Microbiome And Infertility

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The Reproductive Microbiome and Fertility

As a pharmacist who turned holistic, I love to show conventional medicine what it’s missing. I began asking questions while I was still in pharmacy school because I had many health problems of my own, and the system was failing me. In addition, I observed that patients were getting younger and younger, taking more medications, experiencing more side effects and getting no answers. Today, as a holistic pharmacist and functional nutritional therapy practitioner, I try to help people get off of prescription drugs—for cholesterol, high blood pres­sure, pain, migraines, you name it—and return to natural principles.

Let’s look at a major problem we face today: the crisis of infertility. The situation is only getting worse. For those younger than thirty-five, health care providers diagnose infertility after twelve or more months of regular unprotected intercourse have failed to result in pregnancy—the time period shortens to six or more months if the person is thirty-five or older. Worldwide, the World Health Organization (WHO) estimates that one in six people of reproductive age experiences infertility in their lifetime—that’s 17.5 percent of the adult population. In my personal circle, three of my close friends sought fertility treatment just in the past two years. Notably, though, men make up 35 to 50 percent of all infertility cases.

For women, the WHO considers as causes of infertility hormone disorders, ovarian dys­function, fallopian tube problems, uterine condi­tions and cancer or cancer treatment; for men, accepted causes include testicular or ejaculatory dysfunction, “genetic disorders” and cancer. Sexually transmitted infections (STIs) are also on the list of causes for both women and men. Medicine approaches these problems through the lens of “hardware”—whether anatomy, hormones or genetics. However, it cannot ex­plain 30 to 45 percent of infertility. Personally, I don’t like the word “unexplained”—I prefer to say “unexplored.” I believe a missing piece to the infertility puzzle is actually a “software” issue—the reproductive microbiome.

WHAT IS THE REPRODUCTIVE MICROBIOME?

In women and men, the reproductive mi­crobiome maintains homeostasis, regulating the microenvironment within the reproductive tract. It controls inflammation and oxidative stress, and it provides metabolic and nutrient support. Clinical papers and research on the female microbiome started to be published around 2004, and now we’re seeing about two hundred fifty papers per year on that topic. The male reproductive system didn’t start showing up in the literature until around 2017, so we have a lot more data on women.

Looking at the optimal vaginal microbiome, it needs to be Lactobacillus-dominant¹—where “dominant” means greater than 90 percent. Lac­tobacilli produce lactic acid. This tells us that the female reproductive tract likes to be fairly acid­ic.² The pH needs to be somewhere between 3.8 and 4.5. This acidity level, plus what the bacteria secrete—bacteriocins (antimicrobial peptides) and also hydrogen peroxide—eliminate the overgrowth of pathogens and maintain a low-diversity environment. Note that the dominance of Lactobacillus in the vaginal microbiome is very different from the gut microbiome, where we do want more microbial diversity.

Above the membrane of the endometrium is a mucus layer, and that is where the lactobacilli live. They don’t digest the mucus, they just perch there—acting like security guards working arm in arm to protect that mucus layer so that it, in turn, can protect the membrane below. Where there is dysbiosis, there is less Lactobacillus, making more mucus available to pathogens who see this as an opportunity; they start to digest the mucus—made of proteins, sugars and fats—for food. That exposes the endometrial membrane, resulting in a leaky endometrium, inflammation and the release of cytokines—which are signal­ing molecules that tell the body, “alarm, alarm!” A leaky endometrium lets microbes go through the vagina and into the endometrium, and this can damage the uterus. It can also damage the placenta, change hormone production and cause immune disruption.

If we think of the reproductive microbiome as a “house,” where would you rather raise a baby? If the reproductive microbiome is healthy, your house is nice and clean and you have your “security guards”—the lactobacilli. You might occasionally have some visitors—maybe your kids’ friends spend the weekend and make a bit of a mess—but you are able to clean it up and put it back together. If the reproductive microbi­ome is unhealthy, it’s a bit like when a friend or relative overstays their welcome, eats your food and doesn’t clean up after themselves—now, the microenvironment of the uterus and the vagina starts to get damaged.

OPTIMAL AND SUBOPTIMAL

Researchers have determined that the vagi­nal microbiome clusters into five different pro­files, called “community state types.”³ Again, this is unique to this particular microbiome; we don’t see this in the gut microbiome, where researchers have not been able to come up with any consistent profiles.

Each of the five community state types in the vaginal microbiome is dominated by a particular strain:

• Type I: L. crispatus
• Type II: L. gasseri
• Type III: L. iners
• Type IV: Non-Lactobacillus domi­nance
• Type V: L. jensenii

Types I, II and V are optimal, Type III is suboptimal and Type IV is non-optimal. Type IV is characterized as a high pH and low Lacto­bacillus; a high risk of bacterial vaginosis (BV)⁴ (that is, dysbiosis); instability and fluctuations during the menstrual cycle; a strong association with STIs, endometritis and pregnancy loss; and low vaginal mucosal protection. With type III, the pH is at 4.5—at the cusp of an acceptable pH. For this reason, some researchers describe L. iners as only “borderline” beneficial.⁵

The vaginal microbiome changes with each reproductive stage, from youth to reproductive age, and from pregnancy into the postmeno­pausal years. For youth, there is not as much mucus, but upon entering reproductive age, the mucus layer thickens and women start to make estrogen and progesterone. Estrogen plays a ma­jor role in providing a food source for Lactoba­cillus, releasing glycogen from the membranes in the endometrium. When a woman becomes pregnant, she releases even more hormones, sending more blood flow to the area, with more Lactobacillus and a thicker membrane, ensuring that everything is protected. At the postmeno­pausal stage, the picture shifts again.

Another factor influencing the reproductive microbiome, perhaps surprising to some, is our gut microbiome.⁵ There is a 62.5 percent overlap between the gut and urinary microbiota and 32 percent overlap between the gut and vagina microbiota.⁶ The reason is proximity—the vagi­nal opening and urinary tract are close to one another and to the anal opening. Depending on a woman’s habits (whether related to hygiene, sex­ual intercourse or even thong underwear), there can be translocation of microbes. This also helps explain why supporting the gut microbiota can improve the reproductive microbiome. Properly prepared, diverse nutritional sources—along with taking probiotics orally, whether through food or supplements—can positively influence reproductive health.

CONCEPTION

How does the female reproductive microbi­ome affect conception? A 2022 study⁷ in healthy women asked that question, looking at whether the pre-pregnancy vaginal microbiome is as­sociated with time-to-pregnancy (TTP) within a year. The researchers took a cohort of eighty-nine women and swabbed them right before they wanted to get pregnant and then followed them every three months. What they found was that within one year, the 60 percent of women who got pregnant had higher Lactobacillus. The women who did not get pregnant had higher Gardnerella vaginalis, which, when it over-proliferates, leads to bacterial vaginosis (BV). Gardnerella, the literature tells us, “poses distinctive challenges due to its far-reaching implications on women’s reproductive health, susceptibility to sexually transmitted diseases, and potential to give rise to complications during pregnancy.”⁸

Studies on fertility in the context of in vitro fertilization (IVF) can tell us a lot about the role of the reproductive microbiome. Let’s look first at the role of the endometrial microbiome⁹ in the upper genital tract. Note that IVF costs almost twenty thousand dollars a month; from start to implantation, a cycle takes anywhere from six to eight weeks, and only 30 to 35 percent of women who undergo IVF actually achieve a live birth. Those are not good odds. An interesting study published in 2016 asked whether the endometrial microbiota affects IVF outcomes.¹⁰ The researchers took samples from thirty-five infertile women shortly before they were scheduled for their embryo transfer, differentiating between women who were Lactobacillus-dominant (greater than 90 percent) versus non-Lactobacillus-dominant (less than 90 percent). Two weeks after implantation, 60.7 percent of the Lactobacillus-dominant group had implanted, versus just 23.1 percent of the non-Lactobacillus-dominant group. A bit later, they checked women’s pregnancy status via ultrasound and fetal heartbeat, and again, the difference was 70.6 versus 33.3 percent. Next, they looked at the proportion of women who made it to twelve weeks (58.8 vs. 13.3 percent) and to live birth (58.8 vs. 6.7 percent). Lactobacillus dominance improved IVF outcomes.

Going a little lower in the reproductive tract, a 2021 meta-analysis asked, how does the vaginal microbiome affect IVF outcomes? The analy­sis pooled seventeen studies totaling thirty-five hundred women, again divided by Lactobacillus-dominance (greater than 90 percent) versus non-Lactobacillus-dominance.¹¹ To assess vaginal dysbiosis, they also used the Nugent score, which is a measure of BV (bacterial vaginosis) and Gardnerella. The prevalence of vaginal dysbiosis was 18 percent, and that group had a 45 percent lower chance of having a positive heartbeat at ultrasound and a 71 percent increased risk for pregnancy loss. The key takeaway is that the vaginal microbiota strongly influences IVF success, particularly with respect to miscarriage risk.

Another study of vaginal dysbiosis and IVF looked at particular strains,¹² asking: “Is the presence or absence of certain vaginal bacte­ria associated with failure or success to become pregnant after an in vitro fertilization treatment?” In the prospective cohort of one hundred ninety-two women, they could predict, with 94 percent accuracy, who was going to have a successful IVF cycle just by looking at the vaginal microbiota—without knowing who the woman was, what her history was or whether she had previously had IVF miscarriages or failures. For someone who is spending twenty thousand dollars a month, wouldn’t this be a data point that they would want to know?

MISCARRIAGE AND PRETERM BIRTH

Miscarriage is defined as spontaneous loss of pregnancy before twenty weeks. One in five pregnancies end in miscarriage, with the ma­jority (but not all) occurring in the first trimester. I know four women who have had seven miscarriages between them. According to the CDC, half of women will experience at least one miscarriage in their lifetime.

In a study of two hundred fertile women published in 2016, the researchers looked at how BV (that is, Gardnerella) affects first- and second-trimester miscarriage.¹³ Not quite one-third (30.5 percent) of the women had had a miscarriage within the previous six months and a his­tory of recurrent pregnancy loss (at least three). The researchers found that within that group, the presence of BV was significantly associated with miscarriage in the previous six months and with second-trimester miscarriage, but not with repeat pregnancy loss. Notably, the women who had BV were all asymptomatic and did not even know they had it.

A 2023 review paper¹⁴ summarized several key findings related to miscarriage and the reproductive microbiome. Lactobacillus is not the dominant strain in any of these scenarios.

• High-risk pregnancies are linked to the abundance of Gardner­ella.
• In second-trimester miscarriage, there is a much greater fre­quency of vaginal dysbiosis.
• In women with repeated miscarriage, Lactobacillus is absent from the vagina.

Preterm birth, defined as delivery before thirty-seven weeks, is a leading cause of morbidity and mortality in children under five, with nearly one million deaths worldwide in 2022. Approximately one in ten babies are born preterm. Most preterm babies end up in the neonatal in­tensive care unit and may have developmental disorders or delays, vision problems or hearing problems.

A 2023 study looked at how the late-pregnancy vaginal microbiota affected preterm labor.¹⁵ They found that Type I—that is, being L. crispa­tus-dominant—was the most protective, with the lowest risk of preterm birth. Again, with 83 percent accuracy, they were able to use computer modeling to predict who was going to have a preterm birth just by looking at the microbiota. Those who were non-Lactobacillus-dominant (Type IV) had a 15 percent increase in preterm birth. Twenty-nine percent of those who delivered before thirty weeks had a co-infection such as Candida, Ureaplasma or Gardnerella.

BACTERIAL VAGINOSIS AND PROBIOTICS

As already mentioned, most women with BV have no symptoms. In a 2007 study of five hundred randomly selected girls and women ages fourteen to forty-nine who self-collected vaginal swabs, 29.2 percent had BV, but 84 percent of these didn’t have any symptoms.¹⁶ Another small study in the UK recruited twenty-one healthy women (ages twenty-one to thirty-nine) to self-collect vaginal samples; 43 percent had dysbiosis but did not know it.¹⁷ Thus, testing matters, especially if you’re trying to get pregnant (see sidebar on testing).

It goes without saying that a good Wise Traditions diet is important for a healthy re­productive microbiome, and probiotics can also help; whether from food or from supple­ments, probiotics can shift the balance from a disrupted to a balanced vaginal microbiota. A 2019 meta-analysis pooled ten studies and over twenty-three hundred women to look at whether probiotics alone, without antibiotics, were effective in getting rid of BV.¹⁸ This is an important research question because one in three women will experience BV in their lifetime. The standard of care for BV is antibiot­ics—most of which were developed in the 1980s or early 2000s. Because there has been no drug innovation in this area, recurrence is extremely common, with a 50–60 percentt likelihood of reinfection within six months. Additionally, antibiotics do not rebuild Lactobacillus, which is essential for a healthy female microbiome. This meta-analysis found that one month of daily Lactobacillus probiotics—taken either orally or inserted vaginally—resulted in a two-to three-times higher cure rate compared to placebo. This study shows us that we now have an alternative approach to eliminate BV while simultaneously rehabilitating and correcting the female microbiome.

A 2018 randomized controlled trial (RCT) asked, “What if we give women a yogurt drink for four weeks?” This study looked at the very strains—L. crispatus, L. Jensenii, L. Gasseri and also L. rhamnosus—that should be domi­nant in the vaginal microbiota.¹⁹ At one month, 100 percent of the women were without BV and there was a 200 percent reduction in another rat­ing score. There was also significant reduction in discharge and odor.

An earlier RCT from 2006 assessed whether probiotics paired with the antibiotic metronida­zole might help the metronidazole work better.²⁰ Enrolling one hundred twenty-five premeno­pausal women, ages eighteen to forty-four, who had three markers of BV (vaginal irritation, discharge and “fishy” odor), both the control and intervention groups got metronidazole twice a day for seven days; in addition, the interven­tion group took an oral probiotic twice a day for thirty days, while the control group got a placebo. The antibiotic/probiotic combination was indeed more effective (88 percent) than antibiotics alone (40 percent). Further follow-up identified Lactobacillus colonization in the women in the probiotic group, meaning that they had built up their own production.

As already mentioned, BV recurrence is a problem, and women who are sexually active are twice as likely to experience recurrence as women who are not; in fact, studies suggest an increased risk when women have the same part­ner before and after BV treatment.²¹ In March 2025, a cutting-edge Australian study published in the New England Journal of Medicine offered strong evidence that BV is sexually transmit­ted and suggested that treating male partners could reduce recurrence in women.²² The study involved one hundred sixty-four monogamous couples; in the control group, only the women took metronidazole, but in the intervention group, the male partner also received both oral and topical antimicrobial treatment. Treating men reduced recurrence by 50 percent after twelve weeks: although 35 percent of women in the partner-treatment group experienced recur­rence, fully 63 percent of women in the control group had a recurrence. This study illustrates the growing awareness that sexually active couples experience microbiome “interaction,” prompting some researchers to coin the term the “seminovaginal microbiome” to refer to the “collective microbiota of both partners, transferred and shared during sexual interaction.”²³

We know, of course, that antibiotics are very detrimental to the gut microbiome. I’d love to never use them, but in some cases, time is of the essence. Consider someone who has been going through IVF for two or three years and finds out they have BV. They can take an antibiotic, wipe everything out and then start fresh with a protocol that helps repopulate with Lactobacillus right away. There is no predicting the outcome, but it can be an option. Some studies suggest that giving an antibiotic to women who have had repeated miscarriages and IVF failures does increase suc­cess rates.^24,25

Studies have explored whether probiotics can improve on the standard IVF protocol, which uses estrogen and progesterone to prepare the endo­metrium before the embryo transfer. In one RCT, the researchers assigned three hundred sixteen IVF patients, ages eighteen to thirty-nine, to two groups: the control group got the standard IVF protocol plus placebo, while the intervention group got an intravaginal probiotic for six days before the transfer.²⁶ There were no differences in getting pregnant, but the miscarriage rate was significantly lower in the probiotic group (9.5 vs. 19.1 percent) and the live birth rate was higher.

It is important to be careful with intravaginal probiotics, because we don’t want to use just anything. We don’t want bacteria that don’t belong in the vagina or fillers or strange prebiotics. The two brands that I like are VS-01™ and V-Probiotics™. VS-01 contains three different strains of L. crispatus as well as a prebiotic. Strains in V-Probiotics include L. crispatus, L. gasseri, L. jensenii, L. reuteri and L. rhamnosus. You put them in at bedtime, and the next morning, you wear a panty liner be­cause you might have some discharge. The discharge is normal; it could be remnants of the capsule or remnants of what’s being killed off and coming out. Both products will help with Candida infections, itchiness, odor, discharge and even urinary tract infec­tions. For reproductive-age women, the day when her period ends is generally the best time to insert an intravaginal probiotic once a day for a day or two.

THE ALL-IMPORTANT pH

What do hormonal changes, sexual activ­ity, certain hygiene practices, medication and stress have in common? They all do one of two things—or both. First, they increase the vaginal pH above 4.5, which is going to favor the growth of BV. Second, they lower Lactobacillus, either directly or indirectly, which means that the lactobacilli are not going to be there to release lactic acid and keep the pH where it’s supposed to be. Either way, the pH goes up.

With respect to birth control methods, cop­per IUDs have been linked with BV in some patients.²⁷ In addition, the longer a woman uses hormonal birth control methods, including both pills and hormonal IUDs, the more she is at risk for Candida overgrowth. That’s because constantly supplying estrogen releases too much glycogen, which is a food for Candida.

In terms of sexual activity, be cautious of water-based lubricants, which often contain preservatives (another word for “preservative” is “antibiotic”) that will lower Lactobacillus. Most of them have a pH closer to six, which is above where we want it to be. Water-based lubricants also contain glycerin, which is a sugar that again serves as food for Candida and other pathogens. Another concern is frequency of application. Water-based lubricants need to be applied multiple times in the same intercourse session, which amplifies the sugars and can cause even more damage. Some women turn to coconut oil as a more natural lubricant; however, the higher pH of coconut oil poses the same risk of disturbing the more acidic intravaginal pH.²⁸

What are other sexual activity tips?

• Avoid unnatural condoms, which have plastics and act like endocrine-disrupting chemicals. They also may have preservatives.
• Avoid spermicides, which have been shown to lower Lactobacillus levels,²⁹ preventing them from adhering to the mucus layer.
• Be aware that saliva can introduce dif­ferent microbes.
• Wash sex toys shared between partners.
• After being intimate, some women may wish to insert a vaginal probiotic that night or the next day, once a day for a day or two.

With respect to hygiene practices, the top rule is absolutely no douching! Not only is it ineffective, it’s unnecessary and it’s damaging, because it washes everything out, both good and bad. Regular douching is linked to a fivefold increased BV risk.³⁰ Other tips include wiping front to back, changing period products within a reasonable time frame and choosing looser underwear made of breathable natural fabric. Where medications are concerned, ideally one should avoid antibiotics and other drugs that damage the microbiome, such as NSAIDs.³¹

I have been asked about the practice of douching with raw apple cider vinegar or yo­gurt for cervical dysplasia. Apple cider vinegar temporarily makes the vaginal pH more acidic, which is what we want, but it will not necessarily help the vagina repopulate with good flora, so it probably would not produce a long-lasting ef­fect. As for yogurt, even plain yogurt has natural sugars that could feed Candida. That is why I like to use high-quality probiotics, because they provide just the bacteria and nothing else.

WHAT ABOUT MEN?

Men make fifteen hundred sperm every second and can release up to six hundred thou­sand every time they ejaculate. The life cycle of sperm—from origin to ejaculation—is up to ninety days, meaning that men may be ejacu­lating something their bodies made weeks ago. At a minimum, therefore, men’s window for making changes is three months, but I would argue it’s actually at least six months, because we want to change their diet and lifestyle so they can produce healthy sperm.

Standard semen analysis looks at dysfunc­tions in the ejection and quality of semen. Sperm parameters analyzed include total sperm num­ber (in millions), volume, sperm concentration (million/mL), total sperm motility, progressive motility (that is, how many are actually going somewhere?), morphology (shape) and presence of leukocytes (white blood cells) as an indicator of infection. If a man falls below the threshold for one of these parameters, he will be diagnosed with some type of infertility.

It may help men to think of themselves as a delivery company. Their job is to safely get a very important package—their sperm—to the final destination, which is the egg. But in cases of male infertility, the delivery goes wrong. Per­haps the delivery company doesn’t have enough trucks or drivers, or has too few packages (a low sperm count) and thus fewer chances to get to the destination. Perhaps the GPS is broken, or the driver is stuck in traffic or has flat tires, or he’s driving in circles and can’t move forward (low motility or lack of progressive motility). What if he can’t open the doors of the truck? If he can’t get to the destination or he can’t get the packages out, he can’t deliver. And what if the packages are damaged (abnormally shaped)? In that case, it doesn’t matter how perfect the egg is, the package can’t get delivered the right way.

Even if the sperm count is normal, the sperm may not be of sufficient quality, so I recommend paying attention to a critical biomarker: the semen microbiome.³² It encompasses the entire male reproductive tract—from the testicles to the urethra—to provide a full picture from the inside. What are the determinants of high-quality sperm? Lactobacillus, not surprisingly, is critical for indicators of quality such as morphology, concentration, and viscosity, whereas overgrowth of species like Chlamydia, Mycoplasma, Ureaplasma, E. coli, Klebsiella and Pseudomonas are linked to low qual­ity and potentially correlated with indicators of infertility.

Another measure of male infertility is DNA fragmentation—the DNA is damaged or broken, characterized by mutations, deletions, duplications and single-or double-stranded breaks. It’s normal to have some fragmentation (less than 15 percent), but if a man is above 30 percent, this is a problem, doubling the risk of miscarriage. However, no fertility clinic that I know of in the U.S. regularly checks sperm DNA fragmentation. I looked all over the world to find a place where men can get this testing done and finally found a clinic in Greece called Fertilysis (fertilysis. com) that offers shipping to the U.S. They have tests for both the male microbiome and DNA fragmentation.

The “microbiome-gut-testis axis” is a major factor influencing the male microbiome, defined as “a complex, bidirectional communication system where changes in the gut microbiome can promote systemic alterations and inflam­matory responses that negatively affect the testicular environment and sex hormone pro­duction.”³³ Researchers are increasingly inter­ested in looking at how dysbiosis in the gut or testicular microbiomes contributes to hormonal imbalances and other problems, and how the seminal microbiome affects sperm quality and fertility potential.³⁴

As with women, researchers have studied whether probiotic supplementation can help in the treatment of male infertility. A systematic review of four RCTs involving men diagnosed with idiopathic (cause unknown) infertility found that administration of one or two probi­otics protected sperm DNA from the damage that correlates with declining sperm quality.³⁵ In four out of the four studies, there were sig­nificant improvements in motility, and two to four showed improvements across other sperm parameters. In the study with the longest follow-up period—six months—they also observed statistically significant improvements in levels of testosterone and other hormones. This sug­gests that there could be benefits from taking probiotics for a longer period of time.

TAKEAWAYS

The bottom line for women is that dysbio­sis is a hostile environment for pregnancy, and women can be imbalanced without any notice­able symptoms. Unfortunately, fertility clinics do not routinely offer microbiome testing. Women can do vaginal pH testing on their own, as well as at-home vaginal microbiome testing. As for men, I recommend both semen analysis and the DNA fragmentation test. Even if the sperm count is normal, the “package” may be damaged, and that increases risk of miscarriage. For both women and men, a Wise Traditions diet that includes lactofermented foods and a healthy lifestyle will go a long way toward ensuring an optimal reproductive microbiome.

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SIDEBARS

TESTING

How does a woman know what’s going on “down below”? From a home testing standpoint, the most cost-effective thing she can do is buy a pH strip meter for ten to fifteen dollars and start checking her pH. If the pH of the vagina is above 4.5, she knows that she has work to do.

To get a broader picture, vaginal microbiome at-home test kits (BiomeFx or Evvy) are available for somewhere between two hundred and two hundred eighty dollars. The woman inserts a long Q-tip into her vagina, sends off the swab and gets the results in about four weeks. That kind of test can provide information about the microbes living there and the percentage of each. Evvy also offers advanced testing that looks at Ureaplasma,³⁶ Mycoplasma³⁷ and other species that aren’t regularly tested. If a woman wants to get pregnant, that’s the test that I recommend. BiomeFx is fine if she just wants to know whether she is Lactobacillus-dominant or has Candida. To satisfy simple curiosity, this could be done every six months, but if a woman is having problems conceiving, she should probably do it every two to three months to make sure that what she is doing to remediate the situation is working.

Some women ask why they should care if they are not trying to get pregnant or don’t have symptoms. However, BV increases risks for other things like pelvic inflammatory disease (PID), endometriosis, STIs, cancer, yeast, discom­fort and pain. And when pathogens are eating at the mucus layer, that means less lubrication and more discomfort during intercourse.

The next level of testing would be an endometrial microbiome biopsy: either EMMA (Endometrial Microbiome Metagenomic Analysis) or ALICE (Analysis of Infectious Chronic Endometritis). You have to get this done by a doctor, typically mid-cycle. EMMA will tell you about everything, whereas ALICE looks at specific pathogens—all the ones that we’re curious about. These tests also check for antibiotic susceptibility; if you have a specific pathogen, they will see whether an antibiotic would work against it. The Evvy at-home kit does that as well.

THE INFANT MICROBIOME

There are three windows for modulating the infant microbiome: in utero, during delivery and during the first three years of life.

IN UTERO: Whatever the mother’s gut microbiome is, that’s exactly what she’s going to pass on to her baby. In­terestingly, scientists used to believe that the placental microbiome was sterile, but it’s not.³⁸ Some data suggest that it matches what is in the mother’s mouth,³⁹ which is a good reason for mom to take care of her oral health! Studies also have pointed to the role of obesity and excessive weight gain during pregnancy in producing “adverse gut microbiota alterations in mothers and their infants.”⁴⁰

DELIVERY: Birth method matters. Vaginally delivered babies’ microbiota has a higher Bifidobacterium count. The baby passes through the birth canal, swallows some of the mom’s vaginal mucus and fluids, and that’s their “starter pack.” However, the mother’s diet, lifestyle, stress and history of antibiotics will influence whether her vaginal microbiota is optimal. If the baby is born via C-section, the infant microbiota will have a lower Bifidobacterium count and higher pathogen levels. Instead of picking up their “starter pack” in the birth canal, they will get it from the hospital environ­ment. In either mode of delivery, if the mother receives antibiotics, there will be vertical transmission from mom to baby.

INFANCY: During infancy, the first things to look at are whether the baby is breastfeeding or formula feeding. If breastfeeding, what is the mother’s diet like? Is she passing probiotics through the breastmilk (whether from fermented foods or supplements)? If formula feeding, is it one of the WAPF homemade formula recipes or conventional soy for­mula? Is the baby taking antibiotics for any reason? The fact that overweight pregnant women have reduced numbers of intestinal bifidobacteria also has significant implications for their infants: “Decreased Lactobacillus and Bifidobacterium spp. colonization during early infancy is associated with a greater risk for allergies at five years of life.”⁴⁰ In addition to allergies, infant gut imbalances may predict childhood obesity as well as asthma, eczema, infant colic, celiac disease, type 1 diabetes, metabolic syndrome and, in preterm babies, a form of gut inflammation called necrotizing enterocolitis, where the tissues in the lining of the gastrointestinal tract start to die, allowing bacteria into the bloodstream.

If the mother takes probiotics during pregnancy, does it produce healthier outcomes for mom and baby? A study published in 2025 answered yes.⁴¹ When pregnant women began taking a probiotic in the third trimester (at twenty-eight weeks) and continued through the pregnancy, delivery and four to six weeks postpartum, they and their babies were less likely to get sick compared to mothers and babies in the placebo group, and when babies did get sick, it cut their sick days in half. The intervention also improved infant gut colonization, with the C-section babies benefiting the most. Another series of studies showed that giving mothers a Lactobacillus probiotic prenatally as well as postnatally, and giving infants probiotics for six months, helped prevent eczema and other atopic conditions,⁴² with effects that extended well beyond infancy.^43,44 The significance of these studies was that even though the baby stopped taking the probiotics at six months, the effect was seen for years.

For women who have C-sections, exclusive breastfeeding can narrow the differences between C-section and vagi­nally delivered babies due to special sugars in breastmilk (human milk oligosaccharides [HMOs]) that strongly shape gut bacteria. HMOs serve as prebiotics, selectively feeding bifidobacteria. If a baby is born via C-section and the mother can’t breastfeed (for whatever reason), I recommend that she start the baby on probiotics and prebiotics within three months, which can partly restore the gut flora.

REFERENCES

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6. Perez-Carrasco V, Soriano-Lerma A, Soriano M, et al. Urinary microbiome: yin and yang of the urinary tract. Front Cell Infect Microbiol. 2021 May 18;11:617002.
7. Hong X, Zhao J, Yin J, et al. The association between the pre-pregnancy vaginal micro­biome and time-to-pregnancy: a Chinese pregnancy-planning cohort study. BMC Med. 2022 Aug 1;20(1):246.
8. Kairys N, Carlson K, Garg M. Gardnerella vaginalis. Treasure Island (FL): StatPearls Publishing; 2025 Jan-.
9. Toson B, Simon C, Moreno I. The endometrial microbiome and its impact on human conception. Int J Mol Sci. 2022 Jan 1;23(1):485.
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