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A while ago I posted the results of studies showing differences in infant  microbiomes (community of microbes) depending on whether the babies were delivered vaginally or by C-section, and also that "vaginal seeding" may eliminate some of these differences. [C-section babies also have a higher incidence of some health issues, such as allergies, asthma, etc.] Well....that research generated a lot of controversy both for and against, and resulted in many women requesting that "vaginal seeding" be done to their babies after they were delivered by C-section. Even the noted microbiome researcher Rob Knight publicly admitted that the procedure was done to his baby after his partner received a C-section.

Vaginal seeding is the process of swabbing the bodies of C-section babies (including the mouth and nose) with a gauze pad containing the vaginal fluids from their mothers in the minutes after birth - so that the baby is exposed to the same maternal microbes as a baby born vaginally (because mothers transmit microbes to the baby as it moves through the birth canal). Initial research showed this made the microbiomes of the C-section babies look a lot like vaginally born babies, especially their skin and oral microbiomes, but whether these differences persist after a few months is unclear.

Now the American College of Obstetrics and Gynecology (ACOG) has come out with a position paper that vaginal seeding should not be done to babies, except as part of an official clinical trial. Their main opposition to the procedure is fear of transmitting pathogenic bacteria or viruses (e.g. group B streptococci, and STDs). The main reasons in support of doing the  vaginal seeding procedure is the body of research finding differences among C-section and vaginally delivered babies (allergies, asthma, etc.), and the concern that at least some of this may be due to lack of  exposure to maternal vaginal microbes during delivery. Instead, ACOG suggests breastfeeding the baby to transmit maternal microbes to the baby to "seed the gut". And if "a patient insists on performing the procedure herself, ACOG recommends ob-gyns have a documented discussion of the potential risks".

As can be expected, there is an outcry and rejection by some (many?) of the ACOG position paper. At least the ACOG paper acknowledges that every woman can make her own decision regarding this issue, even though they may not support it. And absolutely everyone agrees that more research is needed. From Ars Technica:

Doctors warn new parents: Step away from the vaginal fluid swabs

To slather, or not to slather—that is the question that has been roiling doctors, scientists, and new parents recently. And a new ruling by a doctor’s group stands to muck up the debate further. Amid the birth of microbiome research, some scientists have advocated for smearing bacteria-laden vaginal secretions on any newborns who missed out—namely those born via Caesarian section. Scientists keenly hypothesize that such a gooey glaze can “seed” a more-or-less sterile infant with life-long microbial companions. These wee chums may help train an infant's immune system and dodge issues like allergies and asthma later in life. Several studies have indeed found correlations between C-section deliveries and higher risks of those conditions.

In the latest turn to the controversy, the American College of Obstetricians and Gynecologists’ (ACOG) Committee on Obstetric Practice issued a November opinion firmly wiping up the slimy idea. In its opinion, the committee said it: “…does not recommend or encourage vaginal seeding outside of the context of an institutional review board-approved research protocol, and it is recommended that vaginal seeding otherwise not be performed until adequate data regarding the safety and benefit of the process become available.”

The few studies we do have on infant microbiomes provide no clear answers on the significance of an early “seeding” for health. A 2016 review looking at the patterns of microbial communities in the guts of infants in their first year found that C-section babies did show differences in the first three months. However, those differences disappeared by six months. Similarly, a small study of 18 babies also published last year found that vaginal seeding could eliminate microbial differences between vaginally and C-section delivered babies. But the study only looked at the infants' microbiomes in that first month, and the health effects—if any—are unknown.

The most concerning thing about vaginal seeding, the committee argues, is the potential for transmitting pathogens, such as herpes simplex virus, human papilloma virus (HPV), group B streptococci, and Neisseria gonorrhea. .... If a woman insists on the seeding, the committee recommended she be thoroughly tested and informed of the risks—as well as discouraged.

 A new study has summarized what we know about fungi that live in and on babies - and yes, we all have fungi both on and within us. It's called the mycobiome. In healthy individuals all the microbes (bacteria, viruses, fungi, etc) live in balanced microbial communities, but the communities can become "out of whack" (dysbiosis) for various reasons, and microbes that formerly co-existed peacefully can multiply and become problematic. Or other pathogenic microbes can enter the community, and the person becomes ill.

In healthy adults, approximately 0.1% of the microbes in the adult intestine are fungi, from approximately 60 unique species. Most species live peacefully in the body, and some fungi even have health benefits (e.g., Saccharomyces boulardii prevents gastrointestinal disease). Some fungi that many view as no good and involved with diseases (e.g., Candida and Aspergillus) are also found normally in healthy people. Studies show that normally infants also have fungi. Some fungi that live in the baby's gut (thus detected in fecal samples) are Candida (including C. albicans), Saccharomyces, and Cladosporium. The researchers (from the Univ. of Minnesota) point out that the study of fungi in babies has been neglected and much more research needs to be done.

Whether an infant is born vaginally or through cesarean delivery (C-section) affects the composition of the baby's bacterial communities over the first 6 months of life. And similarly, it looks like when the baby passes through the birth canal, the baby is exposed to the mother's mycobiota (fungi), and then these colonize in the infant's gut. Babies born by C-section have some differences in their fungi, such as being colonized by the mother's skin fungi (such as Malassezia fungi). After birth, a parent kissing and touching the baby (skin to skin contact) also transmits microbes, including fungi, to the baby.

Whether a baby drinks breast milk or formula strongly affects the infant's bacteria within the GI tract. For example, breast-fed infants have more Bifidobacteria and Labctobacilli in their gut compared to formula-fed infants. One study found about 700 species of bacteria in breast milk. Thus, scientists think that human breast milk also influences the infant gut mycobiota (fungi), although this research still needs to be done.

Whether a baby is born prematurely or at term (gestational age) is important. For infants born prematurely, intestinal fungi can cause big problems, such as an overgrowth in the gut. For example, 10% of premature babies get invasive, systemic Candidiasis, and about 20% die. Some factors leading to this are: a naïve immune system, bacterial communities out of whack (dysbiosis) due to antibiotic exposure, and use of parenteral nutrition (because this doesn't contain all the microbes from the mother that are in breast milk). In premature infants, beneficial fungi such as S. boulardii, may help to regulate the growth of opportunistic fungal colonizers such as Candida.

it is clear that whether the baby received antibiotics is important. The bacterial community of infants is altered by exposure to antibiotics in both term and preterm infants. For example, in a lengthy study over the first 3 years of life, infants receiving multiple courses of antibiotics had bacterial community changes following antibiotics and their gut bacterial microbiome became less diverse (fewer species). Although most commonly used antibiotics do not directly act on fungi, anti-bacterial antibiotic exposure is associated with alterations to the mycobiota (fungi) -  such as increased rates of fungal colonization, fungal overgrowth, and changes in the fungal community. For ex., premature infants exposed to cephalosporin antibiotics have an increased risk for invasive Candidiasis (a fungal overgrowth).

Out of whack (dysbiotic) microbial communities, incuding fungi, are found in IBD (intestinal bowel diseases) in children. They have more of some fungi (e.g. Pichia jadinii and Candida parapsilosis) and less of Cladosporium cladosporiodes, and an overall decrease in fungal diversity in the gut, as compared to healthy children.

From BMC Medicine: Infant fungal communities: current knowledge and research opportunities

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research....

 The mother is an important source of the first microbiome for infants by "seeding" the baby's microbiome - from the vaginal birth and then breastfeeding. However, research finds that infants born by C-section acquire bacteria commonly found on skin (Staphylococcus, Corynebacterium, and Propionibacterium) rather than the bacteria acquired during a vaginal birth.

This study examined the source of the skin-type bacteria found on C-section babies. The researchers analyzed the dust from operating rooms (which they collected right after C-sections) and found that it contains deposits of human skin bacteria and human skin flakes. The researchers point out that "Humans shed up to 37 million bacterial genomes into the environment per hour." Operating rooms are occupied by humans, lack natural ventilation, and even though they are regularly cleaned, the humans using the operating rooms shed bacteria and skin flakes. From Microbiome:

The first microbial environment of infants born by C-section: the operating room microbes

Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be seeding C-section born infants. To test this hypothesis, we sampled 11 sites in four operating rooms from three hospitals in two cities. Following a C-section procedure, we swabbed OR floors, walls, ventilation grids, armrests, and lamps....The bacterial content of OR (operating room) dust corresponded to human skin bacteria, with dominance of Staphylococcus and Corynebacterium. Diversity of bacteria was the highest in the ventilation grids and walls but was also present on top of the surgery lamps. 

We conclude that the dust from ORs, collected right after a C-section procedure, contains deposits of human skin bacteria. The OR microbiota is the first environment for C-section newborns, and OR microbes might be seeding the microbiome in these babies. 

In the present study, we used 16S rRNA gene sequencing to show that OR dust, collected right after a C-section procedure, contains bacteria similar to human skin microbiota. Previous studies using culture-dependent methods also showed that over 85 % of air samples from ORs had skin-like bacteria which were mostly coagulase-negative staphylococci and Corynebacterium. These airborne skin-bacteria could be from individuals present during C-section but could also be shed by cleaning personnel between operations.

In our study, 30 % of samples failed to yield sufficient DNA sequences to be analyzed. While there are no published data on the microbiota in operating rooms using 16S rRNA gene sequencing, very few bacteria (average 3.3–3.5 CFU/10 cm2) were detected in ORs after regular decontamination using standard culturing methods, consistent with the low sequence numbers in our study.

In addition, we found that the microbiota of OR samples was more similar to human skin microbiota than oral microbiota and that OR dust contains deposits of human skin flakes. These results reveal that while the use of surgical masks has limited effectiveness at curtailing oral microbial shedding, skin flakes from individuals present during C-section and/or from cleaning personnel between operations could be a more influential factor contributing to the structure of OR microbiota.

Our SourceTracker analysis results suggest that the OR microbes could play a role in seeding infants born by C-section. C-section born infants, in particular, may be solely receiving this inoculum, while vaginally born infants have exposure to vaginal bacteria. The results of these further studies could be relevant to the possible effects on the priming of the immune system by skin bacteria from environmental sources as the primordial inoculum seeding the infant microbiome. This might be relevant to the increased risk of immune diseases observed in C-section born infants.

Currently, during birth there are many potential disruptions to the healthy development of the infant's microbial ecosystem. Some practices to be concerned about: the use of antibiotics during pregnancy and during delivery, c-sections, newborns routinely given antibiotics, and then bottle feeding instead of breastfeeding. Sometimes one or more of these practices are medically necessary, but currently they are being done much too frequently and casually. In these ways we are conducting an experiment on every baby's microbial ecosystem with unknown long-term consequences. The following excerpts from Dr.Martin Blaser's popular 2014 book Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, even though written a year ago, are a nice summary of these issues. From Wired:

The Way You’re Born Can Mess With the Microbes You Need to Survive

THROUGHOUT THE ANIMAL kingdom, mothers transfer microbes to their young while giving birth....And for millennia, mammalian babies have acquired founding populations of microbes by passing through their mothers’ vagina. This microbial handoff is also a critical aspect of infant health in humans. Today it is in peril.

Microbes play a hidden role in the course of every pregnancy. During the first trimester, certain species of bacteria become overrepresented while others become less common. By the third trimester, just before the baby is born, even greater shifts occur. These changes, involving scores of species, are not random. The compositions change in the same direction across the dozens of women who have been studied.... Women of reproductive age carry bacteria, primarily lactobacilli, which make the vaginal canal more acidic. This environment provides a hardy defense against dangerous bacteria that are sensitive to acid. Lactobacilli also have evolved a potent arsenal of molecules that inhibit or kill other bacteria.

Whether the birth is fast or slow, the formerly germ-free baby soon comes into contact with the lactobacilli. The baby’s skin is a sponge, taking up the vaginal microbes rubbing against it. The first fluids the baby sucks in contain mom’s microbes, including some fecal matter.

Once born, the baby instinctively reaches his mouth, now full of lactobacilli, toward his mother’s nipple and begins to suck. The birth process introduces lactobacilli to the first milk that goes into the baby. This interaction could not be more perfect. Lactobacilli and other lactic acid–producing bacteria break down lactose, the major sugar in milk, to make energy. The baby’s first food is a form of milk called colostrum, which contains protective antibodies. The choreography of actions involving vagina, baby, mouth, nipple, and milk ensures that the founding bacteria in the baby’s intestinal tract include species that can digest milk for the baby.

Breast milk, when it comes in a few days later, contains carbohydrates, called oligosaccharides, that babies cannot digest. But specific bacteria such as Bifidobacterium infantis, another foundational species in healthy babies, can eat the oligosaccharides. The breast milk is constituted to give favored bacteria a head start against competing bacteria.

Cesarian delivery is a largely unrecognized threat to the microbial handoff from mother to child. Instead of traveling down the birth canal picking up lactobacilli, the baby is surgically extracted from the womb through an incision in the abdominal wall....For all of these reasons, U.S. C-section rates increased from fewer than one in five births in 1996 to one in three births in 2011—a 50 percent increase.

The founding populations of microbes found on C-section infants are not those selected by hundreds of thousands of years of human evolution. A few years ago in Puerto Ayacucho, Venezuela, my wife, Gloria, conducted the first study of its kind to test whether the microbes found on newborn babies delivered vaginally or by C-section varied in any way....The mouths, skin, and first bowel movements of babies born vaginally were populated by their mother’s vaginal microbes: Lactobacillus, Prevotella, or Sneathia species. Those born by C-section harbored bacterial communities found on skin, dominated by Staphylococcus, Corynebacterium, and Propionibacterium.

In other words, their founding microbes bore no relationship to their mother’s vagina or any vagina. At all the sites—mouth, skin, gut—their microbes resembled the pattern on human skin and organisms floating in the air in the surgery room. They were not colonized by their mother’s lactobacilli. The fancy names of these bacteria don’t matter as much as the notion that the founding populations of microbes found on C-section infants are not those selected by hundreds of thousands of years of human evolution or even longer.

Another threat to a baby’s newly acquired resident microbes involves antibiotics given to the mother. Most doctors consider it safe to prescribe penicillins for all sorts of mild infections in pregnancy—coughs, sore throats, urinary tract infections. Sometimes when doctors think that the mother has a viral infection they also give antibiotics just in case it is actually a bacterial infection.

Then comes the birth itself. Women in labor routinely get antibiotics to ward off infection after a C-section....Antibiotics are broad in their effects, not targeted....The problem, of course, is that we know antibiotics are broad in their effects, not targeted. While the antibiotic kills Group B strep, it also kills other often-friendly bacteria, thus selecting for resistant ones. This practice is altering the composition of the mother’s microbes in all compartments of her body just before the intergenerational transfer is slated to begin.

The baby also is affected in similar unintended ways. Any antibiotic that gets into the bloodstream of the fetus or into the mother’s milk will inevitably influence the composition of the baby’s resident microbes, but we are only beginning to understand what this means.

Finally, the babies are directly exposed. Most parents are not aware that all American-born babies today are given an antibiotic immediately after birth. The reason is that many years ago, before antibiotics, women who unknowingly had gonorrhea would pass the infection to their babies, giving the newborns terrible eye infections that could cause blindness...The dose is low but is likely affecting the composition of the infant’s resident microbes just when the founding populations are developing. We should be able to develop a better way to screen, so we can target those babies at the highest risk, perhaps a few hundred among the millions of births a year.

Although babies are born into a world replete with diverse bacteria, the ones that colonize them are not accidental. These first microbes colonizing the newborn begin a dynamic process. We are born with innate immunity, a collection of proteins, cells, detergents, and junctions that guard our surfaces based on recognition of structures that are widely shared among classes of microbes. In contrast, we must develop adaptive immunity that will clearly distinguish self from non-self. Our early-life microbes are the first teachers in this process, instructing the developing immune system about what is dangerous and what is not.

A newborn infant, seconds after delivery. Amniotic fluid glistens on the child's skin.  Credit: Wikipedia, Ernest F