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Healthy women were followed during their pregnancies and postpartum, and it was found that vaginal microbial communities change over the course of pregnancy, and then really change postpartum. They also found differences in the predominant Lactobacillus bacteria species between the women. In this study it was found that Lactobacillus bacteria were most dominant during pregnancy, especially L. gaserii, L. crispatus, L. iners, and L. jensenii, and there were ethnic differences in the species. And they found that the vaginal microbiome changes postpartum, with bacteria becoming more diverse and the numbers of Lactobacillus dropping. The message here is that what are "normal and healthy" microbial communities can vary between women (in this study which Lactobacillus species were "healthy and normal" varied among women). Remember: dysbiosis means that the normal microbial community is "out of whack". And sequenced the microbiomes means state of the art genetic analysis of the microbial communities From American Microbiome Institute:

The vaginal microbiome changes during and after pregnancy

The vaginal microbiome is critically important to a healthy pregnancy, and studies have shown that vaginal dysbiosis during pregnancy can lead to infection and preterm birth.  In order to help understand what the microbiome looks like throughout and just after pregnancy, researchers from England performed longitudinal studies on 42 pregnant women.  They published their results last week in Nature Scientific Reports.

The scientists sequenced the microbiomes of the 42 women throughout their pregnancies, and then for the 6 weeks afterwards for some of the women.  They discovered, in agreement with other literature on the subject, that the vaginal microbiome becomes dominated by Lactobacilli species during pregnancy.  The Lactobacilli are thought to prevent pathogens from colonizing the vagina because they produce lactic acid which decreases the overall pH of the vagina, and they secrete antibacterial toxins.  These Lactobacilli are also important as they are normally the first to colonize the new infants' guts after they pass through the birth canal. 

The researchers also learned that the microbiome shifts away from Lactobacilli and towards a more diverse microbiome in the period immediately following birthThe new bacteria that colonize are often associated with vaginosis, and these can lead to inflammation and infection of the birth canal in some women.  The scientists suspect this shift occurs because there is a sudden drop in estrogen production upon removal of the placenta.  The increase in circulating estrogen is thought to be important for Lactobacilli colonization, so it makes sense that the rapid decrease in estrogen decreases Lactobacilli abundance.

Finally, this study showed that there were geographic and ethnic variations to the pregnant microbiome.  While each microbiome was associated with a healthy pregnancy, there were important differences, especially on the species level.  For example, Asian and Caucasian women’s pregnant microbiomes were dominated by Lactobacillus gasseri, while this species was absent in black women’s pregnant microbiomes.

The human vagina is another microbial community that is nowhere as simple as earlier thought - and it's not just Lactobacillus bacteria. From The Scientist:

Characterizing the “Healthy” Vagina

For years, researchers characterized the microbial community of women’s vaginas as being dominated by Lactobacillus bacteria, which ferment carbohydrates to lactic acid, yielding a low pH that is toxic to many pathogenic microbes. When levels of Lactobacillus drop, the pH becomes more neutral, and the risk of infection rises.

But with research revealing notable variation among women’s vaginal microbiomes, as well as some interesting dynamics of the microbial communities within a single organ, “that dogma is changing a little bit,” said Gregory Buck of the Vaginal Microbiome Consortium at Virginia Commonwealth University (VCU).

The composition and stability of the vaginal microbiome varies by race, age, even within an individual—and it’s quickly become clear that the formula for a “normal,” “healthy” microbial community cannot be computed by ratios of bacterial species. “In the past we’ve made some generalizations about what kinds of bacteria are found in the vagina, what kinds of bacteria are good or healthy or protective,” said microbial ecologist Larry Forney of the University of Idaho. “What the research is showing is there are tremendous differences between women in terms of the kinds of bacteria that are present and the changes in the communities that occur over time.”

In June 2010, Forney, Jacques Ravel of the University of Maryland School of Medicine, and their collaborators published a survey of the vaginal microbiomes of nearly 400 women and found that the majority harbored bacterial communities dominated by one of four Lactobacillus strains. More than a quarter of the women studied, however, did not follow this pattern. Instead, their vaginas had fewer Lactobacillus and greater numbers of other anaerobic bacteria, although the bacterial communities always included members of genera known to produce lactic acid.

In many ways, the microbiome of these women resembled the bacterial communities of women suffering from bacterial vaginosis (BV), an infection characterized by an odorous vaginal discharge, Buck noted. “By looking at the microbial components, you’d say they have BV, but they have no clinical symptoms,” he said. “These people are not unhealthy.

The researchers also found that the composition of a woman’s vaginal microbiome was linked to her race. Eighty percent of Asian women and nearly 90 percent of white women harbored vaginal microbiomes that were dominated by Lactobacillus, while only about 60 percent of Hispanic and black women did. Moreover, vaginal pH varied with ethnicity as well, with Hispanic and black women averaging 5.0 and 4.7, respectively, and Asian and white women averaging 4.4 and 4.2. 

This raises questions about the role of the commensal bacteria and risk of preterm labor , which has been linked to BV—and to low levels of Lactobacillus in particular—and is one-and-a-half times more common among African American women than Caucasian women.

Meanwhile, the researchers continue to sort through 40,000 swabs from more than 6,000 women to better characterize the bacterial communities living in the vagina. But Fettweis and her colleagues face a common problem in microbiome research. “In many samples, only a fraction of [the genetic sequences] align to anything we have in our databases,” she said. “So I think there’s still a lot of work to be done in terms of actually understanding: What are these organisms?”

Another question facing researchers probing the vaginal microbiome is how it is initially colonized. “Where do [the bacteria] come from?” said Forney.

Many suspect that the process occurs during vaginal childbirth. But the adolescent microbiome does not resemble that of a sexually mature woman, having far less Lactobacillus, leading some to suspect that there may be a second colonization of the vagina later in life. And if the birthing process is important to establish the vaginal microbiome, what happens in the case of C-sections? “We have more questions than answers,” Forney said.

The microbiome is also not stable later in life. It is now well known that the vaginal microbiome changes after menopause, containing fewer Lactobacillus than the vaginas of reproductive-aged women, with the notable exception of women on hormone-replacement therapies.

Moreover, recent research has revealed that the composition of the vaginal microbiome can change in as little as 24 hours.

The temporal dynamics of the vaginal microbiome raise important questions about developing microbiota-based diagnostics and therapeutics, said Forney. “If you perform a diagnostic test, would you get a different result tomorrow or the day after? In some cases, yes. How do you incorporate that into [a] decision about whether some kind of intervention is required?”

Within the past few years there has been an explosion in human microbiome research - looking at the community of microorganisms that live in and on human beings. Within the body of a healthy adult, microbial cells are estimated to outnumber human cells ten to one! This community of microorganisms remains largely unstudied, and so their influence on human development, diseases, immunity, and health are almost entirely unknown.  Some of the latest research looks at the microbiomes of healthy people and those with diseases, seeing how they differ, and from that looking at possible treatments using bacteria.  This is a whole different mind-set from the one we've had for decades that viewed all bacteria as bad (pathogens) and needing to be eliminated. 

An introduction to this emerging area of human microbiome research was written by Gina Kolata in the NY Times, June 13, 2013:  

In Good Health? Thank Your 100 Trillion Bacteria

For years, bacteria have had a bad name. They are the cause of infections, of diseases. They are something to be scrubbed away, things to be avoided. But now researchers have taken a detailed look at another set of bacteria that may play even bigger roles in health and disease: the 100 trillion good bacteria that live in or on the human body.

No one really knew much about them. They are essential for human life, needed to digest food, to synthesize certain vitamins, to form a barricade against disease-causing bacteria. But what do they look like in healthy people, and how much do they vary from person to person?

In a new five-year federal endeavor, the Human Microbiome Project, which has been compared to the Human Genome Project, 200 scientists at 80 institutions sequenced the genetic material of bacteria taken from nearly 250 healthy people. They discovered more strains than they had ever imagined — as many as a thousand bacterial strains on each person. And each person’s collection of microbes, the microbiome, was different from the next person’s. To the scientists’ surprise, they also found genetic signatures of disease-causing bacteria lurking in everyone’s microbiome. But instead of making people ill, or even infectious, these disease-causing microbes simply live peacefully among their neighbors.

"Until recently, Dr. Bassler added, the bacteria in the microbiome were thought to be just “passive riders.” They were barely studied, microbiologists explained, because it was hard to know much about them. 

The work also helps establish criteria for a healthy microbiome, which can help in studies of how antibiotics perturb a person’s microbiome and how long it takes the microbiome to recover.

In recent years, as investigators began to probe the microbiome in small studies, they began to appreciate its importance. Not only do the bacteria help keep people healthy, but they also are thought to help explain why individuals react differently to various drugs and why some are susceptible to certain infectious diseases while others are impervious. When they go awry they are thought to contribute to chronic diseases and conditions like irritable bowel syndromeasthma, even, possibly, obesity.

"The microbiome starts to grow at birth, said Lita Proctor, program director for the Human Microbiome Project. As babies pass through the birth canal, they pick up bacteria from the mother’s vaginal microbiome.

Babies born by Caesarean section, Dr. Proctor added, start out with different microbiomes, but it is not yet known whether their microbiomes remain different after they mature.In adults, the body carries two to five pounds of bacteria, even though these cells are minuscule — one-tenth to one-hundredth the size of a human cell. The gut, in particular, is stuffed with them.

“The gut is not jam-packed with food; it is jam-packed with microbes,” Dr. Proctor said. “Half of your stool is not leftover food. It is microbial biomass.” But bacteria multiply so quickly that they replenish their numbers as fast as they are excreted.

Including the microbiome as part of an individual is, some researchers said, a new way to look at human beings. The next step, he said, is to better understand how the microbiome affects health and disease and to try to improve health by deliberately altering the microbiome. But, Dr. Relman said, “we are scratching at the surface now.”

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FOR THOSE WHO WOULD LIKE TO SEE A VIDEO ON THIS TOPIC, this TED talk given by Dr. Jonathan Eisen  is an excellent introduction to the human microbiome and how we should view ourselves as being covered in a microbial cloud.  And that this microbial community within and on us should be viewed as an organ, and thus should be treated carefully and with respect.

Who are “Me, Myself and Us?”

2012Jonathan Eisen