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This article summarizes some of the same things I've been posting here. From NY Times:

We Are Our Bacteria

We may think of ourselves as just human, but we’re really a mass of microorganisms housed in a human shell. Every person alive is host to about 100 trillion bacteria cells. They outnumber human cells 10 to one and account for 99.9 percent of the unique genes in the body.

Our collection of microbiota, known as the microbiome, is the human equivalent of an environmental ecosystem. Although the bacteria together weigh a mere three pounds, their composition determines much about how the body functions and, alas, sometimes malfunctions. Like ecosystems the world over, the human microbiome is losing its diversity, to the potential detriment of the health of those it inhabits.

Dr. Martin J. Blaser, a specialist in infectious diseases at the New York University School of Medicine and the director of the Human Microbiome Program, has studied the role of bacteria in disease for more than three decades. In his new book, “Missing Microbes,"Dr. Blaser links the declining variety within the microbiome to our increased susceptibility to serious, often chronic conditions,  from allergies and celiac disease to Type 1 diabetes and obesity. He and others primarily blame antibiotics for the connection.

The damaging effect of antibiotics on microbial diversity starts early, Dr. Blaser said. The average American child is given nearly three courses of antibiotics in the first two years of life, and eight more  during the next eight years. Even a short course of antibiotics like the widely prescribed  Z-pack (azithromycin, taken for five days), can result in long-term shifts in the body’s microbial environment.

But antibiotics are not the only way the balance within us can be disrupted. Cesarean deliveries, which  have soared  in recent decades, encourage the growth of microbes from the mother’s skin, instead of from the birth canal, in the baby’s gut, Dr. Blaser said in an interview.

This change in microbiota can reshape an infant’s metabolism and immune system. A recent review of 15 studies involving 163,796 births found that, compared with  babies delivered vaginally, those born by cesarean section were 26 percent more likely to be overweight and 22 percent more likely to be obese as adults. 

The placenta has a microbiome of its own, researchers have discovered, which may also contribute to the infant’s gut health and help mitigate the microbial losses caused by cesarean sections.

Further evidence of a link to obesity comes from farm animals. About three-fourths of the antibiotics sold in the United States are used  in  livestock. These  antibiotics change the animals’ microbiota, hastening their growth. When mice are given the same  antibiotics used on livestock, the metabolism of their liver changes, stimulating an increase in body fat, Dr. Blaser said.

Even more serious is  the increasing number of serious disorders now linked to a distortion in the microbial balance in the human gut. They include several that are becoming more common in developed countries: gastrointestinal ailments like Crohn’s disease, ulcerative colitis and celiac disease; cardiovascular disease; nonalcoholic fatty liver disease; digestive disorders like chronic reflux; autoimmune diseases like multiple sclerosis and rheumatoid arthritis; and asthma and allergies.

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?”

Informing pregnant women about environmental health hazards is absolutely necessary, especially because steps can be taken to avoid them (such as pesticides, mercury in fish, lead and BPA). Why isn't it happening routinely? Hey obstetricians - are you listening? From Huffington Post:

Doctors Fail To Counsel Pregnant Women On Toxic Chemical Risks

...dozens of environmental chemicals can course through a pregnant woman's body, cross the umbilical cord and wreck havoc on a developing fetus. Birth defects, IQ losses and childhood cancers are just some of the potential risks scientists have now tied to even low levels of exposure.

Among more than 2,500 doctors consulted for the survey, nearly all of them reported counseling patients on factors such as diet, exercise and cigarette smoking. However, only about 20 percent said they addressed environmental exposures. They pegged their hesitation to a number of factors, from the fear of overwhelming patients with anxiety-inducing worries to limited appointment time to a lack of environmental health education.

Just one in 15 doctors said they had received training on the harmful reproductive effects of toxic chemicals. "Medical school and residencies tend to frame their curriculum around the boards and required licensing exams," said Stotland. "This material is not yet on those tests." ... The American College of Obstetrics and Gynecologists (ACOG) and the American Society for Reproductive Medicine (ASRM) issued a statement in October that underscored mounting evidence of "significant and long-lasting effects" caused by industrial chemicals, and emphasized doctors' role in protecting pregnant women.

The actual study from Plos One summed up the importance of knowing about exposures to environmental hazards during pregnancy very nicely in the introduction:

Counseling Patients on Preventing Prenatal Environmental Exposures - A Mixed-Methods Study of Obstetricians

Exposure to hazardous environmental chemicals, i.e., manufactured chemicals and metals, is linked to adverse health outcomes across all stages of the human life cycle including fertility, conception, pregnancy, child and adolescent development, and adult health [1][5]. Human exposure to environmental chemicals is ubiquitous. A population-based study found that virtually all pregnant women in the U.S. had measureable levels of at least 43 different environmental chemicals in their bodies, including chemicals that were measured at levels similar to those associated with adverse developmental and reproductive health outcomes in epidemiologic studies [6]. There are currently over 80,000 chemicals in commerce [7][8], and exposure occurs through air, water, food and consumer products in the home and workplace. The majority of industrial chemicals have not been tested for potential reproductive/developmental harm [9].

Obstetricians are uniquely positioned to help prevent exposures to environmental chemicals with adverse developmental and reproductive health effects [2]. Pregnancy is a time when exposure to environmental contaminants can disrupt or interfere with the physiology of a cell, tissue, or organ [4], leading to permanent and lifelong adverse health outcomes that may be passed down to future generations [10]. Pregnancy is also an opportune time to prevent harmful exposures as it is a period when patient interest about health can be extremely high.

The worrisome results are adding up for BPA and BPS. From Environmental Health News:

Miscarriage risk rises with BPA exposure, study finds

Women exposed to high levels of bisphenol A early in their pregnancy had an 83 percent greater risk of miscarriage than women with the lowest levels, according to new research. The scientists said their new study adds to evidence that low levels of the ubiquitous chemical, used to make polycarbonate plastic and found in some food cans and paper receipts, may affect human reproduction. The study involved 115 pregnant women who had visited a Stanford University fertility clinic within about four weeks of fertilization. The more BPA detected in the women’s blood, the higher their risk of miscarriage, according to the researchers.

“Couples suffering from infertility or recurrent miscarriages would be best advised to reduce BPA exposure because it has the potential to adversely affect fetal development,” wrote the scientists, led by Dr. Ruth Lathi, a Stanford University associate professor of obstetrics and gynecology. 

In 2005, a smaller study in Japan found that 45 women who had three or more first-trimester miscarriages had three times more BPA in their blood than 32 women with no history of pregnancy problems. 

From Science Daily:

BPA increases risk of cancer in human prostate tissue, study shows

Fetal exposure to a commonly used plasticizer found in products such as water bottles, soup can liners and paper receipts, can increase the risk for prostate cancer later in life, according to a study. Exposure of the fetus to BPA in utero is of particular concern, because the chemical, which mimics the hormone estrogen, has been linked to several kinds of cancer, including prostate cancer, in rodent models. The new findings show that human prostate tissue is also susceptible.

"Our research provides the first direct evidence that exposure to BPA during development, at the levels we see in our day-to-day lives, increases the risk for prostate cancer in human prostate tissue," Prins said

This study was done in rats, but thought to also apply to humans. From Science Daily:

Common BPA substitute, BPS, disrupts heart rhythms in females

Bisphenol S (BPS), a common substitute for bisphenol A (BPA) in consumer products, may have similar toxic effects on the heart as previously reported for BPA, a new study finds.

There is implied safety in BPA-free products. The thing is, the BPA analogs -- and BPS is one of them -- have not been tested for safety in humans." "Our findings call into question the safety of BPA-free products containing BPS," he said. "BPS and other BPA analogs need to be evaluated before further use by humans."

The researchers of this study looked at proximity to farm fields (how close a pregnant woman lives to a farm) and certain farm pesticides and found a link between exposure to farm pesticides during pregnancy and having a child with autism. But too bad they didn't also include pesticide exposures from homes (for pest control), gardens, and yards which would have given a more accurate measure of total exposure. However, it's a start. From Science Daily:

Association found between maternal exposure to agricultural pesticides and autism

Pregnant women who lived in close proximity to fields and farms where chemical pesticides were applied experienced a two-thirds increased risk of having a child with autism spectrum disorder or other developmental delay, a study by researchers with the UC Davis MIND Institute has found. The associations were stronger when the exposures occurred during the second and third trimesters of the women's pregnancies.

The large, multisite California-based study examined associations between specific classes of pesticides, including organophosphates, pyrethroids and carbamates, applied during the study participants' pregnancies and later diagnoses of autism and developmental delay in their offspring. It is published online in Environmental Health Perspectives. "... the message is very clear: Women who are pregnant should take special care to avoid contact with agricultural chemicals whenever possible."

California is the top agricultural producing state in the nation, grossing $38 billion in revenue from farm crops in 2010. Statewide, approximately 200 million pounds of active pesticides are applied each year, most of it in the Central Valley, north to the Sacramento Valley and south to the Imperial Valley on the California-Mexico border. While pesticides are critical for the modern agriculture industry, certain commonly used pesticides are neurotoxic and may pose threats to brain development during gestation, potentially resulting in developmental delay or autism.

The study was conducted by examining commercial pesticide application using the California Pesticide Use Report and linking the data to the residential addresses of approximately 1,000 participants in the Northern California-based Childhood Risk of Autism from Genetics and the Environment (CHARGE) Study. The study includes families with children between 2 and 5 diagnosed with autism or developmental delay or with typical development. "We mapped where our study participants' lived during pregnancy and around the time of birth. In California, pesticide applicators must report what they're applying, where they're applying it, dates when the applications were made and how much was applied," Hertz-Picciotto said. "What we saw were several classes of pesticides more commonly applied near residences of mothers whose children developed autism or had delayed cognitive or other skills."

Organophosphates applied over the course of pregnancy were associated with an elevated risk of autism spectrum disorder, particularly for chlorpyrifos applications in the second trimester. Pyrethroids were moderately associated with autism spectrum disorder immediately prior to conception and in the third trimester. Carbamates applied during pregnancy were associated with developmental delay.

Exposures to insecticides for those living near agricultural areas may be problematic, especially during gestation, because the developing fetal brain may be more vulnerable than it is in adults. Because these pesticides are neurotoxic, in utero exposures during early development may distort the complex processes of structural development and neuronal signaling, producing alterations to the excitation and inhibition mechanisms that govern mood, learning, social interactions and behavior.

Of course we should expect to find bacteria in a healthy placenta. It only makes sense. But this is interesting stuff - the possibility that the placental biome being out of whack playing a role in preterm birth. From Medical Xpress:

Bacteria live even in healthy placentas, study finds

Surprising new research shows a small but diverse community of bacteria lives in the placentas of healthy pregnant women, overturning the belief that fetuses grow in a pretty sterile environment. These are mostly varieties of "good germs" that live in everybody. But the study also hints that the make-up of this microbial colony plays a role in premature birth.

We share our bodies with trillions of microbes—on the skin, in the gut, in the mouth. These communities are called our microbiome, and many bacteria play critical roles in keeping us healthy, especially those in the intestinal tract. Healthy newborns pick up some from their mother during birth, different bugs depending on whether they were delivered vaginally or by C-section. What about before birth?

Aagard's team earlier had studied the microbiome of the vagina, and learned that its composition changes when a woman becomes pregnant. The puzzle: The most common vaginal microbes weren't the same as the earliest gut bacteria that scientists were finding in newborns. What else, Aagaard wondered, could be "seeding" the infants' intestinal tract?

With colleagues from Baylor and Texas Children's Hospital, Aagaard analyzed 320 donated placentas, using technology that teases out bacterial DNA to evaluate the type and abundance of different microbes. The placenta isn't teeming with microbes—it harbors a low level, Aagaard stressed. Among them are kinds of E. coli that live in the intestines of most healthy people. But to Aagaard's surprise, the placental microbiome most resembled bacteria frequently found in the mouth, she reported in the journal Science Translational Medicine. The theory: Oral microbes slip into the mother's bloodstream and make their way to the placenta.

Why does the body allow them to stay? Aagaard said there appears to be a role for different microbes. Some metabolize nutrients. Some are toxic to yeast and parasites. Some act a bit like natural versions of medications used to stop preterm contractions, she said. In fact, among the 89 placentas that were collected after preterm births, levels of some of the apparently helpful bacteria were markedly lower, she said.

There has been much discussion lately on declining male sperm counts and what it means. From Medical Xpress:

No link found between low sperm count, birth defects

Having a low sperm count doesn't seem to determine whether a man's children will be born with birth defects, a new study indicates.

With infertile couples, men are partially or fully responsible for the inability to conceive about 40 percent of the time. Assisted reproductive technologies such as in vitro fertilization can help couples have children, but research has suggested a possible link between these approaches—when used to treat infertility problems in the male partner—and a higher risk of birth defects.

In the new study, researchers examined a Baylor College of Medicine database in search of possible connections between birth defects and low sperm count. The researchers didn't find any links.

But the following finding is a cause for concern. From Science Daily:

Male infertility linked to mortality, study shows

Men who are infertile because of defects in their semen appear to be at increased risk of dying sooner than men with normal semen, according to a study. Men with two or more abnormalities in their semen were more than twice as likely to die over a roughly eight-year period as men who had normal semen, the study found.

Years ago the advice was to really limit exercise during pregnancy, but times have changed. Now studies find exercise during pregnancy beneficial for both the mother and baby. From Discover:

Exercise During Pregnancy Benefits Mom—And Baby, Too

Women who exercise with baby on board have been known to have, among other things, lower risks of gestational diabetes and pregnancy-induced high blood pressure than those who don’t.

In 1985, the American Congress of Obstetricians and Gynecologists came out with their first set of guidelines for exercise during pregnancy—guidelines, now considered conservative, that included suggestions like keeping strenuous activities to 15 minutes or less. Since then, research has turned that idea on its head. Exercise is now thought to be—for most women with healthy pregnancies—a boon for the mother's health, and for the baby she carries as well.

It’s been known that those who exercise—including pregnant women—tend to have lower resting heart rates than those who don’t. Lower heart rates can be a sign of an efficient heart; high heart rates have been linked to greater risk of cardiovascular disease. May, now at East Carolina University in North Carolina, has long been interested whether benefits like this extended to baby.  In a 2010 study, she and her colleagues collected a group of 26 pregnant women who reported that they’d been exercising three times a week for more than 30 minutes per session.  When researchers brought the moms into the lab at 36 weeks, they found that the babies in their bellies, too, had lower heart rates than those carried by the moms they studied who weren’t regular exercisers.

The results indicate that exercise during pregnancy, far from harming the fetus, can be incredibly beneficial for both mom and baby. And timing matters: exercise during pregnancy, as opposed to pre-pregnancy fitness, seems to be doing something extra-special, May says. In this most recent study, about half of the group hadn’t exercised previously, and still saw similar effects on their babies’ hearts. 

Such benefits to the heart may last into a child’s early life. Earlier this year, May and colleagues found that month-old infants still had higher heart rate variability if they had exercised along with their moms in utero. Another set of results from May’s group, not yet published, suggests that kids up to six years old still carry some of these early workouts with them: youngsters whose moms exercised while pregnant have higher “ejection fractions,” which indicates their hearts are pumping blood more efficiently.

Studies report that only about 10 to 30 percent of pregnant women are following recommended exercise guidelines—for healthy women, at least 30 minutes of moderate exercise most, if not all, days, according to the American Congress of Obstetricians and Gynecologists.. (Of course, some women can’t safely exercise during part or all of their pregnancy, and active women should watch out for warning signs while exercising, such as bleeding or contractions.)

Researchers found that many common chemicals, including Triclosan, interfere with normal sperm function. Perhaps this is contributing to fertility problems.From Science Daily:

Endocrine disruptors impair human sperm function, research finds

A plethora of endocrine-disrupting chemicals interfere with human sperm function in a way that may have a negative impact on fertilization. These are the findings of a German -- Danish team of researchers from the Center of Advanced European Studies and Research in Bonn, Germany, and the University Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark. The work, which is published in EMBO reports,suggests that endocrine disruptors may contribute to widespread fertility problems in the Western world in a way that hitherto has not been recognized.

Endocrine disruptors are present in food, textiles, drugs, household, and personal-care products such as plastic bottles, toys, and cosmetics. Proving the deleterious effects of endocrine disruptors on human beings has been difficult due to a lack of suitable experimental systems.

"For the first time, we have shown a direct link between exposure to endocrine disrupting chemicals from industrial products and adverse effects on human sperm function,'' said Niels E. Skakkebaek, professor and leader of the Danish team.

Hundreds to thousands of chemicals can be rapidly tested for their potential to interfere with human sperm function using the bioassay developed by the researchers. In this initial study, about one hundred chemicals were tested. Around one third, including ultraviolet (UV) filters like 4-methylbenzylidene camphor (4-MBC) used in some sunscreens, the anti-bacterial agent Triclosan used in toothpaste, and di-n-butylphthalate (DnBP), showed adverse actions.

Altogether, the study indicates that endocrine disruptors might disturb the precisely coordinated sequence of events underlying fertilization in several ways: the chemicals might evoke changes in swimming behaviour at the wrong time and wrong place, hinder navigation of sperm towards the egg, and hamper penetration into the protective egg coat.

Different article about the same research, and here they also discuss the very important finding that mixtures of common chemicals have an even stronger adverse "cocktail effect" on sperm. From The Independent:

Chemicals in soap can cause male infertility, claim scientists

They also found that the concentrations needed to trigger these adverse reactions were similar to the very low levels commonly found within the human body. In addition, they showed for the first time that there was a “cocktail effect”, when a number of chemicals worked together to amplify their individual effects.

From NPR:

More Hints That Dad's Age At Conception Helps Shape A Child's Brain

Traditionally, research has focused on women's "biological clock." But in recent years, scientists have been looking more and more at how the father's age at conception might affect the baby, too. A study published Wednesday hints that age really might matter — in terms of the child's mental health.

Researchers from the University of Indiana and the Karolinska Institute found that compared with children fathered by men who were 20-24 years old, kids born to dads who were 45 or older were three times as likely to have autism and 13 times as likely to have ADHD. Kids born to older dads were also more likely to go on to develop substance abuse problems and get lower grades in school. The findings appear in JAMA Psychiatry.

To figure out how paternal age was related to children's psychiatric health, the researchers looked at millions of parents in Sweden who had children between 1973 and 2001. The researchers took into account the mother's age, as well as other demographic factors that might play a role in the child's cognitive development and mental health.

"There's a growing body of literature that suggests that advancing paternal age is associated with a host of problems," D'Onofrio tells Shots. Another study, published in JAMA Psychiatrylast month, found that the children of older fathers seemed to be at greater risk for developing schizophrenia and autism.

D'Onofrio and his colleagues paid special attention to siblings and cousins, and found that even among kids in the same extended family, a dad's age when his child was born made a difference.

The results are in line with a growing body of research linking older fatherhood with various developmental problems in children.

However, the study looks only at how paternal age and children's mental health are associated — it's a correlation, Reichenberg cautions, not a proven causal link. Scientists haven't yet determined the mechanisms of the effect. But it doesn't seem to be simply a matter of overdiagnosis among the children of older parents, the scientists say. Other research has found that as men get older, their sperm cells are more likely to contain random mutations that might, theoretically, contribute to disorders like autism in their kids.

Ultimately, men and women of all ages, he says, should remember that age is only one of many factors influencing the developing baby's health.

"The most important thing is [that] future mothers and fathers should still go ahead and have children, even if the father is older than 45 or 50," Reichenberg says. "Most of these children will be absolutely fine."