill strep B, I’m sure it’s killing a lot more than that community of bacteria.

[Interviewer] If your research pans out, using this gauze technique for C-section babies would seem to be such an easy intervention. I imagine there might already be women saying, ‘I want to do that.’ Possibly even, ‘I want to schedule a C-section and do that.’ What would you say to them?

I would say labor is a very complex process and labor is far more than inoculating the baby. And it’s a process that we don’t fully understandwhat’s its adaptive value, why is it important? There is a lot of stress in labor and some people think that stress is healthy for both the mother and the baby. It’s a long process, so during all those hours, physiological changes occur in the mom and the baby. So I think we have not studied labor enough and tried to understand what it is about labor that is healthy.

Plus, with the restoration we did, we do restore the bacteria partially but not completely. And also, the mother’s body prepares to breastfeed, for example — and who knows how many other things — much better after a natural birth than a C-section. A C-section is a sudden interruption of a process before the process finishes. So the body of the mother doesn’t even know that the baby’s out. It takes a while for the body to realize, ‘Oh, there is no baby.’ 

The basic premise is that babies that should have crossed the birth canal, and for no medical reason they don’t, then this is a restoring intervention. But we still, as with any vaginal delivery, we check for strep B; I would make sure the mother is HIV-negative, strep-B negative, and has an acid, lactobacillus-dominated vagina.So far it’s not a medical practice. It hasn’t been accepted as a standard practice. ..So I don’t know how much it will be regulated, if at all. Some people are doing it more or less individually, independently, because they believe it will be good for the baby.

Another research result from the American Gut Project, an amazing crowdsourced project. While differences were found in the fecal microbiome (microbial community) of adults born by cesarean section vs vaginal delivery, it is unknown whether this has any possible effects on diseases or risks of diseases during adulthood. This study is online as of 8 November 2014, but still In Press. From EBioMedicine:

Diversity and Composition of the Adult Fecal Microbiome Associated with History of Cesarean Birth or Appendectomy: Analysis of the American Gut Project

Adults born by cesarean section appear to have a distinctly different composition of their fecal microbial population. Whether this distinction was acquired during birth, and whether it affects risk of disease during adulthood, are unknown.

Prenatal and early postnatal exposures and events can affect the entire life course. As one example, cesarean birth has been associated with an increased likelihood of asthma and cardiovascular disease in children (Renz-Polster et al., 2005, Thavagnanam et al., 2008 and Friedemann et al., 2012), hypertension in young adults (Horta et al., 2013), and obesity in both children and adults (Pei et al., 2014, Darmasseelane et al., 2014,Blustein et al., 2013 and Mueller et al., 2014). ... As well summarized by Arrieta and colleagues, several studies have noted differences in the neonatal fecal microbiota by route of delivery (Arrieta et al., 2014). ... More recently, with comprehensive analysis based on next generation sequencing of 16S rRNA genes, Dominguez-Bello and colleagues reported that route of delivery was associated with differences in the composition of the microbial populations that initially colonized the offspring. Notably, neonates who were born vaginally were colonized by vagina-associated bacteria, whereas those born by cesarean section were initially colonized by skin-associated bacteria ( Dominguez-Bello et al., 2010).

Early life alteration of the gut microbiota may have a lasting effect. Trasande et al. observed that exposure to antibiotics up to age 6 months was associated with elevated body mass index (BMI) up to age 7 years (Trasande et al., 2013).

The 16S rRNA V4 region was sequenced by the American Gut Project....Of the 1097 participants, cesarean birth was reported as “yes” by 92, “no” by 948, and missing or uncertain by 57. Likewise, appendectomy was reported as “yes” by 155, “no” by 961, and missing or uncertain by 21.

This analysis was primarily motivated by the observation that the composition of the microbiome of neonates differed significantly between those born vaginally and those born by cesarean section (Arrieta et al., 2014 and Dominguez-Bello et al., 2010). With vaginal delivery, the neonatal microbiome resembled the vaginal microbiome, with high relative abundance of Prevotella and especially Lactobacillus taxa. In contrast, cesarean-delivered neonates had a diverse array of taxa resembling the skin microbial community, including Staphylococcus, Streptococcus, Propionibacterineae, Haemophilus, and Acinetobacter ( Dominguez-Bello et al., 2010). Cesarean-delivered neonates and infants typically have a paucity of Bifidobacterium and Bacteroides species ( Arrieta et al., 2014).

In the current analysis, we observed that the fecal microbiome composition differed in adults who reported that they had been delivered by cesarean section. This suggests that a difference by route of delivery may persist into adulthood. Of the taxa noted to be increased in cesarean-delivered neonates and infants ( Arrieta et al., 2014, Penders et al., 2006 and Dominguez-Bello et al., 2010), only Haemophilus and certain Clostridia genera had elevated abundance in the fecal microbiome of cesarean-delivered adults ( Table 3).