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The Development of the Placental Microbiome Lorraine Salterelli 10/5/2015

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Page 1: Development of the Microbiome in Infants

The Development of the Placental Microbiome

Lorraine Salterelli

10/5/2015

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Abstract

Studies have begun to show the presence of bacteria in not only preterm placental tissues,

but in placental tissues from healthy pregnancies that went to term. This has lead researchers to

rethink the idea of the uterine environment, disputing the idea that embryos develop in sterility.

Using culture-based methods, bacteria were recovered from the non-pregnant uterus, indicating

that infection may occur prior to pregnancy, however, even women positive for bacteria within

the endometrium were found to have full, healthy pregnancies (Andrews et al. 2005). Other

studies were able to detect bacterial DNA among placental tissue from preterm and term

pregnancies in the absence of chorioamnionitis, or inflammation of the fetal membranes. It has

been observed that preterm pregnancies tend to have a greater diversity of bacterial species.

Some have begun to believe that the bacteria initiate the microbiome of the developing

fetus, and tried to characterize the species present in healthy term placentas by comparison of the

bacteria found in term placentas. These bacteria may also play a role in pregnancy. For instance,

one bacteria may alter the tissue structure in such a way as to allow other bacteria to colonize

tissue. Unfortunately, it is still unclear what species are necessary to the microbiome and which

are pathogenic, or whether there are other factors that induce pathogenicity of certain bacteria.

The microbiome of a healthy pregnancy appears to be most similar to that of the oral

microbiome. Much more research will be necessary to determine more about the microbiome,

the factors that influence it, and whether it is beneficial, harmless, or harmful.

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Introduction

Little thought is given to the abilities provided to human physiology by microscopic

organisms. It is well-known that bacteria live in our bodies, but what is not often known are the

important functions these bacteria perform for our benefit. Bacteria have the ability to form

colonies that thrive any place, such as on our skin, nose, mouth, guts, and more recently

discovered, the placenta. These communities throughout the human body are referred to as

microbiomes. Though microscopic, these tiny, one-celled organisms overt a great power over us

to which we tend to forget. They can have positive and negative effects on function of the human

body.

One of the most well-known microbiomes is the intestines, which aids in the ability

digest foods and obtain certain vitamins and minerals. Every person has a unique constitution of

the amount and types of bacteria that inhabit their intestines (Hattori and Taylor 2009). The

consequence of this variation can cause some conditions such as irritable bowel syndrome (Iwase

et al. 2010). It has also been observed that alterations to the gut microbiome can have effects in

other areas of the body such as the central nervous system, and is believed to have an influence

on autism, depression, and eating disorders among other psychiatric disorders (Konkel 2013).

Generally, though, the presence and diversity of bacteria is necessary for optimal health

as it provides functions that our body is unable to perform on its own. The human body has a

high degree of complexity, which makes it surprising that each cell within the human body

contains a similar number of genes to that found in the cells of a less complex species such as the

fruit fly. That is to say, the cells within the human body carry only 20,000 genes, which is distant

from what was expected prior to this discovery. When taking into consideration the additional

genes provided by commensal bacteria, this number is likely greater than 100,000, as these

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bacteria outnumber our own cells 10:1 (Belkaid and Hand 2014). These additional genes provide

functions that our body evolved without, such as the ability to produce necessary vitamins and

breakdown complex food material (Turnbaugh et al. 2007). They also act as a boost for the

immune system through initiation and training it to recognize bacterial antigens (Belkaid and

Hand 2014).

The role of these bacteria is so important that scientists have developed the Human

Microbiome Project (HMP). The goal of HMP is to determine the specific bacteria that constitute

the complete microbiome, as well as how they function to improve or compromise human health

(Turnbaugh et al. 2007). Using an advancement in DNA analysis called metagenomics, scientists

are now able to study bacterial genomes within communities from their natural habitat.

Metagenomics has opened doors to ways of studying bacteria that are unable to be cultured. For

instance, many resident species of the gut were not identified previously due to strict

environmental conditions that are not reproducible in a lab setting. Now these species can be

identified from samples taken from the environment. Furthermore, bacteria have been discovered

in places previously thought sterile, such as the placental membranes of infants in utero. Using

advanced DNA Techniques, analysis of the characteristics of the communities have been

performed. (Aagard et al. 2014).

The recently discovered presence of bacteria in the tissue that constitutes the placenta has

led researchers to speculate that the placenta may also harbor a unique microbiome,

distinguished from other microbiomes of the body. It will be important to understand how this

integral part of our body comes about, and the factors that influence community structures during

development. A greater understanding of these aspects of the microbiome will allow us to guide

the development of the microbiome into a community optimal for overall health. Some scientists

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believe the development of the human microbiome may begin in utero. If this is true, there are

reasons to believe current practices are outdated and may impair development, including the use

of antibiotics, maternal diet, and delivery methods, among others. The consequences of

impairment so early in development could lead to a cascade of negative consequences relating to

the microbiome later in life, affecting the necessary attributes they provide.

The goal of this review is to combine the observations of current research concerning the

colonization of the placenta, such as the type of bacteria present, the process through which they

colonize, and their possible role in pregnancy or fetal development. It may now be the case that

development of the human microbiome begins in utero and complete at a point in childhood

where the microbiome reaches stability. This point of stability is characterized by similarity in

dynamics of diversity and bacterial counts through adulthood.

Bacterial Colonization in the Placenta: Simple infection?

The presence of bacteria has been observed in the amniotic fluid and chorioamnion for

quite some time and is believed to be the major cause of preterm-birth (Andrews et al. 2005).

Infection begins early in gestation and is derived from ascension from the upper genital tract.

Women who undergo very early preterm delivery typically experience the same results in

following pregnancies. This, in addition to the occurrence of endometritis in nonpregnant women

suggests that colonization occurs prior to pregnancy and may explain why some women

experience repeat preterm labor. This was not supported by one study, as researchers it was

observed that microbial colonization of the endometrium 3 months after delivery was similar in

frequency between women with recent spontaneous preterm delivery, indicated preterm, and

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spontaneous term birth. They found approximately 80% of women were positive for endometrial

bacterial colonization (Andrews et al. 2005).

Previous studies were able to detect bacteria using culture-based methodology, however,

metagenomics have shown the existence of other bacteria in the placental membrane that were

not observed when culture-based methods were used alone. People have begun research into the

bacteria present in the placental tissues and how they might have migrated to this environment

which was previously believed to be sterile. The studies presented here have shown the presence

of bacteria in placental membranes despite the length of gestation and delivery methods. Many

were quick to assume these were simply the result of infection and led to problems such as

preterm birth. Inflammation caused by infection within the amniotic fluid commonly results in

early delivery. Some of the following studies were performed to investigate the types of bacteria

present in placentas of preterm against term pregnancies. Researchers were then able to

determine if the presence of bacteria could only result in preterm birth or if their presence was

not always infective and therefore may serve a purpose.

As early as 2009, researchers believed that bacteria may not have been the major cause of

preterm birth, that they may serve a higher purpose. One study was performed in which

researchers used broad-range 16S rDNA endpoint PCR followed by species-specific real time

PCR in order to detect the presence of bacteria (Jones et al. 2009). Following broad-range 16S

rDNA PCR, 30% of women showed evidence of bacterial DNA within the fetal and placental

membranes. Using species-specific real time PCR, the percent increased to 43%. Of women in

this study, 72% delivered preterm, compared with the 28% control group which delivered to

term. No bacteria were observed in samples obtained by women who went to term and delivered

by cesarean section, whereas all other groups, including 50% of samples from women who went

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to term and delivered vaginally, exhibited bacterial DNA. 90% of samples from women that

experienced spontaneous preterm birth with intact membranes (all were delivered vaginally)

were positive for bacterial DNA. Furthermore, samples were taken from various locations of the

placental tissue to test for the spread of bacteria along the membrane. Figure 1, taken from their

study, shows that bacterial spread was greater in the preterm labor and preterm prolonged rupture

of membranes (PPROM) groups, whereas the term vaginal deliveries were positive, but exhibited

little spread as indicated by a lower number of samples positive for bacteria. They also found a

greater diversity of species among the woman that delivered preterm (preterm labor and

PPROM).

Figure 1: “The spread of bacteria in placental tissue and fetal membranes from term and very preterm

deliveries. A total of 5 samples were taken from each women. DNA was extracted and then subject to broad-

range 16S rDNA endpoint PCR and species-specific real time PCR. The percentage (and number) of

individuals that had 3–5 samples, 1–2 samples, and 0 samples positive for bacteria are shown for each group.

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(CS) caesarean section, (V) spontaneous vaginal delivery, (PTL) preterm labour with intact membranes,

(PPROM) preterm prolonged rupture of membranes. (Jones et al. 2009)

As for determining the association between bacteria and inflammation, referred to as

chorioamnionitis, these same researchers found a higher prevalence among preterm labor (68%)

and PPROM (88%) groups. Similar to other studies, not all cases were positive for both bacteria

and chorioamnionitis, indicating that bacteria do not always cause inflammation. It can be

inferred then that there are other etiological forces that may have attributed to the resulting

inflammation other than the presence of bacteria. Figure 2, taken from their study, summarizes

the comparison of presence of bacteria, chorioamnionitis, or both among preterm groups.

Figure 2: “The presence of histological chorioamnionitis in fetal membranes from very preterm

deliveries. Fetal membranes of all deliveries before 32 weeks gestation were assessed routinely for histological

chorioamnionitis. Here we show the association between the presence of bacteria in fetal membranes and

placental tissue and histological chorioamnionitis in preterm labour with intact membranes (PTL), preterm

prolonged rupture of membranes (PPROM), and indicated preterm delivery.” (Jones et al. 2009)

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Their final conclusions were that bacterial presence and diversity is greater among

preterm labor and PPROM groups. Furthermore, they determined that there is a positive

correlation of bacterial presence and chorioamnionitis, and that infection of the membranes is

more common than amniotic fluid in cases of preterm delivery. They suggest that the action of

labor may play a role in bacterial colonization, as intraamniotic infection is higher in active labor

in contrast to those delivered by cesarean section. Ultimately, they also concluded that though

there was a high correlation between chorioamnionitis and bacterial colonization, bacterial

colonization did not necessarily result in an established infection and result in preterm labor.

Similarly, Stout et al. (2013) began research to determine if bacteria were present in the

basal plate of the placenta specifically, and whether these bacteria were associated with preterm

birth. They found both gram positive and gram negative bacteria in all shapes present both as

individuals and as a biofilm in 27% of the placental samples. In all samples, only 17% were

diagnosed with choriamnionitis, or evidence of an intraamniotic infection. This provides further

evidence that the presence of bacteria did not always result in intraamniotic infection. About

35% of the samples were from preterm births, whereas the remaining 65% were from

pregnancies that made it to full-term. They concluded that preterm birth occurred regardless of

the presence of bacteria in the basal plate; though they did note high prevalence of bacteria in the

basal plate of pregnancies delivered at less than 28 weeks.

Satokari et al. (2009) looked specifically for Bifidobacterium and L. rhamnosus in

placentas of healthy term pregnancies and found that most samples were positive for both

regardless the mode of delivery. Neither were able to be cultured, but were discovered by use of

species specific DNA analysis using PCR. They discuss failures of cultivation due to freezing of

samples for storage as well as the possibility that the DNA detected were from dead cell parts

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and not from viable cells. They hypothesize that the bacterial DNA may facilitate development

of the immune system of the fetus while still in utero.

To sum, it has been shown that bacteria invade the endometrium of non-pregnant women,

however this is not believed to be associated with preterm birth. Bacteria have been observed in

placental samples despite gestation length or delivery method, even in the absence of

inflammation of the membranes. Bacteria have been observed in healthy, full-term placental

samples and in the absence of chorioamnionitis supports the hypothesis that bacteria do not

always cause preterm birth, and that their presence may play a physiological role in pregnancy or

infant development.

Microbiome Development Begins in the Placenta

Aagaard et al. (2014) hypothesized these bacteria were the beginning of development of

the infant microbiome, and constitute the placental microbiome. They found a distinct difference

in the gut microbiome of full-term infants in their first week compared to infants weighing less

than 1200g, suggesting that development of the infant microbiome begins in utero through the

placenta. They then performed research to identify the bacterial species and the community

construction found among the placental microbiome. It was observed in their findings that

individuals varied in species composition, however, most exhibited E. coli in the greatest

abundance. Oral species Prevotella tannerae and Neisseria (nonpathogenic) were also common.

They further determined that typical phyla include Proteobacteria and Tenericutes such as

Mycoplasma and Ureaplasma, Firmicutes, Bacteroidetes, and Fusobacteria. The researchers

concluded that altogether these form a placental microbiome consisting of nonpathogenic

bacteria with little diversity.

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Another study was performed to detect bacteria in the placental membranes of preterm

and term pregnancies and characterize the differences between them. The bacteria were also

compared in relation to how each pregnancy was delivered (Doyle et al. 2014). They discovered

a greater abundance as well as a more diverse group of bacteria in placental membranes of

preterm infants compared with term infants. Recall that this increased diversity was also seen in

the previous study by Jones et al. (2009). Term placental membranes did not differ greatly in

genera observed by different delivery methods, and exhibited Streptococcus, Microbacterium,

Rhodococcus, and Corynebacterium. Preterm placental membranes exhibited increased amounts

of Fusobacterium, Streptococcus, Mycoplasma, Aerococcus, Gardnerella, and Ureaplasma

genera as well as the family Enterobacteriaceae compared to term placental membranes.

Sequences found specific to preterm infants delivered vaginally were determined to represent F.

nucleatum, Mycoplasma hominis, Aerococcus christensenii, Streptococcus anginosus,

Streptococcus agalactiae, Gardnerella vaginalis, and Streptococcus itis. Figure 3 shows their

results indicating the abundance of various bacteria detected by sequencing analysis of two 16s

hypervariable regions in placentas of term infants delivered vaginally or through cesarean

section, and preterm infants delivered vaginally. Bacteria that were observed in the study by

Aagard et al. (2014) are marked with a blue star, and bacteria observed in the study by Jones et

al. (2009) are marked with a red star

They have noticed the species detected in this study resemble other studies which

associated bacteria to the placenta or preterm birth, including S. agalactiae, S. mitis group, and

Mycoplasma hominis. For the first time, A. christenensii was observed. They concluded that

bacteria are an important aspect in preterm birth, however there are distinct species composition

associated with preterm birth, differing from those observed in term births. Furthermore there are

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no significant differences observed in relation to different methods of delivery. They also noted

that the genera observed by Aagard et al. (2014) are dissimilar to those observed in this study,

though the same regions were sequence and analyzed. They believe the two 16S hypervariable

regions used do not allow for observation of the diversity present in completeness.

In a previously mentioned study (Jones et al. 2009), other researchers found that that the

most common species detected were U. parvum, Fusobacterium spp. Furthermore, most of the

species observed are associated with the vaginal tract, and have been linked to bacterial

vaginosis and a change in the vaginal microbiome; both of which are already known as important

factors of preterm birth. Some organisms present were associated with the upper respiratory

tract. Most of the species found to make-up the nonpathogenic microbiome of the placenta in the

research by Aagard et al. (2014) closely resembled the oral microbiome

These bacteria are believed to travel to the placenta from their respective microbiomes

via the blood, or hematogenous transmission. There has been a mechanism proposed by Perez et

al. (2007) in which viable bacteria from the intestinal lumen are transported by mononuclear

phagocytes such as dendritic cells to the mammary glands, where they can be secreted in breast

milk. This same mechanism, or perhaps a similar mechanism, may also serve as a transport

system to the placenta.

To sum, multiple phyla have been observed in the healthy term placenta with much

variation between individuals. Two studies found common phyla which include Fusobacterium,

Mycoplasma, Prevotella, Bacteroides, and Ureaplasma. These were also present in placenta

samples from preterm birth however they were observed in larger abundance. So far the

placental biome is most similar to that of the oral microbiome, and bacteria are believed to travel

to the placenta from various locations around the body through the blood.

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Figure 3 A) Bacteria found through amplification of two variable regions within samples of both term elective

caesarean sections (T CS) and vaginal deliveries (TL V). The bacteria observed were amplified by the two variable

regions shown as either red or blue; with varying shades of each to represent the abundance of the specific bacteria

observed. B) Bacteria found through amplification of two variable regions within samples of both preterm (PTL V)

vaginal deliveries as well as term vaginal deliveries for a direct comparison. Figures from Doyle et al. 2014. Stars

indicate bacteria in which

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The final Answer: Are these bacteria commensal or pathogenic?

Some studies, such as Onderdonk et al. (2008), found that preterm delivery was

positively correlated with high rates of colonization. In their research, they seen that colonization

of the placental parenchyma decreased as gestational age at birth increased. In that study,

however, culture-based methods were used, and researchers did not observe placentas from

pregnancies that went to term. While it is undoubtedly true that bacteria play a role in preterm

birth, they are not exclusive causes (Payne and Bayatibojakhi 2014), and they may play different

roles in the placenta as well.

Thus far, what is shown is that there is a great diversity among specimens in the bacteria

species present, and a greater diversity within a sample may indicate preterm birth. As many

studies could not detail specific bacterial species that are associated with either the preterm or

term placentas, we see a few genera overlap between the two such as Fusobacterium,

Mycoplasma, Ureaplasma, Streptococcus. This may just simply be that some species within

these genera are non-pathogenic, whereas the others are pathogenic and may result in preterm

birth. Another possible reason could be the genetic variation found within species. Different

bacterial taxa as well as species can vary widely in their DNA content. (Allen-Daniels et al.

2015). Bacteria have the ability to transfer DNA both between and within species, pick it up

from the environment, and evolve quickly due to their quick and constant reproduction. This

results in multiple strains of the same species. It is not unreasonable, nor uncommon, to find that

different strains of the same bacteria then may be pathogenic whereas some may be commensal.

Mycoplasma hominis, a species which has been heavily associated with preterm risks, is

one such species that is not always pathogenic. Harmless in nonpregnant women, it has been

shown to cause intraamniotic infection and result in chorioamnionitis (Allen-Daniels et al. 2015).

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Allen-Daniels et al. (2015) set out to find genes specific to intraamniotic infectious strains of

Mycoplasma hominis compared to a previously genetically sequenced strain, PG21. The three

experimental strains were referred to as AF1, AF3, and PL5. For the most part, all four strains

were genetically similar, however there were three genes found within the infectious strains that

were absent in PG21. These genes encoded alanine racemase (alr), a second gene (designated as

goiB) which may encode a secreted protease, and a third gene (designated as goiC) which is also

unknown in function and dissimilar to any known proteins. Researchers then looked attempted to

determine the association of these genes with preterm outcome. Vaginal flora samples were

obtained (n=58), 17 of which were positive for M. hominis. Of these 17, 4 samples were from

women that delivered preterm. The gene alr was present in 2 of the preterm samples and 5 of the

term samples. 3 and 4 preterm samples were positive for the genes goiB and goiC respectively,

while in term pregnancies, 6 and 4 were positive, respectively. GoiC was associated significantly

with preterm birth samples. Further research showed that the gene may facilitate colonization of

the placenta or in amniotic fluid preferentially than to the vagina.

Another factor that may cause some bacteria to become pathogenic could be bacteria

found within the community. For instance, pregnant woman with bacterial vaginosis are at

higher risk of having a pre-term birth when they are colonized by bacteroides and M. hominis.

(Hillier et al. 1995). The study performed by Allen-Daniels et al. (2015) found that the strain of

M. hominis that carried goiC had greater survival over Ureaplasma, indicated by a negative

correlation between the presence of the two. This is odd in that M. hominis and Ureaplasma are

often observed simultaneously in preterm samples. The sample size (n=4) that provided

evidence of presence of goiC in the absence of Ureaplasma was very small, however, and may

need to be researched further.

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Still, there are other reasons that may explain the overlap in genera observed in preterm

and term placentas. One explanation is that these bacteria serve a role in the development of the

microbiome, such as initiating colonization. It turns out that there may be a bacteria able to

perform such a role; the mechanism for colonization or infection of bacteria has been proposed

by Fardini et al. (2011). Fusobacterium nucleatum is a gram-negative bacteria found in the oral

microbiome that contains a molecule on its cell surface called FadA. Only F. nucleatum oral

species have shown this molecule as well as an increased ability to bind and penetrate host cells.

Furthermore, it was shown in their research that F. nucleatium binding increases the ability of

other bacteria to spread through these tissues. It is proposed that F. nucleatum as well as other

bacteria travel via the blood from the oral microbiome to the placenta using hematogenous

transmission; F. nucleatum bind to the endothelium of placental tissue and indirectly allow

passage to other bacteria which then colonize or infect the placental tissue.

In their review, Prince et al. (2014) describes a mechanism in which bacteria may even

aid in the maintenance of pregnancy. The bacteria described however were located in the vaginal

microbiome and authors expected them to colonize the infant during delivery. It may not be

unreasonable to extend this idea of maintenance to bacteria that inhabit the placenta.

Final Conclusions

At least one author is still skeptical and questions the validity of Aagard et al. (2014)

findings, as well as Stout et al. (2013). Kliman (2014) remarks that the methods used in the study

performed by Aagard et al. (2014) do not distinguish living, dead, ruptured or fragmented

bacteria; all of which would produce positive signals. In addition, these bacteria discovered

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could be from contamination of maternal blood, and a control should have been performed in

order to test for the bacteria present in a remote vein. This would make their findings of live

bacteria invalid. Kliman (2014) also questions whether intact live bacteria are able to be

observed in tissue samples only 5µm (Stout et al. 2013). Aagard (2014) retorted, explaining that

procedures performed in order to prevent contamination were initiated during collection of

samples, and that available evidence made the control for small samples of maternal blood

unnecessary. Furthermore, Aagard (2014) reports the HMP showed that there was a distinct lack

of colonization of other body sites by bacteria in the oral microbiome, and no evidence of oral

bacterial DNA fragments found within the gut or the venous system have been observed by other

researchers that they are aware. He does acknowledge that they made no conclusions as to

whether these bacteria were living or dead in their research (Aagard et al. 2014), however they

are not the first to observe the placenta is non-sterile.

Indeed, they were not the first to observe bacteria of the placental membranes. All studies

discussed here have evidenced the prevalence of bacteria in the placentas of both preterm and

healthy term labors. Whether bacteria are present or not is no longer a question. The question

that remains unanswered is which bacteria are harmful, or what bacterial interactions may result

in infection, inflammation, and finally preterm labor. Knowing this, we then ask ourselves what

can be done to stop this from occurring. There has been a great diversity of bacteria in samples

both within studies and between studies. This may be due to differences in methodology; as

some studies amplified and sequenced general DNA regions whereas others looked for DNA

sequences specific to bacteria identities previously associated with intraamniotic infection and

preterm labor.

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Several studies have observed the colonization of the placenta by a large proportion of

species associated with the oral microbiome. Though many studies do not mention a reason for

this in terms of the development of the microbiome as a starting point, one can be hypothesized

for testing. For instance, if placental colonization does initiate the start of the infant microbiome,

these species could aid in digestion or development of the infant microbiome following birth by

acting as competitive selectors of bacteria that may try to colonize other parts of the infant such

as the gut. To test this, the oral microbiome of the neonate can be compared to that of placenta.

It is clear that multiple, more definitive studies must be performed in order to clarify if

there are specific bacteria that lead to preterm labor, or if it is simply the result of colonization by

a greater diversity and multitude of bacteria. To do this, it may be necessary to try and obtain

samples during pregnancy, although this will be difficult as sampling may be dangerous to the

pregnancy. Sampling may be taken when procedures such as amniocentesis are ordered, however

this is usually done only in cases where there are already risks to the infant or pregnancy, and

thus the results may be biased. Furthermore as many studies have observed the placental

microbiome to resemble that of the oral microbiome, it may be beneficial to obtain parallel

samples of the mother’s oral microbiome in addition to placental specimens for direct

comparison.

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