Optimizing Maternal Microbiome: Role in Improved Conception and Pregnancy Outcome.

Preventive evaluation of the oral cavity with special attention to teeth/gums is required prior to conception where dental caries and abscess are prevented. This is important since with pregnancy dental caries that are not treated easily can become an abscess and this can spread causing systemic infection even affecting the heart. In case of abscess development, antibiotics and even surgery will be required. Therefore, having proper oral hygiene has major importance since if it is not addressed complications can take place. This was recently reported by a systematic review of pregnant women with periodontal disease. Data demonstrated no increased maternal or fetal death; however, it significantly demonstrated that those at increased risk of developing preeclampsia and delivering a preterm and/or low birth weight neonate. However, those suggestions were not fully confirmed in other studies. The microflora was examined throughout pregnancy in the saliva. The data showed in 101 women in both preconception and pregnancy. There was a reduced microbial diversity in the third trimester; pathogens Prevotella and Atopobium parvulum were increased. Improved oral hygiene showed lower bacterial diversity. Oral hygiene is important to be maintained prior and during pregnancy; it may reduce complications [ 83 , 84 , 85 , 86 ]. Table  2 describes the healthy microbiome in the vaginal tract, GI, urine, and oral cavity. Address therapeutic measures that can improve the microflora. The microbiome and its role in reproductive health. L. crispatus , L. rhamnosus , L. fermentum , L. gasseri Bacteria causing vaginosis or UTIs Protective: Prevent vaginitis, maintain urinary microbiome. Proper hydration, prevent infection. Cultures based treatment. Harmful: Ascending vaginal pathogens. Dehydration, carbonated drinks. Non targeted antibiotics. Note: This table highlights the different sites of the microbiome, the specific microorganisms involved, and their impact on pregnancy.

Until recently it was viewed that the uterus, specifically that the endometrium should have a sterile environment. This is challenged by finding frequently ascending bacteria in the endometrium‐in many cases this can be indolent. Until endometrial biopsy and/or cultures are performed, the diagnosis is not made‐ which is rarely conducted. This is because there is a high risk of contamination. Such is further emphasized by the presence of microbiomes also in the placenta. Importantly, this is a common finding observed also in uncomplicated pregnancies. Precise mechanism of systemic microbiome transfer to both uterus and the fetus remain not fully understood. It even continues to be challenged and it is not supported by recent data. This indicates that endometrial microbiota is innate and becoming pathogenic in only selective cases. This is true only for bacteria and not for fungi, viruses, or parasites [ 54 ]. Ascending diverse vaginal bacteria to the endometrium takes place through the endocervix. The exposure to diverse local pathogens makes the ascending bacteria to the endometrium vulnerable for infection. Such is different from the local vaginal environment which has its own innate microflora (lactobacilli dominant crispatus genus). Those bacteria are protective and frequently negate other pathogens' effects. In contrast, the endometrium does not have a defined resident bacterium; therefore, any ascending pathogen will not be able to be counteracted through the presence of a beneficial innate microbiome. The clinical symptoms range from an indolent infection to acute endometritis. In contrast to the vagina where the mucosa is a highly effective barrier in preventing systemic infection, the endometrium is different. In the endometrium, a local infection can become systemically symptomatic evidenced by fever, abdominal pain, and an increase in peripheral WBC, a rare event in the vagina. Consequently, all endometritis treatments require systemic administration as compared with local antibiotics administration for a defined vaginal infection. The endometrium is vulnerable to infection since there are no protective layers. This is since the endometrial lining changes through the menstrual cycle from proliferative and estrogen‐dependent events; thereby, the cervical mucus enables ascending sperm as well as potential pathogens access. Followed by the secretory phase, where through progesterone‐dependent action it alters the cervical mucus, creating a defensive barrier against sperm access and pathogens' entry. However, those pathogens that have already reached the endometrium will benefit from the presence of the menstrual blood, a rich culture medium [ 55 , 56 ]. Blastocyst implantation requires specific embryo maternal signaling to enable maternal recognition of pregnancy and promote endometrial receptivity in a narrow‐targeted implantation window [ 55 ]. The presence of local pathogens in the endometrium can significantly affect embryo implantation and prevent embryogenesis. Overall, the embryo requires a secretory endometrium creating a local immune tolerant environment through local progesterone dominant action. In contrast, pathogens' presence in the endometrium causes local inflammatory changes associated with immune reactivity, negating the embedding process. The decidua, which is the mucosal lining of the uterus, is populated by many maternal immune cells during pregnancy. In this context, increased natural killer (NK) cells and macrophage presence assists the uterine vasculature in adjusting embryo/fetus access to oxygen and nutrition, thus facilitating fetal growth. Trophoblastic cells detach from the developing placenta and penetrate deeply into the endometrium, interacting with immune cells. Beyond maintaining homeostasis, decidual NK cells can counteract pathogens supporting fetal and placenta development. Otherwise, pathogens can activate NK cells for inflammatory signaling, affecting the pregnancy [ 57 ]. The consequence is failed effective interaction between the implanted blastocyst and the endometrium through controlled invasion of the trophoblast leading later to vascularization and placenta formation [ 58 ]. Once embryogenesis is completed, the uterus should adapt to pregnancy to enable fetal development until term. Consequently, altered local microbiomes can significantly alter this stepwise progression to term, and it was documented that the altered vaginal microbiome reaches the endometrium early on, leading to recurrent pregnancy loss if it persists without treatment. Also, it has later adverse ramifications causing preterm birth with or without leading to chorioamnionitis [ 6 , 58 , 59 ]. The cause of endometritis in general is due to chlamydia and/or gonorrhea or other bacteria like BV, among others. Bacterial vaginosis is a highly frequent vaginal pathogen. It is associated with local symptoms of discharge odor and is detected in culture. The high 50% presence of BV biofilm in the endometrium supports ascending infection. This was also found during pregnancy, increasing preterm birth risk. BV infection was documented in fallopian tube samples reaching also the peritoneal cavity. Such support systemic exposure through the vaginal ascending route. Therefore, systemic metronidazole administration would be preferable to a local cream, thereby also an ascending endometrial BV and possibly an associated polymicrobial infection already present could be eradicated. This should specifically be emphasized in view of an impending conception [ 60 ]. Endometrial positive cultures results are clearly informative and require therapy. A more detailed gene analysis defines at a high accuracy the diverse microbiota and not only mostly the dominant species usually are identified in culture. In nineteen sub‐fertile and non‐pregnant asymptomatic women, endometrial samples were collected through hysteroscopy followed by deep sequencing V1‐2 hypervariable regions of the 16S ribosomal RNA (rRNA) analysis. Data revealed a high polymicrobial flora presence. Fifteen phylotypes were present in all samples. The presence of Bacteroides genus, xylanisolvens, B. thetaiotaomicron , and B. fragilis reflected endometrial bacteria. L. crispatus or L. iners combined with Bacteroides was present only in six women. Others had a diverse variety of bacteria. Thus, local microbiome mostly remains undetected unless such complex analysis—which is rarely available—takes place. Such data could be related to the reduced fertility observed in these patients. The presence of endocervical bacteria (possible contaminant) also raises the possibility that the Lactobacilli found in the vagina may confer a local protective role also in the endometrium thus supporting fertility and protection against STI. Such require further confirmation [ 61 , 62 ]. When cervical cultures document a specific infection (i.e., BV, Chlamydia, Gonorrhea) the treatment can directly eradicate the pathogen. However, in other cases cultures may not be fully informative and thereby systemic broad‐spectrum antibiotics are used. When infection results in acute endometritis it is associated with clinical symptoms such as abdominal pain, fever, and vaginal discharge. Consequently, due to their emergent clinical status, patients' systemic antibiotics will be used. Frequently, by the time the diagnosis is made, infection has already spread into the peritoneum as well as affecting the fallopian tubes causing pelvic inflammatory disease (PID). Even following the resolution of the acute infection, damage has already frequently occurred affecting the uterine lining as well as causing pelvic adhesions, further pain, fever, and altered bowel function. Such spread infection also damages the fallopian tubes causing obstruction, adhesions, and even hydrosalpinx. Overall, PID reduces the chances of conception and favorable pregnancy outcomes. The presence of hydrosalpinx, once it is identified, poses a risk for pregnancy and is associated with symptoms of abdominal pain. Therefore, in these patients with past PID, prior to considering conception, testing for STI should be conducted to document that the infection has been resolved. In addition, it is advisable to perform a vaginal ultrasound since the risk of ectopic pregnancy is increased and thereby if conception occurred it is important to follow with serial bhCG levels and confirmation of gestational sac presence by using vaginal ultrasound, since there is an increased risk for a clinically severe ectopic pregnancy. Patients at risk with a careful and specific timely approach would mitigate the risk of a ruptured ectopic pregnancy since the rupture rate is high. It is imperative to prevent tubal rupture which is associated with high morbidity and mortality. To resolve such serious conditions frequently it requires the performance of operative laparoscopy to remove the affected tube. When the risk of rupture with an ectopic is lower, Methotrexate injections administration can be contemplated, provided that careful follow‐up is made serially following the bhCG levels until they become non‐detectable. It is advisable to remove the affected fallopian tube to reduce the risk of future ectopic pregnancy, especially in the case of hydrosalpinx presence. Not only due to the risk of future ectopic pregnancy, but it is also compounded by the presence of the adverse inflammatory fluid and possible residual pathogens residing in the tube, which is demonstrated to impair future pregnancy success [ 63 ]. In the case of chronic endometritis, ranging from being symptomatic resembling PID to being indolent while creating a progressive pathology and failed implantation up to early pregnancy loss. In general, indolent endometritis is identified during hysteroscopy and in patients that are undergoing fertility therapy, also including IVF. Here, endometrial cultures are informative even though contamination from the vaginal microbiome can alter information gained unless collection is performed under meticulous methods. When this is performed and infection and local pathology are diagnosed, the use of systemic antibiotics is effective, but for a chronic condition, long‐term treatment will be required. This will be followed by repeat cultures to confirm that the infection was already resolved and pregnancy could be safely pursued [ 63 , 64 , 65 ]. Emerging evidence supports the view that patients who are undergoing fertility management, especially those with a history of recurrent pregnancy failure, may benefit from hysteroscopy. Beyond histology, immunohistochemistry and cultures are required. Based on diagnostics, antibiotic treatment increased pregnancy and live birth rates. Therefore, hysteroscopy should be the gold standard in these patients' management [ 65 ]. The endometrium where the embryo implants is not a sterile environment; however, as described below, the meconium mostly remains sterile until birth. This indicates that there is not a noticeable maternal‐fetal transmission of pathogens: bacteria and others, unless there is significant pathology leading to maternal‐fetal transfer, also evidenced by ascending infections such as chorioamnionitis. Advanced sequencing techniques for bacteria and virus compared with buffer controls and pediatric stool samples done at both mid‐gestation and term pregnancy found only occasional viral signatures reflecting the maintained fetal environment sterility. Thus, meconium also stays sterile and acquires microflora mostly in the post‐natal period within the first 24–48 h after birth [ 66 , 67 , 68 ]. This would indicate that there is an intimate mechanism that creates an environment favorable to the embryo/fetus in the uterus which preserves in general and specifically the gastrointestinal tract from exposure to bacteria from both beneficial and pathogenic genus. However, the presence of ascending infection affecting the amniotic fluid can cause severe infection in the fetus and newborn; therefore, the vulnerability is high when there is inappropriate access of pathogens [ 58 ]. The evidence as shown with Covid19 infection is highly demonstrative. We reported that despite maternal infection, which can be very severe leading to high circulating virus titer and infected immune cells, such is associated with placental infection at ~100%. On the other hand, viral transmission to the newborn is extremely low, only 2%–2.5%. Therefore, the placenta has an important function as a barrier; in this case, the newborn is not to be exposed to pathogens. However, the placenta does not always serve such a protective barrier since in other infections when they are severe, such as Zika, HIV, Syphilis, Toxoplasmosis, and measles affecting the mother, the infection can also be transmitted to the fetus, causing even death. So therefore, we must view the placenta as a semi‐permeable barrier that can be a protector to a large degree, while in other cases, it is a transmitter of pathogens [ 69 ].

The obesity epidemic continues affecting both LMIC and high resource countries. This was further aggravated during the Covid‐19 epidemic, and it continues until the present. The associated poor‐quality nutrition that is easily accessible plays a key role. Such an imbalance leads to significant periconceptual to conceptual issues. The resulting high BMI or already present related pathologies in lower fertility require advanced medical interventions to achieve conception. These are associated with poor ovulation, chemical pregnancy, and embryopathy, including miscarriage occurring at the early stage of pregnancy. Furthermore, prediabetes can lead to diabetes and hypertension in pregnancy, causing fetal pathologies like growth restriction or macrosomia. Such high‐risk conditions are frequently associated with an altered vaginal microbiome associated with fungal and bacterial infections. Adjustment of the underlying conditions by improving diet habits, exercise aiming to reduce BMI based on local ethnic standards, hormonal work‐up and appropriate diabetes control can improve both conception and pregnancy outcome. Treatment of fungal infections causing vaginal itching, burning and discharge by local treatment is effective since in pregnancy systemic treatment is not feasible. The gut microbiome is also frequently affected due to poor quality food intake which can be restored using good quality nutrition and supplemental micro and macronutrients. As for diabetes, there is a propensity to develop other infections beyond the vagina, also in urine, oral cavity, and even skin. The second aspect is the GI tract, since the poor‐quality imbalanced nutrition causes altered flora, increased bowel inflammation, and GI symptomatology which becomes more evident during pregnancy and is manifested by abdominal pain, bloating, and altered bowel movement. Correcting the altered GI microbiome by proper nutrition can make a major difference. Thus, improving the High BMI/polycystic ovary syndrome (PCOS)/Diabetes spectrum can go a long way to adjust the microbiome and thereby reducing additional complications in these at‐risk patients [ 7 ]. There is a growing problem of antibiotic resistance development due to excessive antibiotic use. Importantly, repeated antibiotic use subsequently reduces their efficacy. Therefore, the need to use more antibiotics including second and third line that may have toxic side effects leads to multidrug resistance. It is evident that managing such resistance as pregnancy initiates becomes more difficult since certain antibiotics can also have teratogenic and significant toxicity, minimizing their safe utilization, especially during embryogenesis. Thereby, it will be more difficult to eradicate resistant pathogens, and the used antibiotics will only be partially effective in adjusting the altered microbiome. Prevention of antibiotic resistance in these cases should be strongly implemented. There are two interconnected aspects: first, the offending agents are difficult to treat and second, the altered microbiome present on site exerts negative effects on the maternal system. This is emphasized since there is an increased vulnerability to infection due to pregnancy and compounded by the associated physiologic changes. The solution is avoiding unnecessary antibiotic use, especially those related to mild viral conditions that can be successfully addressed by simple and local measures. Furthermore, proper infection diagnostics prior to treatment are essential. Another important aspect in addressing the issue is preventing antibiotic resistance through exposure to beneficial gut bacteria intake [ 8 , 9 ]. It is important to mention the role of vaccination here. Timely vaccination can reduce the need of using advanced potentially harmful medications during the gestational period, especially in the first trimester. The current recommendations on vaccine use, their safety use at an appropriate time in a gestation is recently reported; such preventive measures can make a major positive influence on maternal health [ 2 ]. When clinically indicated, there is a need to use appropriate medications. However, many of them, beyond causing adverse effects, alter both vaginal and the GI flora. Based on clinical judgment the exposure to medications per force should be limited since there is always some concern regarding embryopathy. Minimizing the use of medications is advisable when conception is planned. They should not be drastically stopped, since that would be ill advised, but a gradual decrease should follow in view of the planned pregnancy where possible. Such an approach will enable microbiome recovery, benefiting the impending gestation. These specifically are related to steroids and immune suppressive drugs which are used for treatment of inflammatory diseases which clearly alter the microbiome. This causes a lower immune response which promotes pathogen resurgence. Especially during pregnancy, due to anatomic and immunological changes, certain pathogens can become more virulent and are less likely to be eradicated. Therefore, the use of medications should be minimized as much as is feasible. Patients that are currently on medications for other diverse diseases should consult prior to stopping any medication that would affect their general health. Furthermore, in certain conditions patients should aim to conceive, preferably only when a given medication has been ‘washed out’ of the system, minimizing the risk of exposure. Overall sound clinical judgment should prevail balancing need for medication use to address medical conditions, the desire for pregnancy and improving maternal microbiome to minimize pregnancy associated pathologies [ 10 , 11 , 12 , 13 ]. There is a difference between poor nutrition that alters the microbiome and malnutrition that reduces access to dietary macro and micronutrients, leading to weight loss and is documented to increase pregnancy pathologies. Since what is consumed as food creates the environment for the microbiome, access to food is imperative with effective food consumption of decent quality. The problem of lack of access to nutritious food is pervasive in many countries and not only in LMIC and rural settings but also in high‐resource countries. Efforts should be made to put a special emphasis on young women seeking fertility for their access to high‐quality nutrition. Defining the required food and any supplements in a clearly described manner, specifically affected populations in need, can make a major difference to the outcome with optimization of the microbiome. In diverse populations, the ability to access appropriate nutrition will be significantly different. For example, access to milk and milk products, a major source of lactobacilli, is not available in many countries; thereby, adequate substitutes are needed. The specific nutrients and supplements beyond the currently offered prenatal vitamins will be in the later part of the paper. The avoidance of trans fats, simple carbohydrates while increasing plant‐based proteins, dietary fiber, folic acid, vitamin D, vitamins, minerals, and Omega‐3 that are plant based. Overall, sometimes simple adjustments can make a major difference in maternal and newborn outcomes [ 10 ]. In its other manifestation, malnutrition also exists in high resource countries where individuals are spoiled for choice with an overwhelming supply of fast and instant food depriving them of the recommended dietary allowances of vital nutrients, leading to chronic illnesses such as obesity and metabolic syndrome and their disease sequelae. The challenges in high resource countries are that the widespread decrease in the prevalence of malnutrition has been counteracted by the disproportionately increasing prevalence of obesity, and it is expected that the gap between obesity and malnutrition will continue to expand in the next ten years [ 11 ]. Infertility is a growing problem, and diet can play a significant role in female fertility. Research shows that unhealthy diets high in trans fats, refined carbs, and added sugars can negatively impact fertility, while diets rich in fiber, omega‐3s, plant‐based protein, vitamins, and minerals have a positive effect. The gut microbiota's role in fertility warrants further investigation. While folic acid supplementation is recommended, and vitamin D and iodine deficiencies should be addressed, the impact of gluten (in the absence of celiac disease), moderate caffeine, and alcohol on fertility needs more research. Phytoestrogens may be beneficial, but more research is needed on supplements. Overall, diet and lifestyle are key factors in fertility, making further research in this area crucial. Similar conclusions can be found in another review paper which analyzed the relationship between diet and environmental factors, including nutrition, and women's reproductive health [ 12 ] It is claimed that consumption of polyunsaturated fatty acids, fiber, and the generally Mediterranean diet is beneficial for female fertility. It is also explored how dietary components affect female reproduction and assisted reproductive technologies outcomes, including the complex interactions between diet, genes, gene expression, and gut microbiota. The impact of nutrition on microbiota was also explored in [ 13 ] where it was examined how the mother's gut microbiota is passed on to the fetus and how this impacts the fetus' health. That research examines how the maternal diet during pregnancy influences both her own and her fetal gut microbiota and the fetus's overall health. Specifically, it claims that a typical Western diet, containing significant amounts of processed foods and sugars, is related to adverse maternal and child health outcomes, such as fetal overgrowth, macrosomia, congenital defects, and stillbirth, among others. Another adverse effect of abnormal gut microbiota in pregnant women is potentially gestational diabetes mellitus (GDM). Also, in this case, diet impacts the onset of GDM, and dietary supplements like probiotics, prebiotics, and symbiotics might help to regulate the microbiota and help prevent or even treat GDM. The impact of these supplements not only on GDM but also on other health risk factors such as obesity and type 2 diabetes has been explored to support possible efficacy [ 14 , 15 , 16 ]. Vaginal progesterone is commonly used by obstetricians and infertility specialists to improve pregnancy outcomes. It is often prescribed without a proper indication. However, there are doubts as to whether the administration of vaginal progesterone could alter the vaginal microbiome [ 17 ] While, according to [ 18 ], the microbiome does not seem to be altered during pregnancy when a woman uses vaginal progesterone. Contraception is a tool for women who do not want to get pregnant. Most available contraceptives contain hormones in their composition. Therefore, there are doubts as to whether combined contraceptives or those that only contain progesterone can alter the vaginal microbiome, since this is naturally influenced by the woman's natural hormones during the menstrual cycle [ 19 ]. Generally different contraceptive methods, whether long‐acting reversible contraception (LARC) or not, whether combined or only progesterone, do not alter the vaginal microbiome during their use. The exception is the copper intrauterine device (IUD), which increases the incidence of bacterial vaginosis. The hormonal progesterone‐based IUD apparently has the same effect; additional studies are needed to confirm [ 20 ]. Table  1 describes modifiable factors that can negatively affect the microbiome and preconception and pregnancy. Key factors affecting the maternal microbiome. Note: This table summarizes the various factors that can negatively impact a woman's microbiome, which are crucial to address for a healthy pregnancy.

It is viewed that during pregnancy the fetus is in a sterile environment with no evidence of an in utero microbiome transfer. The first meconium of the baby is sterile and then the neonate gut microbiome is quickly colonized [ 70 ]. Factors important in promoting transfer between mother and newborn include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Currently there is unambiguous evidence that the vaginal delivery route offers a highly beneficial environment to the newborn by exposure to bacilli, potentially lactobacilli [ 70 ]. Once the microbiome is once acquired, it will exert long term beneficial ramifications lasting through adulthood [ 71 ]. In contrast, following C‐section, the vaginal flora exposure is minimal to absent and therefore skin bacteria are acquired mostly by the newborn. Such limited first exposure to high quality bacteria leads to disorders through increased pathogens exposure, causing inflammatory and connective tissue disorders among others later in life. Consequently, avoidance of a C‐section, unless it is necessary and medically indicated, should not be pursued [ 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 ]. If there is premature rupture of membranes, at that point, ascending bacteria reach the amniotic fluid, and if it is not pathogenic, it will enable beneficial bacteria exposure even if cesarean section follows [ 6 ]. Such acquisition of the right microflora by the newborn will guide colonization throughout life. The acquired GI microbiome, when it is beneficial to the host, has a dual action. One enables better absorption of nutrients through creation of microbiome microfilm, where a mutual benefit takes place where the bacteria thrive and hosts enable to have a good digestive system mostly segregated to the colon thereby well‐being preserved. To achieve that goal, the beneficial microbiome must also prevent pathogens' access and their colonization. Thereby they exert in addition an important anti‐pathogenic activity. Consequently, the host benefits also by being protected against an adverse microbiota. However, this balance is delicate since it can be easily disrupted. It is enough to consume contaminated food or drink, and the gut microflora can be severely affected even in the long term. This delicate balance is further shifted during pregnancy especially in the first trimester and even prior to conception. Significant attention should be paid to keep in check the GI tract which will be challenged mostly in the first trimester. This is shown since young women in their reproductive age are prone to inflammatory bowel disease and related inflammatory conditions affected by the presence of an altered microflora. The adult GI microflora is complex; the content is 10‐fold lower in the upper intestine as compared with the colon. It is composed of 1000–1500 types of bacteria, viruses, fungi, and archaea. Firmicutes (Clostridiales, Lactobacillus, Enterococcus) and Bacteroidetes are most abundant while Bifidobacteria, Escherichia coli , Fusobacteria, and Verrucomi are less abundant. The presence of the gut biota is not only relevant locally, but it has a leading role in systemic immunity and metabolism as well [ 73 ]. Pregnancy poses a major challenge to the GI tract. There is evidence that preconception and first trimester microbiota are similar which will change in later trimesters where Proteobacteria, Bifidobacteria, and Lactobacilli crispatus increase. The result is better control of insulin levels which is required as the calorie intake increases at the II and III trimesters associated with increased weight gain. Further, there is a beneficial effect on the systemic immunity promoting tolerance and minimizing proinflammatory milieu [ 74 ]. Pregnancy has a major impact on the digestive tract. Both must adjust to increased macro and micronutrients intake, but also to the significant physiological changes related to bowel function that also take place. This is mostly manifested already in early pregnancy but can also last even throughout pregnancy. This is related to indigestion, food aversion, nausea, vomiting, bloating, abdominal pain, diarrhea, and constipation. Consequently, during pregnancy, dietary habits must change, but it is difficult to adjust in a healthy manner if the digestive tract is already altered and the microbiome is affected. Therefore, it is strongly advised that any GI problem should be addressed prior to conception since thereafter corrective measures are limited. Among them gastritis caused by the presence of the helicobacter that would require multiple antibiotic treatments to eradicate. Otherwise, it can cause severe upper intestinal problems of nausea and vomiting up to hyperemesis that severely affect mother and fetus. Another disorder is small intestine bacterial overgrowth (SIBO). This also may require antibiotics, adjusted diet, and even steroids in severe cases. The lower GI tract, especially the colon where adverse bacteria are present can cause diarrhea, dehydration, and significant weight loss. This can be corrected by diet adjustment and the use of certain probiotics. The use of the right proportion of food groups combined with micronutrients has a significant role in maintaining the local microflora. Overall, targeted GI cultures are informative and enable specific treatment [ 74 ]. In female anatomy there is a close contact among the urethra, vagina, cervix, and rectum. Testing of the microflora in those different sites compared fertile vs. infertile patients, where follicular fluid was also collected, ( N  = 22) and 10 controls. The urethra, vagina and rectum as expected had a lactobacilli johnsonii dominance in fertile patient's vs. BV in the urethra and vagina in infertile patients. A specific bacterium, Geobacillus thermogeniticans, was widely detected in infertile patients. The L Acidophilus presence in follicular fluid may have reduced fertility as well: A strong indicator of an ascending microflora. Such indicates that adverse bladder‐genital‐rectal flora impairs conception and may increase risk for pregnancy complications as amply documented for BV infection. Another study showed that increased intake of partially hydrolyzed guar gum improved gut dysbiosis and increased in vitro fertilization success rate by increasing Bifidobacterium and reducing Paraprevitella and Blautela genus [ 75 ]. Examination of the microbiome provides valuable information whether there is an association between adverse microflora and evolving pregnancy pathologies. Data showed that ( N  = 39/group) maternal and infant stool microbiome was analyzed. There was a strong association between higher BMI and altered microbiome in the stool. There was increased Bacteroides and lower Phascolarctobacterium Acidaminococcus and Dialister in normal weight women. As for infants' stool, it differed based on mode of delivery and whether there was a vaginal delivery, breastfeeding or not. Such variance is expected since postpartum exposure is enforced by a combined vaginal birth combined with breastfeeding. Specifically, normal weight women had lower Megasphaera genus vs. other groups where Streptococcus and Staphylococcus were of low abundance. Thus, BMI correlates with bacterial diversity both in mother and newborn. This may be related also to the type of nutrition that patients are exposed to causing the variability in BMI—likely balanced diet vs. fast food diet—the major cause of obesity. For example, obesity led to decreased beneficial bacteria leading to gestational diabetes. The change in the bacteria genus is significant and it involves increased Parabacteroides , Dialister , Akkermansia , and reduced Pseudomonades order and Acinetobacter genus among several others [ 76 ]. There is evidence pregnancy‐associated disorders are associated with altered GI microbiome. The altered microbiome not only modifies the GI function and inflammation, but also has significant systemic effects affecting both cytokines, shifting toward inflammatory markers as well as the systemic immunity. What remains unclear is whether this is due to pregnancy pathology or the altered microbiome. Women in reproductive age have increased incidence of GI pathologies among them IBS, ulcerative colitis, and Crohn disease, and such conditions are frequently expected to be aggravated if severe during pregnancy, also due to pregnancy physiology and the excess calories that are consumed. There is an abundance of Acinetobacter , Enterococci , and Paenibacillus , and the reduced Blautia and Collinsella genus; those bacteria reflect a negative biomarker [ 77 ]. Overall, improved BMI, proper diet adjustment, and no processed food play a major protective role in reducing pregnancy‐associated pathologies and GI pathologies. The pregnancy environment has a fundamental impact on the fetus which also persists to adulthood. Beyond exposure to pathogens causing up to congenital anomalies, for example the role of altered microbiome that is associated with pregnancy pathologies and is termed the fetal origin of adult disease. With respect to the altered maternal microbiome, there is evidence that bowel inflammation during pregnancy due to the altered microbiome can be related to increased incidence of colitis in adulthood. Altered maternal microbiomes have significant systemic effects affecting development and effective systemic adaptive immunity; in addition, there is evidence that the maternal microbiome can also alter newborn brain development by interaction with brain microglia activating inflammatory signals in a complex manner [ 77 , 78 , 79 , 80 ].

The urinary biome plays a crucial role in preserving the health of the urothelium and avoiding urinary tract infections (UTIs), while also enhancing the immune response in the urinary tract. An imbalance of microbe populations in this site increases UTI, kidney stone formation (nephrolithiasis), and lower urinary tract dysfunction/infection. The urine is not sterile and has its own microbiome conferring a local protective environment against infection. The presence of local Lactobacillus emerged as a major potential antipathogen similar to that in the vagina. A recent study analyzing large‐scale urinary microbiomes in women with urinary incontinence revealed the presence of a diverse number of bacteria. Specifically, in those without symptoms leading to leaks, there was a low diversity and Lactobacilli were dominant [ 81 ]. The other bacteria identified were highly diverse. Those included Streptococcus, Staphylococcus, Bacteroides, several Actinobacteria such as Gardnerella, and Escherichia. Such analysis indicates that all bacteria in the urine causing bacteriuria do not necessarily lead to infection while they ascend from the vaginal flora. Based on recent data, suspected urine infections are not treated by antibiotics but by measures that minimize symptoms, increasing hydration, electrolytes, and agents that acidify the urine, and even anti‐inflammatory agents. However, beyond urinary frequency and some dysuria, presence when severe pain, fever, and risk of pyelonephritis are present antibiotics are required. The empiric use of antibiotics should be minimized, and the antibiotic administration should be based on urine culture that should be collected aseptically since the likelihood of vaginal contamination is high. In general, colonies that are single bacteria are best to be treated which are sensitive to a given antibiotic. Consequently, treatment by antibiotics when > 30,000 colonies of a specific genus are identified, and unless it is a major pathogen, lower number of colonies are also treated. This increase in the number of bacteria identified in the urine culture may be more complex to treat, likely due to contamination, and therefore a repeat culture is advised using aseptic technique. While prior pregnancy increased hydration and maintaining urine acidity with also cranberry use but not chronically can be corrective; however, in pregnancy this may not be the case [ 82 ]. The urinary system low grade infection must be addressed since it is not done prior to pregnancy during pregnancy due to altered kidney activity, increased partial bladder prolapse, and ureter stasis; there is an increased rate of urinary tract infections, which can be severe, leading up to pyelonephritis causing septicemia and premature birth. Also, starting antibiotic treatment becomes more difficult with less access to safe antibiotics. Moreover, improving the vaginal flora can play a key role in preventing urinary infection. The urinary tract microbiota has a substantial influence on bladder homeostasis, which is crucial for sustaining overall health.

For conception to take place, the vaginal flora must be favorable. This is followed by the uterus where the endometrium should be an environment free of pathogens. Further, the fallopian tubes/ovaries peritoneum must be free of infection through ascending infection. Vaginal microbiome dynamic changes routine testing is needed. The vaginal microbiome is complex and changing, and is continuously exposed to the local, external environment as well as altered by sexual activity. In addition, exposure to menstrual blood occurs in general on a regular basis. In any given time, there are multiple species of bacteria present, thus it is important to recognize that their proportion and not their absolute number of a given subspecies reflect a normal microbiome. As for specific species, the presence of any fungus, viruses, and parasites reflects local pathology. Therefore, only bacterial species in a favorable ratio would indicate health. Also, this ratio changes continuously. There is a perception that an apparently healthy microbiome is present when there is no significant vaginal discharge, itching, burning, pain, or odor. However, is this a clear indicator that there is no abnormal flora or serious pathology? The answer is no. Since cultures are periodically not performed, there is no unmistakable evidence whether there is or is not an altered microbiome. The substantial experience gathered by introducing periodic cervical cancer screening to assess human papilloma virus (HPV) presence is compelling. Herein, in general, there are no symptoms while the pathology can be severe. The pap smear, if atypical squamous cells of undetermined significance (ASCUS) and HPV is positive, then cervical colposcopy and biopsy are followed. Since if active cervical cancer is present, surgery will have to follow, and conception will not be immediately pursued. Prior to pregnancy, pap smear performance is advised, based on risk group and age. This is because managing abnormal findings is difficult during pregnancy [ 21 ]. For conception to take place, the vaginal flora must be favorable. This is followed by the uterus where the endometrium should be an environment free of pathogens. Further, the fallopian tubes/ovaries peritoneum must be free of infection through ascending infection. Vaginal microbiome dynamic changes routine testing is needed. The vaginal microbiome is complex and changing, and is continuously exposed to the local, external environment as well as altered by sexual activity. In addition, exposure to menstrual blood occurs in general on a regular basis. In any given time, there are multiple species of bacteria present, thus it is important to recognize that their proportion and not their absolute number of a given subspecies reflect a normal microbiome. As for specific species, the presence of any fungus, viruses, and parasites reflects local pathology. Therefore, only bacterial species in a favorable ratio would indicate health. Also, this ratio changes continuously. There is a perception that an apparently healthy microbiome is present when there is no significant vaginal discharge, itching, burning, pain, or odor. However, is this a clear indicator that there is no abnormal flora or serious pathology? The answer is no. Since cultures are periodically not performed, there is no unmistakable evidence whether there is or is not an altered microbiome. The substantial experience gathered by introducing periodic cervical cancer screening to assess human papilloma virus (HPV) presence is compelling. Herein, in general, there are no symptoms while the pathology can be severe. The pap smear, if atypical squamous cells of undetermined significance (ASCUS) and HPV is positive, then cervical colposcopy and biopsy are followed. Since if active cervical cancer is present, surgery will have to follow, and conception will not be immediately pursued. Prior to pregnancy, pap smear performance is advised, based on risk group and age. This is because managing abnormal findings is difficult during pregnancy [ 21 ]. Certain medical conditions may be affected by altered vaginal and cervical microbiota‐dysbiosis. Endometriosis is a progressive inflammatory disease causing progressive pain, spread of endometriosis in the pelvis causing severe dysfunction. An advanced case is considered when the 3 or 4 stage is present. Studies using V3 and V4 regions of the 16S rRNA gene were amplified following the 16S genes and analyzed. Fourteen patients with endometriosis were compared to fourteen healthy controls where the Atopobium genus was absent in the cervix while increased Gardnerella, Streptococcus, and Ureaplasma were detected. Further Escherichia and Shigella increases were found in both the cervix and stool. What remains to be confirmed is whether the altered microbiome is a cause or effect of the pathology. But also suggest that additional gynecological pathologies may also be causal to the altered microbiome. This is also evident since the pregnancy of patients with active endometriosis doubles the rate of miscarriage [ 22 ]. Other disorders related to lack of optimal microbiome presence with absence of Lactobacillus bacteria in the vaginal microbiome have been associated with adverse outcomes related to vaginal health, such as preterm birth (PTB), bacterial vaginosis (BV), and an elevated risk of sexually transmitted diseases [ 23 ]., Lactobacillus crispatus bacteria secrete lactic acid and other substances that effectively inhibit bacterial species associated with BV. Consequently, women who have L. crispatus bacteria in their vagina are less prone to developing such an infection [ 24 ]. Certain strains of Lactobacillus, such as L. gasseri , may aid in the elimination of HPV. The probiotic can modify the tumor microenvironment and help clear the predominance of HPV in vaginal and cervical epithelium [ 25 ]. Therefore, it is imperative to develop a novel approach for treating diseases by closely monitoring the specific bacterium linked to HPV infection and regulating the vaginal microbiota [ 26 ]. Only Lactobacillus crispatus M247 has been researched for its capacity to facilitate the elimination of HPV, making it the sole properly studied probiotic. Furthermore, the LC bacteria have a significant propensity to colonize the vaginal environment, establishing a favorable environment that effectively inhibits many pathogens causal for vaginal infections [ 27 ]. The vaginal microbiome is essential for health. Having a proper flora is a major protection against disease, importantly including STI. However, a detailed flora analysis reveals the presence of multiple types of bacteria at the same time therefore lack of dominance of protective or altered genus can be a major cause of vulnerability. Lactobacillus Crispatus appears to be dominant in a healthy environment, resistant in general to change, and has also anti‐inflammatory properties exerting beneficial effects when present in pregnancy. In contrast to the other L. iners are more likely to be modified toward pathogens establishment [ 28 ]. Vaginal health and associated healthy microbiomes are strongly related to age. Throughout the menstrual cycle there is estrogen dominance as compared with progesterone which is a post ovulatory phase steroid. The vaginal microbiome in healthy pregnancy remains stable. This is due to stability of the vaginal environment by the combined estrogen/progesterone presence as compared to the dynamic changes present throughout the menstrual cycles. As pregnancy progresses toward term after 36 weeks, Lactobacilli decreases, and anaerobes increase which continues also after delivery until menstrual cyclicity resumes. Therefore, throughout reproductive age local estrogen action plays a major protective role. This is in contrast to prepuberty and following menopause where vulnerability to infection is significantly increased. The estrogen function acting on the epithelial cells is to promote glycogen synthesis and related metabolites (a‐destrins and maltose and derivatives) that serve as substrates to convert to lactic acid by the lactobacilli. In addition, the action of estrogen is to provide a protective immune environment that is lost at menopause [ 29 ]. As for ethnicity, especially in non‐Caucasian women, the lactobacilli are less prevalent. However, a US study comparing four different ethnicities (Caucasian, African American, Hispanic, and Asian) showed that through diverse communities, mostly lactobacilli presence exposure to milk products could also be an underlying cause for the increased vaginal acidity by lactose activity [ 28 , 29 , 30 ]. However, another study showed diverse bacteria in different ethnic groups. Overall Lactobacilli subgenus crispatus in Caucasian, and subgenus iners in African Americans, and subgenus acidophilus in Hispanic population were observed. This healthy microbiome presence is associated with decreased Ureaplasma and mycoplasma presence in healthy pregnancy [ 31 ]. The vaginal mucosa is resistant to infection, which is preserved despite menstrual blood, sexual activity, rectal contamination, and childbirth, which persists until menopause where vulnerability to infection significantly increases. The lactobacilli create vaginal acidity (pH < 4.5), counteracting pathogens of diverse nature effectively. Case in point is that the local microbiome is highly effective in most circumstances; thereby, overall infection rates are low, and unless significant risk factors are present, the physiology is maintained [ 32 , 33 , 34 , 35 , 36 ]. What are the specific mechanisms involved? The formation of a protective layer of microcolonies attached to the epithelial cells shield against pathogens access. Further, lactobacilli induced acidity < 4.5 pH is effective. It is well known that fungus thrive in a high pH, alkaline environment. A local production of bacteriocins that is effective against both bacteria and viruses is complementary. There is also evidence that through action on the vaginal environment Lactobacilli are able also to reduce local inflammatory cytokines (TNF‐a, IL‐6, IL‐8)—shown in vitro post activation by bacterial pathogens [ 36 , 37 ]. The uterine cervix as a site of microbiota is rarely studied and based on current data it is similar to the vaginal microbiome. Therefore, as discussed below it serves as a port of entry of infection into the endometrium. Overall, despite the continuous potential exposure to pathogens the vaginal microbiome is preserved unless significant pathogens and risk factors are present. There is evidence that fertility can be affected by vaginal dysbiosis, namely the reduced Lactobacilli and presence of G. vaginalis , which reduced 2‐fold chances of pregnancy compared to control patients with a healthy microflora, L. crispatus , and L. iners [ 38 ]. Adverse microbiomes cause multifaceted vulnerability to both local and systemic pathologies which have significant ramifications. Thus, lack of awareness and local symptoms does not exclude the presence of adverse flora. If the woman is having local symptoms, discharge, itching, burning, pain it is a clinical advantage since in that case women will seek specific diagnosis and therapeutic resolution. However, the frequent use of over‐the‐counter medications without proper diagnosis leads to nonspecific treatment and increases the resistant species presence. The aim once symptoms are present which would be the right clinical approach is to conduct a gynecological exam obtaining proper evaluation and cultures as well assess for HPV risk for cervical neoplasia development by performing a pap smear. Such information would provide targeted treatment aiming to eradicate the offending organism or frequently, which is the case, both bacteria like BV, fungus and even HPV may coexist. Such clinical exams with cultures should importantly be conducted prior to a patient considering conception. This became evident since L crispatus presence is associated with fertility, while pathogens presence exerts an adverse effect reducing rates of conception such as in the presence of C. trachomatis , BV, and various Ureaplasma species. In a controlled study infertile patients microbiome analysis showed lactobacilli decreased while BV and Atopobium genus increased. This diversity including Geobacillus thermogenic also in rectal cultures reflect diverse microbiome interaction. In contrast, Lactobacillus johnsonii dominated in fertile patients [ 39 , 40 ]. Adjustment prior to pregnancy addressing fungal infection is important since if it remains untreated it becomes more symptomatic as pregnancy initiates, beyond discharge, causing itching and burning. Local antifungal creams are frequently of limited utility requiring long‐term use. The use of oral antifungal medications is contraindicated due to concern for teratogenicity. The use of douching is not recommended. Also, the use of local soap or detergent should be avoided. Bacterial infection such as BV can adversely affect pregnancy. In general, such an infection beyond discharge is associated with odor. Culture in general is confirmatory of infection. As recently reported, the presence of vaginal BV biofilm has a high correlation and was found in 50% of cases when uterine biopsy samples were cultured and fallopian tubes analyzed. This implies that addressing the local microbiota has significant implications throughout gestation. Bacterial vaginosis presence is associated with miscarriage and preterm birth or other pregnancy‐related complications which are reduced by the presence of Lactobacillus crispatus creating a stable microbiome. There is also evidence that vitamin D levels are associated with reduced rates of BV infection. Therefore, sunlight exposure when accessible and vitamin D use should be encouraged since it would also help improve the vaginal microbiome by increasing the Lactobacillus crispatus . Adjustment prior to pregnancy addressing fungal infection is important since if it remains untreated it becomes more symptomatic as pregnancy initiates, beyond discharge, causing itching and burning. Local antifungal creams are frequently of limited utility requiring long‐term use. The use of oral antifungal medications is contraindicated due to concern for teratogenicity. The use of douching is not recommended. Also, the use of local soap or detergent should be avoided. Bacterial infection such as BV can adversely affect pregnancy. In general, such an infection beyond discharge is associated with odor. Culture in general is confirmatory of infection. As recently reported, the presence of vaginal BV biofilm has a high correlation and was found in 50% of cases when uterine biopsy samples were cultured and fallopian tubes analyzed. This implies that addressing the local microbiota has significant implications throughout gestation. Bacterial vaginosis presence is associated with miscarriage and preterm birth or other pregnancy‐related complications which are reduced by the presence of Lactobacillus crispatus creating a stable microbiome. There is also evidence that vitamin D levels are associated with reduced rates of BV infection. Therefore, sunlight exposure when accessible and vitamin D use should be encouraged since it would also help improve the vaginal microbiome by increasing the Lactobacillus crispatus . In addition, any sexually transmitted disease that is not treated prior to pregnancy can severely affect both mothers and their fetuses. This also includes syphilis, hepatitis, HIV, and others. Measures must be taken to ensure that these infections are already under treatment at the onset of pregnancy. Otherwise, serious consequences such as maternal disease or congenital infections are known to occur. It is recognized that Lactobacillus crispatus and Lactobacillus gasseri are significant protectors against major pathogens. When examined, those bacterial genera inhibited adhesion to vaginal cells of several major pathogens that may cause systemic disease like Streptococcus agalactiae , Staphylococcus aureus , Escherichia coli , and Enterococcus. The protection against BV and Candida albicans is well documented widely in a clinical setting. As for the L. iners genus, it may be a pathogen. Therefore, not all Lactobacilli serve the same function. L crispatus also protects against sexually transmitted infections: Chlamydia trachomatis , HIV, Neisseria gonorrhoeae , and HSV‐2. Importantly, they also decrease HPV infection and the risk for LGSIL development [ 41 ]. Smoking, multiple sexual partners, and vaginal douching increase infection risk while L Crispatus decreases the STI risks. Consumption of dairy and milk products and sitz bathing also decrease STI risks [ 42 , 43 , 44 ]. Initially, syphilis is frequently indolent; therefore, there is a significant increase in the risk of having an infection caused by such a major pathogen, since it is frequently asymptomatic [ 45 ]. This bacterium does not modify the vaginal flora, but it is a point of entry for the infection. A lesion located in the vagina or any region of the perineal region—anal or oral—can lead to infection. The major increase in the rate of infection stems from the fact that routine exams are not performed at regular intervals around the world, and blood tests are not performed to diagnose the infection. At initial stages of infection, it is easily treated with antibiotics. However, if this is not accomplished, it will lead to chronic secondary and tertiary disease. As infection progresses, it will cause, among other things, arthritis in joints and even neurosyphilis, which is not possible to totally eradicate. Syphilis is a significant sexually transmitted disease. Patients who are at risk of developing the disease or having symptoms need specific blood tests (RPR, TPHA), and in some cases, local cultures are needed for confirmation. In the absence of proper diagnosis, exposure to the pathogen carries major risks for the mother. As for the fetus, if syphilis remains untreated, it can cause congenital syphilis. Therefore, it is imperative that proper therapy using penicillin should be used, which was shown to be curative in the initial stages of the disease. Thus, safe sex practices are important in prevention prior to considering conception. Overall, periodic testing when at risk can lead to early identification and effective treatment. As is the case for other STI it would be expected that a healthy vaginal microbiome Lactobacillus dominated should be able also to lower the risk of such infection [ 43 , 44 , 45 ]. HIV remains a major problem affecting both peri and prenatal care. In certain African countries, up to one out of four pregnancies may be affected. The microbiome changes due to the presence of HIV, and whether anti‐HIV medications (anti‐Retroviral Therapy (ART)) affect the disease course is unclear. This is being examined in view of whether preventive measures could reduce the risk of this sexually transmitted infection. This is especially important if the pregnancy is planned and/or it is already ongoing. Studies documented that in women with HIV infection, there is vaginal dysbiosis associated with both BV and moniliasis. In a recent study, data showed that the most common bacteria in all HIV+ women collected two times during gestation in the second and third trimester was L. iners ; this was associated with Gardnerella bacteria, whose presence increases the preterm birth rate. It was not clear whether ART led to the observed altered local inflammation and changes in the vaginal microbiome. Also, an important unanswered question is whether the presence of HIV leads to the altered local microbiome or the altered microbiome causes the increased susceptibility to infection. This is important to state that not all lactobacilli subtypes are protective as is the case when compared to L crispatus. Therefore, beyond ART it is important to diagnose and treat vaginal dysbiosis in this high‐risk population. This is to further reduce the risk of preterm birth which is already elevated in this population. Overall, the early restored microbiome could both protect against HIV as well as reduce pregnancy‐related complications [ 46 , 47 ]. Genital herpes is a common STI associated by painful vulvar and vaginal lesions. Otherwise, the infection can be dormant and is still infectious. Once a lesion is identified it needs to be treated with antiviral medications. Both sexual partners require treatment to prevent reinfection. The relevance of presence of multiple STI in couples was determined. As data showed, 231 couples were documented having anti‐HSV II antibodies by serum testing. Cultures were collected which showed 33% infection rate in both partners, in females alone it was 22% and in males alone was 11%—Still being a significant reservoir for infection. The HIV rate was 11% in both partners. The associated vaginal culture showed preponderance of BV and L. iners being the major pathogens. In contrast L crispatus appears to confer protection against infection. This confirms the pathogenic genus presence that is found also in other STI. Thus, once acute symptoms of infection are resolved the risk of transmission is still present. Such frequently would require continued suppressive daily therapy especially when there is frequent recurrence. The use of condoms is useful, but it is not completely protective. This risk of infection is important to resolve before conception is considered, since risk of vertical transmission is high, and treatment should be continued during pregnancy when it is symptomatic. In preparation for labor, suppressive therapy should start at 36 weeks of gestation. Case in point those with suspected lesions are provided antiviral medication and undergo cesarean section. Overall, the altered microbiome is a major contributor for HSV2 infection which becomes a chronic disease requiring life‐long management [ 48 , 49 ]. It is expected that an altered vaginal microbiome will increase the likelihood of such a highly common STI rate. The presence of Lactobacilli crispatus should be a major protector against this pathogen. However, this does not appear to be the case. As analyzed in detail, it showed no significant differences between the diversity of the microbiome of infected as compared to non‐infected women, where an increase in L. iners was found. As shown, this is before an increase in the likelihood of infection was found. Due to its indolent but serious nature causing frequent tubal pathology and pelvic inflammatory disease (PID) testing should be part of a routine gynecological exam and once identified treated by antibiotics. The partner must also be treated. Post treatment a test of cure should be carried out to ascertain infection resolution [ 50 , 51 ]. The GC is a highly prevalent infection that if it is not treated in a timely manner the infection can become systemic. The current limitation is that in 50% of cases the infection is asymptomatic in both males and females. Such leads to a rapid spread of infection in an indolent manner. Data showed that L. iners presence was associated with clinical symptoms. This genus is considered a facilitator of STI as compared with L. crispatus . The symptomatic GC was also due to BV associated clinical symptoms. This further confirms BV's facilitating role in STI development. Similarly, to chlamydia, this is part of the routine cultures performed in a gynecological exam. Once identified, antibiotics are needed for the patient and partner. Following resolution, repeated culture should be carried out to verify infection resolution [ 51 , 52 ]. BV is a highly common infection that not only leads to local symptoms, but it is also a major cause of the altered vaginal microbiome leading to increased susceptibility to several STI described above. Consequently, early diagnosis and treatment preferentially by systemic antibiotics not only can resolve the local infection but also reduce the risk of associated endometritis, a common finding. Also, BV creates a local proinflammatory environment leading to an increase of several inflammatory cytokines and is involved in several pregnancy pathologies. Therefore, a recent clinical trial documented that BV recurrence, which is common, was prevented by administration of lactobacilli in a controlled study. The implications of such a study are important since restored vaginal microbiome beyond BV could also lead to a decrease of various STI rates which have more severe consequences [ 53 ].

Preconception until the end of the first trimester is the most critical part of gestation. Diagnosing infections and respective treatment during preconception can make a major difference in both the mother and embryo's health. Encouraging women seeking conception to undergo preventive exams would go a long way in reducing risk. This should eventually be the standard of care. On the other hand, when there is a failure to diagnose pathogens and the microbiome is altered, conception starts under suboptimal conditions; it can potentially affect both pregnancy and beyond. Therefore, if any infection is identified and treated and the microbiome is hopefully optimized, this since the lower genital tract from the vagina to the endometrium and pelvis are the most vulnerable sites. Diagnosing and treatment of STI such as chlamydia and gonorrhea can prevent endometritis leading to early pregnancy failure and ectopic pregnancy. In addition, testing for HIV, syphilis, and herpes simplex when a patient is at risk are especially important since once pregnancy occurs, unless it is addressed prior, significant maternal and fetal disease follows, and requiring significant treatment. Syphilis can cause vertical transmission and congenital syphilis. In genital herpes, when there are active perineal lesions, it requires treatment and a cesarean section if present at the time of birth. On the other hand, HIV is not cured, requiring continued treatment throughout pregnancy to reduce adverse effects. Local vaginal infections such as Gardnerella can cause endometritis and are later involved in preterm labor, facilitating other pathologies. Fungus and trichomonas are described below; their elimination to optimize the microbiome frequently requires short term treatment. Overall, early microbiome optimization can prevent/minimize pregnancy loss, congenital anomalies and late pregnancy pathologies. Specific items are addressed below.

Optimum microbiome is essential for life where presence and abundance of beneficial bacteria play a key role. Risk reduction by improved lifestyle, minimizing adverse exposure to antibiotics, teratogenic, toxic agents and vaccination are important in view of planned conception and pregnancy. Such factors should be coupled with proper nutrition avoiding adverse over and under nutrition. Pregnancy requires a healthy microbiome in a challenging environment. The primary vulnerable sites are the vagina and endometrium, which is not sterile, where altered microbiome impairs and facilitates sexually transmitted infections from conception onwards. Diagnosis and prevention/treatment should optimize the microbiome already at conception, reducing pregnancy‐associated risks. Urine sterility should be maintained by reducing pregnancy‐associated vulnerability to infection. Dental care and effective oral microbiome may reduce beyond local and systemic vulnerability. Optimal GI function combined with a healthy gut microbiome is essential for life. Reducing vulnerability of first trimester GI symptoms, coupled with increased safe macro and micronutrients intake, should be pursued. Addressing the altered gut microbiome, which has significant systemic effects, is important since it affects the mother and fetus both during and after birth [ 101 ]. We provide a structural approach minimizing risks, maximizing opportunity through diagnostics and practical, preventive/therapeutic measures, since otherwise, pregnancy may be affected. Overall, simple steps properly executed, also in LMIC and rural areas, can have a positive influence since small simple measures can have a major positive beneficial role.

Gut and vaginal microbiome are influenced by diet and lifestyle factors, though there is a paucity of good clinical evidence of the optimal diets to promote a healthy microbiome. A diet based on the Mediterranean dietary patterns, i.e., rich in dietary fiber, omega‐3 (ɷ‐3) fatty acids, plant‐based protein, and vitamins and minerals, is thought to have a positive impact on female fertility [ 87 ] and forms the basis of healthy nutritional advice. Probiotics are live microorganisms that are intended to have health benefits when consumed and hold potential to improve the microbiome. However, in healthy women of reproductive age, no impact on metabolic health was noted [ 87 ] and among those seeking pregnancy, no statistically significant improvements were seen in pregnancy rates [ 88 ]. In pregnancy there is more data to support the role of nutritional supplements. A recent review found an association between the maternal diet and gut microbiome. High‐fat diets (% fat of total energy), fat‐soluble vitamins (mg/day), and fiber (g/day) were the most significant nutrients associated with the gut microbiota composition of both neonates and mothers. High‐fat diets were significantly associated with a reduction in microbial diversity, while fiber intake may be positively associated with microbial diversity. These results show promise for dietary intervention and microbial manipulation in order to favor an increase of health‐associated taxa in the gut of the mother and her infant [ 89 , 90 ]. Probiotics in pregnancy in many studies have found health benefits for the mother, in terms of improved lipids and possibly improved glycemic control [ 90 ]. In pregnancies among high BMI women no improvement was noted with lactobacillus salivarius supplementation on fasting glucose levels [ 91 ]. However, among women with a recent diagnosis of gestational diabetes the same probiotic was noted to ameliorate the gestational‐related rise in lipids, showing potential for improved metabolism among women with insulin resistance [ 92 ]. Other probiotic strains have shown similar metabolic benefits in at‐risk women [ 93 ]. For mother to child transmission of microbiota, factors important in transfer between mother and newborn include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics [ 94 ]. Breastfeeding is an additional important mode of transfer which is facilitated by maternally provided human milk oligosaccharides [ 95 , 96 ]. Until recently it was not known if maternal oral supplementation with probiotic could result in transfer to the neonatal gut [ 97 ]. However recently it has been shown conclusively with a clinical randomized control trial that Bifidobacterium breve can transfer from mother to infant, robust data provided from the MicrobeMom trial [ 96 , 97 ]. The tagged maternal ingested probiotic was evident in a small number of infant stools, showing that direct mother to infant bacterial strain transfer occurred. Further research will continue to identify those strains with optimal mother to child transfer. The GI tract due to the altered microbiota leads to an increase in multiple diseases. Aiming to counteract such pathologies, examination of the gut microflora showed that there is a reduced rate of a specific bacterium Akkermansia muciniphila . Increased intake of such types of bacteria improved several medical conditions including Type I and type II diabetes, bowel inflammation, among others. The bacteria act through interaction with gut membranes to maintain the barrier through interaction with local proteins and receptors. This is important since gut leak is a major source of systemic inflammation. That creates a vicious cycle where the systemic and local inflammation enforce each other, perpetuating the disease. Thus, potentially a simple intervention using not live but pasteurized sources of bacteria can exert a major positive impact. However, the use of this supplement as a capsule needs to be confirmed in larger studies [ 98 ]. On the other hand, although the administration of probiotics does not affect gestational outcomes per se, the administration of probiotics containing Lactobacillus crispatus reduces the recurrence of bacterial vaginosis. This shows that the administration of these supplements can improve vaginal symbiosis. Future studies need to be conducted in an attempt to understand whether the administration of probiotics during pregnancy actually improves intestinal symbiosis in women without a history of bacterial vaginosis, with the aim of evaluating a reduction in vaginal infections and better maternal and fetal outcomes. In addition to studies that define the best composition of probiotics and whether they require vaginal or oral administration [ 99 ]. Based on recent study, confirm earlier observations; use of probiotics is most effective only after BV is already treated with metronidazole [ 100 ]. Therefore, first, remain a clear target is to cure an infection prior to considering probiotics as long‐term prevention. Table  3 proposes steps in improving the microbiome that leads to better preconception and pregnancy outcomes. Table  4 addresses nutrition and how improved food intake can prevent and mitigate pregnancy‐associated pathologies [ 101 ]. Summary of proposed solutions. Note: This table outlines the key preventative and therapeutic measures that are recommended to optimize the maternal microbiome. Nutrition during preconception and pregnancy.

Preparation for pregnancy by optimizing the microbiome plays a critical role in a gestation's successful outcome. Such is required since the maternal organism undergoes significant changes throughout pregnancy to accept, adapt, nurture, and successfully deliver the mature fetus at term. Therefore, any failure to timely correct may cause significant adverse effects. A healthy pregnancy requires that all maternal organ systems and the whole body be in good health. This is to be achieved beyond the innate body properties whereby the healthy embryo transitions to the fetal stage where the external environment plays a critical part in maintaining health vs. disease. Among them, there is a beneficial interaction between the defenders of the body, such as beneficial microbiome versus potential offenders caused by adverse microbiome exposures affecting health. This balance always remains at risk unless it is addressed in a timely manner before damage occurs, which can be severe and irreversible [ 1 ]. Throughout evolution until the present there is a vital interaction between the presence and action of endogenous beneficial bacteria and mammalian survival. In addition, exposure to yeast in food products such as bread and cheese is also an integral part of the standard diet when consumed in moderation. In contrast, the offending agents are highly diverse, ranging from pathogenic bacteria, and additionally three major classes of pathogens: viruses, fungi, and parasites are involved. Such adverse pathogens are unable to create a beneficial balance between their acceptance and the host's well‐being and survival. Instead, the host serves as a vehicle for their survival, replication, and transmission of disease both horizontally and vertically during pregnancy to the fetus. Thereby, offending microbiota unless promptly counteracted will often cause pathology—it is a matter of whether the infection is acute, subacute, or chronic, symptomatic, or indolent. Indolence is the most dangerous status since if not diagnosed in a timely manner, the infection can become severe. Furthermore, not all pathogens lead to noticeable symptoms. Their transmission, with minimal initial symptoms, has led to a Covid‐19 infection major epidemic [ 2 ]. Therefore, to prevent and reduce adverse microbiome‐induced pathology, vaccinations are administered from early childhood through adulthood with special emphasis on the pregnancy. While several vaccines can be administered prior to pregnancy, others can also be administered during pregnancy protecting both mother and fetus [ 3 ]. Pathogens are identified mostly by culture, histology, and blood tests. Such testing can be carried out when the infection is asymptomatic, preventive, or as part of a targeted approach when the condition is acute/chronic. For conception and pregnancy, the genital tract including vagina and endometrium are the primary sites, followed by the gastrointestinal tract, urinary tract and oral cavity. The respiratory, skin, and other sites as needed are important but are beyond the scope of the current narrative. Upon detection of pathogens in most cases, specific therapy can be given aiming to eradicate the disease as much as it is feasible. Preferentially, the therapy should be specific and is based on proper and accurate diagnostics avoiding empiric interventions that can perpetuate the damage. The body continually needs to protect itself, especially in pregnancy when adverse microbiomes can affect both the mother and fetus. Thus, pre‐conception onward preventing and/or minimizing adverse effects caused by bacteria, fungi, viruses, and parasites is needed. Thus, the aim is to optimize the beneficial maternal microbiome environment as preparation toward a healthy pregnancy and preserving such throughout until delivery. During the recent Covid‐19 epidemic and the aftermath, important preventive care for patients in the reproductive age group significantly decreased, leading to a resurgence of several diseases. It is imperative to restore such periodic preventive care which will improve fertility and minimize high‐risk pregnancies such as high BMI, hypertension, diabetes, and autoimmunity among others. Optimizing the microbiome is also a highly important aspect of addressing preventive care. Unfortunately, only prenatal vitamins and cursory nutrition advice is offered when pregnancy is planned, and the interaction between primary and advanced care, where significant pathologies can be adequately addressed prior and during pregnancy, are not well managed; care remains fragmented and not integrated [ 4 ]. There is an emerging problem: fertility is frequently pursued only in late reproductive age when chronic diseases may already be present, reducing conception rates and potentially increasing pregnancy pathologies. Improving the couple's general health through an optimized microbiome should further increase the odds of counteracting diminished conception rates. Preconception consultation is rarely performed, so the question arises: should this be routine in primary care, where advice is offered and also advice on optimization of the microbiome? As conception is envisaged, preventive steps are required to optimize the microbiome. These include an improved healthy lifestyle, stopping smoking, alcohol, and drugs, avoiding exposure to adverse environments while promoting good nutritional habits described below. The following conditions that need to be addressed to improve the microbiome: (1) Reproductive‐age women are prone to obesity, polycystic ovaries, and prediabetes, thereby increasing the risk of pregnancy loss and other later‐life pathologies causing altered vaginal and gut microbiome. (2) Excess antibiotic use, exposure to potential teratogens, and (3) immune‐suppressive drugs which lower internal body defenses make it prone to infection and altered microbiome. (4) Malnutrition is pervasive leading to poor quality nutrition of not only due to scarcity of food but also due to use of processed food (5) use of medication to support early pregnancy at risk‐ progesterone and (6) Effect of use of contraceptive to the microbiome are presented. This is followed by defining the healy vaginal microbiome and the conditions that lead to a pathological environment. Diagnosis and timely treatment of vaginal infections and sexually transmitted infections (STI) that can be clinically silent but still can affect mother and fetus throughout pregnancy. (4) Evaluation of the endometrium as an emergent site of infection that requires proper systemic treatment to prevent pregnancy loss and associated pathologies. (5) The gastrointestinal tract: starting from the oral cavity, stomach, intestine, and colon is a major source of altered microbiomes that need to be diagnosed in a timely manner and properly adjusted. (6) Additional targets for preventing offending microbiota access are in the urinary system as well as any other site in the body, like skin, where if not addressed adverse effects may follow. Herein we delineate the delicate but necessary balance between defending and offending microorganisms, especially in women intending to pursue pregnancy, recognizing that an effective microbiome improves pregnancy outcome. This is important since the vaginal microbiome frequently is only partially changed throughout pregnancy, unless further exposure occurs; thereby, prevention prior to conception can make a major positive impact throughout gestation. The current call to action is to close the ongoing gap in microbiome optimization by describing effective and simply applicable diagnostic tests and proposing practical preventive and intervention measures with special emphasis in low‐ and middle‐income countries (LMIC) and rural areas. This is in view of the known reduced resources, lack of access to care, good nutrition, and increased exposure to diverse endemic infections, clean water/food; therefore, the need is and remains acute [ 5 ]. This is also supported by the compelling data since high maternal and newborn morbidity and mortality is closely associated both with altered microbiome and increased rate of horizontal/vertical infection leading to major differences in pregnancy outcome in low middle income countries (LMIC) as compared with high resource countries [ 6 ]. We propose that improved access to care, patient and staff education will significantly reduce risks preferentially prior to pregnancy and during embryogenesis at the most vulnerable period and also improve overall pregnancy outcome. Herein we delineate that starting care prior to conception, instituting practical, effective and easily implementable diagnostic and preventive and/or therapeutic measures will optimize maternal microbiome and pregnancy outcome. Finally, the use of safe and proper nutrition combining it with emerging therapies that optimize the microbiome is presented.

The authors declare no conflicts of interest.