The vaginal microbiome as a predictor for outcome of in vitro fertilization with or without intracytoplasmic sperm injection: a prospective study

The impact of caesarean scar niche on fertility - a systematic review

BACKGROUND

The trend of increasing caesarean section (CS) rates brings up questions related to subfertility. Research regarding the influence of CS on assisted reproduction techniques (ART) is conflicting. A potential mechanism behind CS-induced subfertility is intra uterine fluid resulting from a caesarean scar defect or niche. The vaginal microbiome has been repeatedly connected to negative ART outcomes, but it is unknown if the microbiome is changed in relation to a niche.

METHODS

This systematic review describes literature investigating the effect of a niche on live birth rates after assisted reproduction. Furthermore, studies investigating a difference in microbial composition in subfertile persons with a niche compared to no niche are evaluated. Pubmed, Embase and Web of Science were searched on March 2023 for comparative studies on both study questions. Inclusion criteria were i.e., English language, human-only studies, availability of the full article and presence of comparative pregnancy data on a niche. The quality of the included studies and their risk of bias were assessed using the Newcastle-Ottawa scale for cohort studies. The results were graphically displayed in a forest plot.

RESULTS

Six retrospective cohort studies could be included on fertility outcomes, with a total of 1083 persons with a niche and 3987 without a niche. The overall direction of effect shows a negative impact of a niche on the live birth rate (pooled aOR 0.58, 95% CI 0.48-0.69) with low-grade evidence. Three studies comparing the microbiome between persons with and without a CS could be identified.

CONCLUSION

There is low-grade evidence to conclude that the presence of a niche reduces live birth rates when compared to persons without a niche. The theory that a caesarean has a negative impact on pregnancy outcomes because of dysbiosis promoted by the niche is interesting, but there is no sufficient literature about this.

Is there an association between vaginal microbiome community state types and diversity and preterm birth: A non-systematic literature review

Worldwide, preterm birth (PTB) is a significant cause of neonatal mortality and morbidity. Surprisingly, the rate of PTB in the United States is among the top 10 nations in the world, comparable to those of the Democratic Republic of the Congo, Bangladesh, India, and Nigeria. However, there is no predictive biomarker or understanding of the mechanisms of PTB. Recent evidence suggests that the vaginal microbiome can be clustered into Community State Types (CST) and is altered in various obstetrical syndromes. The review aimed to summarize multiple studies on the vaginal microbiome and PTB and identify a particular microbe or CST associated with PTB. We hypothesized that there exists a specific microorganism that, when dominant within the vaginal microbiome, is protective against PTB. We hypothesized that the absence of a particular microbe or CST is a risk factor for PTB. To answer this question, we reviewed the current literature aiming to identify such a microorganism or a group of microorganisms. Our results indicate that no particular microbe or CST can be implicated in PTB. However, the review suggests that an increase in alpha and beta diversity of the vaginal microbiome can be predictive and involved in the pathogenesis of PTB.

Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes

BACKGROUND

Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.

PURPOSE

This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.

METHODS

We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.

RESULTS

Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC = 0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.

CONCLUSIONS

This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.

Effect of Waiting Period on Initial Adverse Vaginal Microbiome Composition in IVF-ICSI Patients

Background/Objectives: In this observational prospective cohort study, conducted at the Fertility Centre of the University Hospital, Duesseldorf Germany, the spontaneous reversal capacity and the effect of waiting time on an adverse vaginal microbiome profile in subfertile patients were investigated. Methods: Vaginal swabs of 76 patients were obtained before starting a fertility treatment using a commercially available test to perform a microbiome analysis. Patients with a favorable microbiome profile ("medium" or "high profile") according to the manufacturer's algorithm proceeded with the fertility treatment. Patients with an unfavorable microbiome profile ("low profile") postponed their fertility treatment and were sampled up to four times in each successive cycle or until a shift to a more favorable profile was detected. Results: Initially, 54/76 subjects had a high or medium profile and 23/76 had a low profile. Within 3 months, 75% of patients with an initial low profile shifted to a more favorable profile (7/23 dropouts). The presence of Lactobacillus crispatus in the initial sample was associated with a higher likelihood of a spontaneous shift to a more favorable profile. Conclusions: The vaginal microbiome is subject to strong fluctuations. Even an unfavorable microbiome profile can develop into a favorable microbiome profile within a few months without treatment.

Contribution of the seminal microbiome to paternal programming

The field of Developmental Origins of Health and Disease has primarily focused on maternal programming of offspring health. However, emerging evidence suggests that paternal factors, including the seminal microbiome, could potentially play important roles in shaping the developmental trajectory and long-term offspring health outcomes. Historically, the microbes present in the semen were regarded as inherently pathogenic agents. However, this dogma has recently been challenged by the discovery of a diverse commensal microbial community within the semen of healthy males. In addition, recent studies suggest that the transmission of semen-associated microbes into the female reproductive tract during mating has potentials to not only influence female fertility and embryo development but could also contribute to paternal programming in the offspring. In this review, we summarize the current knowledge on the seminal microbiota in both humans and animals followed by discussing their potential involvement in paternal programming of offspring health. We also propose and discuss potential mechanisms through which paternal influences are transmitted to offspring via the seminal microbiome. Overall, this review provides insights into the seminal microbiome-based paternal programing, which will expand our understanding of the potential paternal programming mechanisms which are currently focused primarily on the epigenetic modifications, oxidative stresses, and cytokines.

Testing on bacterial vaginosis in a subfertile population and time to pregnancy: a prospective cohort study

PURPOSE

This study aimed to investigate the influence of bacterial vaginosis on time to pregnancy in subfertile couples.

METHODS

Couples attending a teaching hospital in the Netherlands having an initial fertility assessment (IFA) between July 2019 and June 2022 were included in this prospective study, with follow-up of pregnancies until June 2023. Vaginal samples at IFA were analyzed on pH, qPCR BV, and 16S rRNA gene microbiome analysis of V1-V2 region. Main outcome measures were time from initial fertility assessment to ongoing pregnancy at 12 weeks and live birth, analyzed by Kaplan-Meier and Cox regression with adjustment for potential confounders.

RESULTS

At IFA, 27% of 163 included participants tested positive for BV. BV status had no influence on time to ongoing pregnancy (HR 0.98, 0.60-1.61, aHR 0.97, 0.58-1.62). In persons with unexplained subfertility, positive BV status had a tendency of longer time to pregnancy. When persons had an indication for fertility treatment, positive BV status (HR 0.21, 0.05-0.88, aHR 0.19, 0.04-0.85) and microbiome community state type III and type IV had significant longer time to pregnancy.

CONCLUSION

This study indicates that BV may have a potential negative impact on time to live birth pregnancy in subfertile persons with an indication for fertility treatment. This study did not find an association between BV and time to live birth pregnancy in a general group of subfertile couples or in unexplained subfertility. More research should be done in persons with unexplained subfertility and if treatment improves time to pregnancy.

A Standard Pipeline for Analyzing the Endometrial Microbiome

The endometrial microbiome is a rapidly advancing field of research, particularly in obstetrics and gynecology, as it has been found to be linked with obstetric complications and potential impacts on fertility. The diversity of microorganisms presents in the endometrium, along with their metabolites, can influence reproductive outcomes by modulating the local immune environment of the uterus. However, a major challenge in advancing our understanding of the endometrial microbiota lies in the heterogeneity of available studies, which vary in terms of patient selection, control groups, collection methods and analysis methodologies. In this study, we propose a detailed pipeline for endometrial microbiome analysis, based on the most comprehensive prospective of 64 studies that have investigated the endometrial microbiome up to the present. Additionally, our review suggests that a dominance of Lactobacilli in the endometrium may be associated with improved reproductive prognosis, including higher implantation rates and lower miscarriage rates. By establishing a standardized pipeline, we aim to facilitate future research, enabling better comparison and correlation of bacterial communities with the health status of patients, including fertility-related issues.

Assessing vaginal microbiome through Vaginal Microecology Evaluation System as a predictor for in vitro fertilization outcomes: a retrospective study

Objective

This study aims to evaluate the effectiveness of the Vaginal Microecology Evaluation System (VMES) in assessing the dynamics of the vaginal microbiome (VM) throughout the process of in vitro fertilization and embryo transfer (IVF-ET). Furthermore, it seeks to explore the potential correlation between distinct types of VM ecology and the success rate of IVF-ET.

Methods

This study employed VMES to ascertain the composition of the VM. Data were collected from infertile women who underwent their initial IVF-ET treatment for tubal factor between January 2018 and December 2021. A retrospective analysis of pregnancy outcomes resulting from their fresh embryo transfer was conducted to determine the predictive significance of the vaginal microenvironment.

Results

We demonstrate that VMES is able to predict IVF-ET outcomes in patients diagnosed with Bacterial Vaginosis (BV). Notably, a discernible shift in the VM was observed in a decent subset of patients following Controlled Ovarian Stimulation (COS), though this phenomenon was not universal across all participants. Specifically, there was a noteworthy increase in the proportion of patients exhibiting BV and uncharacterized dysbiosis subsequent to COS. Furthermore, our investigation revealed a significant correlation between VM and both the live birth rate and early miscarriage rate. Employing a multivariable logistic regression model, we identified that VM status pre-COS, VM status post-COS, patient age, and the number of embryos transferred emerged as independent predictors of the live birth rate.

Conclusion

Our study suggests that, during IVF-ET treatment, the VMES can effectively detect changes in the VM, which are strongly correlated with the pregnancy outcome of IVF-ET procedures.

Pilot Study on Next-Generation Sequencing Analysis of Vaginal Microbiota in Clinically Infertile Patients Treated with Probiotics

Background: In this investigation, we aimed to understand the influence of oral probiotic supplementation on the vaginal microbiota of women preparing for assisted reproductive technology (ART) procedures. Given the importance of a healthy microbiome for reproductive success, this study sought to explore how probiotics might alter the bacterial composition in the vaginal environment. Methods: We recruited a cohort of 30 women, averaging 37 years of age (ranging from 31 to 43 years), who were scheduled to undergo ART. Using 16S ribosomal RNA (rRNA) sequencing, we meticulously analyzed the vaginal microbiota composition before and after the administration of oral probiotic supplements. Results: Our analysis identified 17 distinct microorganisms, including 8 species of Lactobacillus. Following probiotic supplementation, we observed subtle yet notable changes in the vaginal microbiota of some participants. Specifically, there was a decrease in Gardnerella abundance by approximately 20%, and increases in Lactobacillus and Bifidobacterium by 10% and 15%, respectively. Additionally, we noted a significant reduction in the Firmicutes/Bacteroidetes (F/B) ratio in the probiotic group, indicating potential shifts in the overall bacterial composition. Conclusions: These preliminary findings suggest that oral probiotic supplementation can induce significant changes in the vaginal microbiota of middle-aged women undergoing ART, potentially improving their overall bacterial profile. Future studies should consider a larger sample size and a narrower age range to validate these results. Investigating factors related to female hormone production could also provide deeper insights. Understanding the effects of probiotics on the vaginal microbiota in patients with ovarian aging may lead to personalized interventions and better reproductive outcomes.

Vaginal dysbiosis - the association with reproductive outcomes in IVF patients: a systematic review and meta-analysis

PURPOSE OF REVIEW

To examine impact of vaginal dysbiosis (VD), including bacterial vaginosis (BV) and aerobic vaginitis (AV) on reproductive outcomes of in vitro fertilization (IVF) patients.

RECENT FINDINGS

BV-bacteria (e.g. Gardnerella ) and AV-bacteria (e.g. Streptococci and Enterococci ) have been identified in the endometrium. However, there is inconclusive evidence whether IVF patients with VD have lower success rates.

SUMMARY

The present systematic review and meta-analysis of PubMed/Medline, until December 2023 included 25 studies, involving 6835 IVF patients. Overall VD was defined as an approximation of community state type IV, including BV and AV-type dysbiosis based on either molecular or microscopy methods. Outcomes were live birth rate (LBR), early pregnancy loss (EPL), clinical pregnancy rate (CPR), and biochemical pregnancy rate (BPR).Vaginal dysbiosis prevalence was 19% [1271/6835, 95% confidence interval (CI) 18-20%]. Six studies examined AV-type dysbiosis with a prevalence of 4% (26/628, 95% CI 3-6%). Vaginal dysbiosis correlates with a higher EPL [relative risk (RR) = 1.49, 95% CI 1.15-1.94] and lower CPR (RR = 0.82, 95% CI 0.70-0.95). No statistically significant impact of VD, BV, or AV was found on LBR and BPR.Thus, the association between VD and reproductive outcome remains puzzling as it is difficult to explain how VD impacts CPR and EPL but not LBR and BPR.

Vaginal microbiota are associated with in vitro fertilization during female infertility

The vaginal microbiome plays an essential role in the reproductive health of human females. As infertility increases worldwide, understanding the roles that the vaginal microbiome may have in infertility and in vitro fertilization (IVF) treatment outcomes is critical. To determine the vaginal microbiome composition of 1411 individuals (1255 undergoing embryo transplantation) and their associations with reproductive outcomes, clinical and biochemical features are measured, and vaginal samples are 16S rRNA sequenced. Our results suggest that both too high and too low abundance of Lactobacillus is not beneficial for pregnancy; a moderate abundance is more beneficial. A moderate abundance of Lactobacillus crispatus and Lactobacillus iners (~80%) (with a pregnancy rate of I-B: 54.35% and III-B: 57.73%) is found beneficial for pregnancy outcomes compared with a higher abundance (>90%) of Lactobacillus (I-A: 44.81% and III-A: 51.06%, respectively). The community state type (CST) IV-B (contains a high to moderate relative abundance of Gardnerella vaginalis) shows a similar pregnant ratio (48.09%) with I-A and III-A, and the pregnant women in this CST have a higher abundance of Lactobacillus species. Metagenome analysis of 71 samples shows that nonpregnant women are detected with more antibiotic-resistance genes, and Proteobacteria and Firmicutes are the main hosts. The inherent differences within and between women in different infertility groups suggest that vaginal microbes might be used to detect infertility and potentially improve IVF outcomes.

Association between bacterial vaginosis, Chlamydia trachomatis infection and tubal factor infertility in Bukavu, Democratic Republic of Congo

BACKGROUND

Tubal factor infertility (TFI) is common in sub-Saharan Africa and often secondary to pelvic inflammatory disease (PID). Anaerobes associated with bacterial vaginosis (BV) are also found in PIDs widely dominated by Chlamydia trachomatis (C. trachomatis), whose role in TFI is better demonstrated than that of BV.

OBJECTIVES

To determine the prevalence of BV and C. trachomatis and to investigate the association between BV, C. trachomatis and TFI.

METHODS

We included 137 patients treated for infertility between January 2020 and November 2021. Cases were defined as women with infertility aged 18-45 years presenting with TFI (n = 52), and controls as infertile women in the same age groups without TFI (n = 85). Data on social habits, life style and infertility parameters were collected, and we performed screening for BV and C. trachomatis. Multiple regression was used to measure associations.

RESULTS

The prevalence of BV and C. trachomatis was 42.3% (58/137) and 23.4% (32/137), respectively. BV (61.5% vs 30.6%, p<0.001) and C. trachomatis (48.1 vs 8.2%, p<0.001) were more frequent in cases of TFI. BV and C. trachomatis increased the risk of TFI approximately 4-fold [aOR: 3.77 (1.61-8.83), p=0.002] and 14-fold [aOR: 13.77 (4.59-41.27), p<0.001], respectively.

CONCLUSION

BV and C. trachomatis infection are strongly associated with TFI in Bukavu. Prevention and screening should be implemented to reduce the risk of TFI.

Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies

The microbiome plays a critical role in the process of conception and the outcomes of pregnancy. Disruptions in microbiome homeostasis in women of reproductive age can lead to various pregnancy complications, which significantly impact maternal and fetal health. Recent studies have associated the microbiome in the female reproductive tract (FRT) with assisted reproductive technology (ART) outcomes, and restoring microbiome balance has been shown to improve fertility in infertile couples. This review provides an overview of the role of the microbiome in female reproductive health, including its implications for pregnancy outcomes and ARTs. Additionally, recent advances in the use of microbial biomarkers as indicators of pregnancy disorders are summarized. A comprehensive understanding of the characteristics of the microbiome before and during pregnancy and its impact on reproductive health will greatly promote maternal and fetal health. Such knowledge can also contribute to the development of ARTs and microbiome-based interventions.

Bacterial vaginosis in a subfertile population undergoing fertility treatments: a prospective cohort study

PURPOSE

This study investigates the role of bacterial vaginosis (BV) on pregnancy rates during various fertility treatments. BV is known to influence several obstetric outcomes, such as preterm delivery and endometritis. Only few studies investigated the effect of BV in subfertile women, and studies found a negative effect on fecundity especially in the in vitro fertilisation population.

METHODS

Observational prospective study, 76 couples attending a fertility clinic in the Netherlands between July 2019 and June 2022, undergoing a total of 133 attempts of intra uterine insemination, in vitro fertilization or intra cytoplasmatic sperm injection. Vaginal samples taken at oocyte retrieval or insemination were analysed on qPCR BV and 16S rRNA gene microbiota analysis of V1-V2 region. Logistic regression with a Generalized Estimated Equations analysis was used to account for multiple observations per couples.

RESULTS

A total of 26% of the 133 samples tested positive for BV. No significant differences were observed in ongoing pregnancy or live birth rates based on BV status (OR 0.50 (0.16-1.59), aOR 0.32 (0.09-1.23)) or microbiome community state type. There was a tendency of more miscarriages based on positive BV status (OR 4.22 (1.10-16.21), aOR 4.28 (0.65-28.11)) or community state type group III and IV. On baseline qPCR positive participants had significantly higher body mass index and smoked more often. Odds ratios were adjusted for smoking status, body mass index, and socioeconomic status.

CONCLUSION

Bacterial vaginosis does not significantly impact ongoing pregnancy rates but could affect miscarriage rates.

Sequencing and culture-based characterization of the vaginal and uterine microbiota in beef cattle that became pregnant or remained open following artificial insemination

IMPORTANCE

Emerging evidence suggests that microbiome-targeted approaches may provide a novel opportunity to reduce the incidence of reproductive failures in cattle. To develop such microbiome-based strategies, one of the first logical steps is to identify reproductive microbiome features related to fertility and to isolate the fertility-associated microbial species for developing a future bacterial consortium that could be administered before breeding to enhance pregnancy outcomes. Here, we characterized the vaginal and uterine microbiota in beef cattle that became pregnant or remained open via artificial insemination and identified microbiota features associated with fertility. We compared similarities between vaginal and uterine microbiota and between heifers and cows. Using culturing, we provided new insights into the culturable fraction of the vaginal and uterine microbiota and their antimicrobial resistance. Overall, our findings will serve as an important basis for future research aimed at harnessing the vaginal and uterine microbiome for improved cattle fertility.

Longitudinal analysis of vaginal microbiota during IVF fresh embryo transfer and in early pregnancy

IMPORTANCE

Infertility is a global public health issue which leads many couples to seek fertility treatments, of which in vitro fertilization (IVF) is considered to be the most effective. Still, only about one-third of the women achieve live birth after the first IVF embryo transfer (IVF-ET). Factors affecting embryo implantation are poorly known, but the female reproductive tract microbiota may play a key role. Our study confirms the beneficial role of vaginal lactobacilli, especially Lactobacillus crispatus, in the probability of achieving clinical pregnancy and live birth following IVF-ET. Our findings regarding the intra-individual shift of vaginal microbiota between non-pregnancy and pregnancy states are novel and provide new information about the dynamics of microbiota in the early steps of human reproduction. These findings may help clinicians in their attempts to optimize the conditions for ET by microbiota screening or modulation and timing the ET when the microbiota is the most favorable.

Assessing the endometrium: An update on current and potential novel biomarkers of receptivity

A cyclical evolvement of the endometrium into a transient state of receptivity is crucial for acceptance of the semi-allogeneic foetus, conducive to pregnancy. Despite documentation of aberrances in this process within patients experiencing repeated embryo implantation failures and miscarriages, the endometrium is often overlooked in IVF clinics as the cause for failure. Focus instead is usually given to embryo-derived factors, such as aneuploidy. Nevertheless, failure of approximately 30 % of euploid embryos to implant demonstrates that other factors such as the endometrium require clinical exploration. Here, we review both traditional and novel methods used to assess endometrial receptivity such as identifying the WOI, endometrial immune profiling and transcriptomics panel testing. Where reported, we will also discuss their clinical application, as well as novel potential biomarkers within the pre-clinical research stages which show promise in their ability to assess endometrial receptivity.

Characterization of vaginal Lactobacillus species as a predictor of fertility among Iranian women with unexplained recurrent miscarriage and fertile women without miscarriage history using machine learning modeling

BACKGROUND

Lactobacillus spp. are the predominant bacteria of the vaginal tract, the alteration of which has been previously linked to miscarriage. Here, we investigated differences between selected vaginal Lactobacillus species of women with a history of recurrent miscarriages and fertile women without a history of miscarriage in Iran.

METHODS AND RESULTS

Vaginal swabs were taken from 29 fertile and 24 infertile women and quantitative real-time PCR (qPCR) assay was used to determine a selection of vaginal Lactobacillus species in both groups. The logistic regression (LR) model, Naive Bayes (NB) model, support vector machine model (SVM), and neural network model (NN) were developed to predict disease outcome by selected variables. LR analysis was used to construct a nomogram indicating predictions of the risk of miscarriage. The most abundant species among the patients were L. rhamnosus, L. ruminis, and L. acidophilus, while L. gasseri, L. vaginalis, L. fermentum, and L. iners were more abundant in healthy subjects. The distribution of L. ruminis, L. iners, and L. rhamnosus was higher in patients, while L. acidophilus, L. gasseri, and L. fermentum were highly distributed among healthy subjects. Higher AUC in predicting the disease outcome was observed for L. gasseri, L. rhamnosus, L. fermentum, and L. plantarum.

CONCLUSION

Our findings provide experimental evidence of vaginal Lactobacillus imbalance in infertile women and a suitable predictor for miscarriage based on the AUC algorithms. Further studies with larger sample size and using high-throughput technologies are needed to boost our understanding of the role of lactobacilli in miscarriage.

Endometrial microbiota profile in in-vitro fertilization (IVF) patients by culturomics-based analysis

Introduction

It is well recognized that the human uterus and adjoining tissues of the female reproductive tract exist in a non-sterile state where dysbiosis can impact reproductive outcomes. The endometrial microbiota is a part of this greater milieu. To date, it has largely been studied using 16S rRNA or metagenomics-based methodologies. Despite the known advantages of sequencing analysis, several difficulties have been noted including sample contamination and standardization of DNA extraction or sequencing. The aim of this study was to use a culturomics-based method to analyze the endometrial microbiota and correlate the results with ongoing pregnancy rates.

Methods

A prospective cohort study was performed at the University of Naples from June 2022 to December 2022. Ninety-three patients undergoing an IVF cycle with single embryo transfer (ET) (fresh or frozen) were enrolled in the study. Following ET, the catheter tip was inserted into brain heart infusion (BHI) medium under sterile conditions for culture. After 24h and 48h of incubation the microorganisms in the colonies were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

Results

Overall, 68 (73,92%) patients resulted positive for one or more microbes and 25 patients (26,08%) had no microbial growth. Across all participants, the four most important phyla were Firmicutes (87,76%), Proteobacteria (27,94%), Actinobacteria (10,29%) and Ascomycota (8,82%). Lactobacillus species, in particular, was significantly correlated with ongoing pregnancy rate (p=0,05). On the other hand, Staphylococcus subspecies (spp.) (p<0,05) and Enterobacteriaceae (p<0,001) were found to have a negative impact on the implantation rate.

Discussion

Detection of bacteria by culturomics from catheter tips used for embryo transfer has been shown to be a reliable method to detect pathogen growth. Endometrial microbiota testing in clinical practice could certainly offer a means to further improve diagnosis and treatment strategies in IVF patients.

Vaginal microbiome in obesity and its impact on reproduction

A number of reproductive outcomes have been increasingly found to be affected by the vaginal microbiota. Obesity has become a global epidemic, affecting increasing numbers of reproductive-age women, and has been shown to be a risk factor for a number of adverse female health outcomes. A healthy vaginal microbiome is characterized by Lactobacillus-dominance, in particular Lactobacillus crispatus; obesity has been found to be associated with higher diversity and a lower likelihood of Lactobacillus-dominance. In this review, we summarize the evidence on the vaginal microbiome in obese women and the impact on reproductive outcomes such as conception rates, early pregnancy, and preterm birth. We further explore the mechanisms by which obesity may result in an altered microbial composition and highlight future avenues for therapeutic targeting of the vaginal microbiota.

Characterization of the follicular fluid microbiota based on culturomics and sequencing analysis

Introduction. The human oocyte microenvironment is follicular fluid, which is important for follicle growth, ovulation and maturation of the oocyte. The micro-organisms present in follicular fluid could be a predictor of in vitro fertilization outcomes.Hypothesis/Gap Statement. Women with follicular fluid colonized with micro-organisms can be asymptomatic, but the presence of some genera in the follicular fluid correlates with in vitro fertilization.Aim. To confirm the existence of micro-organisms in follicular fluid, and to profile the micro-organisms present in follicular fluid sampled from women undergoing in vitro fertilization with different outcomes.Methodology. Women undergoing in vitro fertilization (n=163) were divided into different subgroups according to their in vitro fertilization outcomes. Their follicular fluid samples were collected, and among them, 157 samples were analysed by 16S rDNA sequencing, and 19 samples were analysed using culturomics.Results. The culturomics results suggested that the 19 follicular fluid samples were not sterile. The isolation rates for Streptococcus, Finegoldia and Peptoniphilus were >50 % in the 19 samples. Linear discriminant analysis effect size analysis showed differential bacteria abundance according to the pregnancy rate, the rate of normal fertilization, the rate of high-quality embryos and the rate of available oocytes. The sequencing results showed that micro-organisms could be detected in all 157 samples. Pseudomonas, Lactobacillus, Comamonas, Streptococcus and Acinetobacter were detected in all of the samples, but with a wide range of relative abundance. Pseudomonas, Lactobacillus, Ralstonia and Vibrio constituted a notable fraction of the microbiota.Conclusions. Follicular fluid is not sterile. Micro-organisms in follicular fluid could be a predictor of in vitro fertilization outcomes.

The female upper reproductive tract harbors endogenous microbial profiles

Introduction

The female reproductive tract harbours unique microbial communities (known as microbiota) which have been associated with reproductive functions in health and disease. While endometrial microbiome studies have shown that the uterus possesses higher bacterial diversity and richness compared to the vagina, the knowledge regarding the composition of the Fallopian tubes (FT) is lacking, especially in fertile women without any underlying conditions.

Methods

To address this gap, our study included 19 patients who underwent abdominal hysterectomy for benign uterine pathology, and 5 women who underwent tubal ligation as a permanent contraceptive method at Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA). We analyzed the microbiome of samples collected from the FT and endometrium using 16S rRNA gene sequencing.

Results

Our findings revealed distinct microbiome profiles in the endometrial and FT samples, indicating that the upper reproductive tract harbors an endogenous microbiome. However, these two sites also shared some similarities, with 69% of the detected taxa Being common to both. Interestingly, we identified seventeen bacterial taxa exclusively present in the FT samples, including the genera Enhydrobacter, Granulicatella, Haemophilus, Rhizobium, Alistipes, and Paracoccus, among others. On the other hand, 10 bacterial taxa were only found in the endometrium, including the genera Klebsiella, Olsenella, Oscillibacter and Veillonella (FDR <0.05). Furthermore, our study highlighted the influence of the endometrial collection method on the findings. Samples obtained transcervically showed a dominance of the genus Lactobacillus, which may indicate potential vaginal contamination. In contrast, uterine samples obtained through hysterescopy revealed higher abundance of the genera Acinetobacter, Arthrobacter, Coprococcus, Methylobacterium, Prevotella, Roseburia, Staphylococcus, and Streptococcus.

Discussion

Although the upper reproductive tract appears to have a low microbial biomass, our results suggest that the endometrial and FT microbiome is unique to each individual. In fact, samples obtained from the same individual showed more microbial similarity between the endometrium and FT compared to samples from different women. Understanding the composition of the female upper reproductive microbiome provides valuable insights into the natural microenvironment where processes such as oocyte fertilization, embryo development and implantation occur. This knowledge can improve in vitro fertilization and embryo culture conditions for the treatment of infertility.

ESHRE good practice recommendations on recurrent implantation failure

STUDY QUESTION

How should recurrent implantation failure (RIF) in patients undergoing ART be defined and managed?

SUMMARY ANSWER

This is the first ESHRE good practice recommendations paper providing a definition for RIF together with recommendations on how to investigate causes and contributing factors, and how to improve the chances of a pregnancy.

WHAT IS KNOWN ALREADY

RIF is a challenge in the ART clinic, with a multitude of investigations and interventions offered and applied in clinical practice, often without biological rationale or with unequivocal evidence of benefit.

STUDY DESIGN SIZE DURATION

This document was developed according to a predefined methodology for ESHRE good practice recommendations. Recommendations are supported by data from the literature, if available, and the results of a previously published survey on clinical practice in RIF and the expertise of the working group. A literature search was performed in PubMed and Cochrane focussing on 'recurrent reproductive failure', 'recurrent implantation failure', and 'repeated implantation failure'.

PARTICIPANTS/MATERIALS SETTING METHODS

The ESHRE Working Group on Recurrent Implantation Failure included eight members representing the ESHRE Special Interest Groups for Implantation and Early Pregnancy, Reproductive Endocrinology, and Embryology, with an independent chair and an expert in statistics. The recommendations for clinical practice were formulated based on the expert opinion of the working group, while taking into consideration the published data and results of the survey on uptake in clinical practice. The draft document was then open to ESHRE members for online peer review and was revised in light of the comments received.

MAIN RESULTS AND THE ROLE OF CHANCE

The working group recommends considering RIF as a secondary phenomenon of ART, as it can only be observed in patients undergoing IVF, and that the following description of RIF be adopted: 'RIF describes the scenario in which the transfer of embryos considered to be viable has failed to result in a positive pregnancy test sufficiently often in a specific patient to warrant consideration of further investigations and/or interventions'. It was agreed that the recommended threshold for the cumulative predicted chance of implantation to identify RIF for the purposes of initiating further investigation is 60%. When a couple have not had a successful implantation by a certain number of embryo transfers and the cumulative predicted chance of implantation associated with that number is greater than 60%, then they should be counselled on further investigation and/or treatment options. This term defines clinical RIF for which further actions should be considered. Nineteen recommendations were formulated on investigations when RIF is suspected, and 13 on interventions. Recommendations were colour-coded based on whether the investigations/interventions were recommended (green), to be considered (orange), or not recommended, i.e. not to be offered routinely (red).

LIMITATIONS REASONS FOR CAUTION

While awaiting the results of further studies and trials, the ESHRE Working Group on Recurrent Implantation Failure recommends identifying RIF based on the chance of successful implantation for the individual patient or couple and to restrict investigations and treatments to those supported by a clear rationale and data indicating their likely benefit.

WIDER IMPLICATIONS OF THE FINDINGS

This article provides not only good practice advice but also highlights the investigations and interventions that need further research. This research, when well-conducted, will be key to making progress in the clinical management of RIF.

STUDY FUNDING/COMPETING INTERESTS

The meetings and technical support for this project were funded by ESHRE. N.M. declared consulting fees from ArtPRED (The Netherlands) and Freya Biosciences (Denmark); Honoraria for lectures from Gedeon Richter, Merck, Abbott, and IBSA; being co-founder of Verso Biosense. He is Co-Chief Editor of Reproductive Biomedicine Online (RBMO). D.C. declared being an Associate Editor of Human Reproduction Update, and declared honoraria for lectures from Merck, Organon, IBSA, and Fairtility; support for attending meetings from Cooper Surgical, Fujifilm Irvine Scientific. G.G. declared that he or his institution received financial or non-financial support for research, lectures, workshops, advisory roles, or travelling from Ferring, Merck, Gedeon-Richter, PregLem, Abbott, Vifor, Organon, MSD, Coopersurgical, ObsEVA, and ReprodWissen. He is an Editor of the journals Archives of Obstetrics and Gynecology and Reproductive Biomedicine Online, and Editor in Chief of Journal Gynäkologische Endokrinologie. He is involved in guideline developments and quality control on national and international level. G.L. declared he or his institution received honoraria for lectures from Merck, Ferring, Vianex/Organon, and MSD. He is an Associate Editor of Human Reproduction Update, immediate past Coordinator of Special Interest Group for Reproductive Endocrinology of ESHRE and has been involved in Guideline Development Groups of ESHRE and national fertility authorities. D.J.M. declared being an Associate Editor for Human Reproduction Open and statistical Advisor for Reproductive Biomedicine Online. B.T. declared being shareholder of Reprognostics and she or her institution received financial or non-financial support for research, clinical trials, lectures, workshops, advisory roles or travelling from support for attending meetings from Ferring, MSD, Exeltis, Merck Serono, Bayer, Teva, Theramex and Novartis, Astropharm, Ferring. The other authors had nothing to disclose.

DISCLAIMER

This Good Practice Recommendations (GPR) document represents the views of ESHRE, which are the result of consensus between the relevant ESHRE stakeholders and are based on the scientific evidence available at the time of preparation. ESHRE GPRs should be used for information and educational purposes. They should not be interpreted as setting a standard of care or be deemed inclusive of all proper methods of care, or be exclusive of other methods of care reasonably directed to obtaining the same results. They do not replace the need for application of clinical judgement to each individual presentation, or variations based on locality and facility type. Furthermore, ESHRE GPRs do not constitute or imply the endorsement, or favouring, of any of the included technologies by ESHRE.

Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods

Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.

The Impact of the Female Genital Microbiota on the Outcome of Assisted Reproduction Treatments

The vaginal microbiota plays a critical role in the health of the female genital tract, and its composition contributes to gynecological disorders and infertility. Lactobacilli are the dominant species in the female genital tract: their production of lactic acid, hydrogen peroxide, and bacteriocins prevents the invasion and growth of pathogenic microorganisms. Several factors such as hormonal changes, age of reproduction, sexual practices, menstrual cycle, pregnancy, and antimicrobial drugs use can cause imbalance and dysbiosis of the vaginal microbiota. This review aims to highlight the impact of the vaginal microbiota in Assisted Reproductive Technology techniques (ART) and it examines the factors that influence the vaginal microbiota, the consequences of dysbiosis, and potential interventions to restore a healthy female genital tract.

Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling

Bacterial vaginosis (BV) is characterized by depletion of Lactobacillus and overgrowth of anaerobic and facultative bacteria, leading to increased mucosal inflammation, epithelial disruption, and poor reproductive health outcomes. However, the molecular mediators contributing to vaginal epithelial dysfunction are poorly understood. Here we utilize proteomic, transcriptomic, and metabolomic analyses to characterize biological features underlying BV in 405 African women and explore functional mechanisms in vitro. We identify five major vaginal microbiome groups: L. crispatus (21%), L. iners (18%), Lactobacillus (9%), Gardnerella (30%), and polymicrobial (22%). Using multi-omics we show that BV-associated epithelial disruption and mucosal inflammation link to the mammalian target of rapamycin (mTOR) pathway and associate with Gardnerella, M. mulieris, and specific metabolites including imidazole propionate. Experiments in vitro confirm that type strain G. vaginalis and M. mulieris supernatants and imidazole propionate directly affect epithelial barrier function and activation of mTOR pathways. These results find that the microbiome-mTOR axis is a central feature of epithelial dysfunction in BV.

The role of microbiota in the pathophysiology of uterine fibroids - a systematic review

For a long time, the uterus had been considered a sterile organ, meaning that under physiological conditions the uterus would not be colonized by bacteria. Based on available data, it may be concluded that the gut and uterine microbiome are related, and that the role of this microbiome is greater than expected. Despite being the most common pelvic neoplasms in women of reproductive age, uterine fibroids (UFs) are still poorly understood tumors whose etiology has not been fully determined. This systematic review presents the relationship between intestinal and uterine dysbiosis and uterine fibroids. A systematic review of three medical databases was carried out: the MEDLINE/PubMed, Scopus and Cochrane. In this study, 195 titles and abstracts were reviewed, including only original articles and clinical trials of uterine microbiome criteria. Finally, 16 studies were included to the analysis. In recent years, researchers dealing with reproduction in a broad sense have focused on the microbiome in various locations to study its role in the pathogenesis and, consequently, the prevention and treatment of diseases of the genital organ. Conventional microbial detection methods are not suitable for identifying bacteria, which are difficult to culture. Next-generation sequencing (NGS) provides an easier and faster and more informative analysis of bacterial populations. It seems that gut microbiota dysbiosis has the potential to be a risk factor for uterine fibroids or affect the disease process. Some changes were shown in many types of bacteria, such as Firmicutes, Proteobacteria, Actinobacteria and Verrucomicrobia detected in fecal samples in patients with uterine fibroids. In view of the few results on the link between the microbiome and uterine fibroids, further intensive studies in humans and animal models are necessary, including the possible use of different microbiome modulations in the prevention or treatment of uterine fibroids.

The Impact of the Microbiological Vaginal Swab on the Reproductive Outcome in Infertile Women

BACKGROUND

The thesis on which this paper is based intended to investigate whether the result of the microbiological vaginal swab has an influence on the outcome of the fertility treatment.

METHODS

The microbiological vaginal swabs of patients who received fertility treatment at Saarland University Hospital were evaluated. Depending on the microorganisms detected, the swab result was classified as inconspicuous, intermediate, or conspicuous. The SPSS software was used to determine the correlation between the swab result and the outcome of the fertility treatment.

RESULTS

Dysbiosis was associated with a worse outcome of fertility treatment. The pregnancy rate with a conspicuous swab was 8.6%, whereas it was 13.4% with an inconspicuous swab. However, this association was not statistically significant. Furthermore, an association of endometriosis with dysbiosis was found. Endometriosis was more frequent with a conspicuous swab result than with an inconspicuous result (21.1% vs. 17.7%), yet the correlation was not statistically significant. However, the absence of lactobacilli was significantly associated with endometriosis (p = 0.021). The association between endometriosis and a lower pregnancy rate was also statistically significant (p = 0.006).

CONCLUSION

The microbiological vaginal and cervical swabs can be used as predictors for the success of fertility treatments. Further studies are needed to assess the impact of transforming a dysbiotic flora into a eubiotic environment on the success of fertility treatments.

Vaginal microbes confounders and implications on women's health

The vagina has diverse vaginal microbes (Vm). A disturbance in the delicate balance maintained in Vm is linked to women's obstetrical and reproductive tract problems. Vaginal microbes play an essential role in protecting the health of the female reproductive tract by alleviating gynecological infection. However, Vm profiling has many confounders that need to be addressed during sampling, including age, race, pregnancy, medical illness, and smoking. Vm profiling improves reproduction odds, may serve as a marker for genital malignancies and have a therapeutic application in menopausal women and women with cervical cancers.

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain

In this study, we evaluated the seminal and fecal microbiota in yearling beef bulls fed a common diet to achieve moderate (1.13 kg/day) or high (1.80 kg/day) rates of weight gain. Semen samples were collected on days 0 and 112 of dietary intervention (n = 19/group) as well as postbreeding (n = 6/group) using electroejaculation, and the microbiota was assessed using 16S rRNA gene sequencing, quantitative PCR (qPCR), and culturing. The fecal microbiota was also evaluated, and its similarity with seminal microbiota was assessed. A subset of seminal bacterial isolates (n = 33) was screened for resistance against 28 antibiotics. A complex and dynamic microbiota was detected in bovine semen, and the community structure was affected by sampling time (R2 = 0.16, P < 0.001). Microbial richness increased significantly from day 0 to day 112, and diversity increased after breeding (P > 0.05). Seminal microbiota remained unaffected by the differential rates of gain, and its overall composition was distinct from fecal microbiota, with only 6% of the taxa shared between them. A total of 364 isolates from 49 different genera were recovered under aerobic and anaerobic culturing. Among these seminal isolates were pathogenic species and those resistant to several antibiotics. Overall, our results suggest that bovine semen harbors a rich and complex microbiota which changes over time and during the breeding season but appears to be resilient to differential gains achieved via a common diet. Seminal microbiota is distinct from the fecal microbiota and harbors potentially pathogenic and antibiotic-resistant bacterial species. IMPORTANCE Increasing evidence from human and other animal species supports the existence of a commensal microbiota in semen and that this seminal microbiota may influence not only sperm quality and fertility but also female reproduction. Seminal microbiota in bulls and its evolution and factors shaping this community, however, remain largely underexplored. In this study, we characterized the seminal microbiota of yearling beef bulls and its response to the bull age, different weight gains, and mating activity. We compared bacterial composition between seminal and fecal microbiota and evaluated the diversity of culturable seminal bacteria and their antimicrobial resistance. Our results obtained from sequencing, culturing, and antibiotic susceptibility testing provide novel information on the taxonomic composition, evolution, and factors shaping the seminal microbiota of yearling beef bulls. This information will serve as an important basis for further understanding of the seminal microbiome and its involvement in reproductive health and fertility in cattle.

A pilot study using unique targeted testing of the urogenital microbiome has potential as a predictive test during IVF for implantation outcome

PURPOSE

This pilot study aimed to develop a methodology characterising the urogenital microbiome as a predictive test in the IVF workup.

METHODS

Using unique custom qPCRs, we tested for the presence of specific microbial species from vaginal samples and First Catch Urines from the male. The test panel included a range of potential urogenital pathogens, STIs, 'favourable bacteria' (Lactobacillus spp.) and 'unfavourable bacteria' (anaerobes) reported to influence implantation rates. We tested couples attending Fertility Associates, Christchurch, New Zealand for their first round of IVF.

RESULTS

We found that some microbial species affected implantation. The qPCR result was interpreted qualitatively using the Z proportionality test. Samples from women at the time of Embryo Transfer who did not achieve implantation had significantly higher percent of samples that were positive for Prevotella bivia and Staphylococcus aureus compared to women who did achieve implantation.

DISCUSSION

The results provide evidence that most other microbial species chosen for testing had little functional effect on implantation rates. The addition of further microbial targets (yet to be determined) could be combined in this predictive test for vaginal preparedness on the day of embryo transfer. This methodology has a substantial advantage of being affordable and easily performed in any routine molecular laboratory. This methodology is most suitable as a foundation on which to develop a timely test of microbiome profiling. Using the indicators detected to have a significant influence, these results can be extrapolated.

CONCLUSION

Using a rapid antigen test, a woman can self-sample prior to embryo transfer and obtain an indication of microbial species present which could influence implantation outcome.

Correlations of joint detection of 22 vaginal microbes with routine examination results of vaginal secretions and assisted reproductive outcomes

The correlations of joint detection of 22 vaginal microbes with routine examination results of vaginal secretions and assisted reproductive outcomes were investigated. There were 37 samples with abnormal vaginal microecology in 107 vaginal secretion samples. The top 5 detection rates of microorganisms were Ureaplasma urealyticum (73.83%), Prevotella sp. (70.09%), Gardnerella vaginalis (53.27%), L. crispatus (52.34%) and L. inerts (51.40%). When the levels of Bacillus and hydrogen peroxide in vaginal secretions decreased or pH increased, the abnormal rates of vaginal microecology increased significantly (P < 0.01). The clinical pregnancy rate (53.66%, 22/41) in the women with normal vaginal microecology was higher than that (37.5%, 9/24) with abnormal vaginal microecology. In conclusions, the joint detection of 22 vaginal microbes can quickly and effectively determine whether the vaginal microecology is normal or not. The evaluation of vaginal microecology may be valuable in predicting the assisted reproductive outcomes of infertile women.

The endometrial microbiota of women with or without a live birth within 12 months after a first failed IVF/ICSI cycle

The endometrial microbiota composition may be associated with implantation success. However, a 'core' composition has not yet been defined. This exploratory study analysed the endometrial microbiota by 16S rRNA sequencing (V1-V2 region) of 141 infertile women whose first IVF/ICSI cycle failed and compared the microbiota profiles of women with and without a live birth within 12 months of follow-up, and by infertility cause and type. Lactobacillus was the most abundant genus in the majority of samples. Women with a live birth compared to those without had significantly higher Lactobacillus crispatus relative abundance (RA) (p = 0.029), and a smaller proportion of them had ≤ 10% L. crispatus RA (42.1% and 70.4%, respectively; p = 0.015). A smaller proportion of women in the male factor infertility group had ≤ 10% L. crispatus RA compared to women in the unexplained and other infertility causes groups combined (p = 0.030). Women with primary infertility compared to secondary infertility had significantly higher L. crispatus RA (p = 0.004); lower proportions of them had ≤ 10% L. crispatus RA (p = 0.009) and > 10% Gardnerella vaginalis RA (p = 0.019). In conclusion, IVF/ICSI success may be associated with L. crispatus RA and secondary infertility with endometrial dysbiosis, more often than primary infertility. These hypotheses should be tested in rigorous well-powered longitudinal studies.

Urogenital tract and rectal microbiota composition and its influence on reproductive outcomes in infertile patients

Introduction

Microbiota in the human body are closely related to human diseases. Female urogenital tract and rectal microbes have been considered as important factors affecting female pregnancy, but the mechanism is unknown.

Methods

Cervical, vaginal, urethral, and rectal swabs were collected from 22 infertile patients and 10 controls, and follicular fluid was extracted from 22 infertile patients. The microbial composition of different sampling sites of infertile patients was examined. By comparing the microbial composition difference between infertile patients and controls and combining bioinformatics methods to analyze the potential impact of the female urogenital tract (cervical, vaginal and urethral) and rectal microbial diversity on female infertility and pregnancy outcomes.

Results

Lactobacillus predominated in the female urogenital tract, but its abundance decreased in infertile patients, whereas the abundance of Gardnerella and Atopobium increased. The microbial changes in the urethra had the same trend as that in the vagina. Compared with healthy controls, the cervical and rectal microbial diversity of infertile patients were significantly increased and decreased, respectively. There might be interactions between microbes in different parts of female. Geobacillus thermogeniticans was enriched in the urogenital tract and rectum of infertile patients, and has a good predictive effect on infertility. Compared with infertile patients, L. johnsonii was enriched in the vagina, urethra, and intestine of the control group. L. acidophilus in follicular fluid might be associated with Non-pregnancy.

Conclusion

This study found that the microbial composition of infertile patients was changed compared with that of healthy people. The translocation of Lactobacillus between the rectum and urogenital tract might play a protective barrier role. The changes of Lactobacillus and Geobacillus might be related to female infertility or pregnancy outcome. The study provided a theoretical basis for the future treatment of female infertility from the perspective of microorganisms by detecting the microbial changes associated with female infertility.

Variable Selection for Sparse Data with Applications to Vaginal Microbiome and Gene Expression Data

Sparse data with a high portion of zeros arise in various disciplines. Modeling sparse high-dimensional data is a challenging and growing research area. In this paper, we provide statistical methods and tools for analyzing sparse data in a fairly general and complex context. We utilize two real scientific applications as illustrations, including a longitudinal vaginal microbiome data and a high dimensional gene expression data. We recommend zero-inflated model selections and significance tests to identify the time intervals when the pregnant and non-pregnant groups of women are significantly different in terms of Lactobacillus species. We apply the same techniques to select the best 50 genes out of 2426 sparse gene expression data. The classification based on our selected genes achieves 100% prediction accuracy. Furthermore, the first four principal components based on the selected genes can explain as high as 83% of the model variability.

The Vaginal Microbiome in Health and Disease-What Role Do Common Intimate Hygiene Practices Play?

The vaginal microbiome is a dynamic, sensitive microenvironment. The hallmark of a 'healthy' vaginal microbiome is currently believed to be one dominated by Lactobacillus spp., which acidifies the vaginal environment and help to protect against invading pathogens. However, a 'normal' microbiome is often difficult, if not impossible, to characterise given that it varies in response to numerous variables, including pregnancy, the menstrual cycle, contraceptive use, diet, ethnicity, and stress. A Lactobacillus-depleted microbiome has been linked to a variety of adverse vaginal health outcomes, including preterm birth (PTB), bacterial vaginosis (BV), and increased risk of sexually transmitted infections. The latter two of these have also been associated with feminine intimate hygiene practices, many of which are practised without any evidence of health benefits. The most extensively studied practice is vaginal douching, which is known to cause vaginal dysbiosis, predisposing women to BV, pelvic inflammatory disease, and PTB. However, little is known of the impact that intimate hygiene practices and associated products have on the vaginal microbiome. This review aims to outline the major factors influencing the vaginal microbiome and common vaginal infections, as well as to summarise current research surrounding the impact of hygiene products and practices on the vaginal microbiome.

The Implication of Mechanistic Approaches and the Role of the Microbiome in Polycystic Ovary Syndrome (PCOS): A Review

As a complex endocrine and metabolic condition, polycystic ovarian syndrome (PCOS) affects women's reproductive health. These common symptoms include hirsutism, hyperandrogenism, ovulatory dysfunction, irregular menstruation, and infertility. No one knows what causes it or how to stop it yet. Alterations in gut microbiota composition and disruptions in secondary bile acid production appear to play a causative role in developing PCOS. PCOS pathophysiology and phenotypes are tightly related to both enteric and vaginal bacteria. Patients with PCOS exhibit changed microbiome compositions and decreased microbial diversity. Intestinal microorganisms also alter PCOS patient phenotypes by upregulating or downregulating hormone release, gut-brain mediators, and metabolite synthesis. The human body's gut microbiota, also known as the "second genome," can interact with the environment to improve metabolic and immunological function. Inflammation is connected to PCOS and may be caused by dysbiosis in the gut microbiome. This review sheds light on the recently discovered connections between gut microbiota and insulin resistance (IR) and the potential mechanisms of PCOS. This study also describes metabolomic studies to obtain a clear view of PCOS and ways to tackle it.

The function and mechanism of action of uterine microecology in pregnancy immunity and its complications

The human microbiota influences physiology, disease, and metabolic reproduction. The origin of uterine bacteria is controversial. The main assumption is that the germs enter the uterine cavity from the vagina through the cervical canal, bloodstream, fallopian tubes, and gynecological surgical channels. Understanding the microbiota at various anatomical sites is critical to the female reproductive system and pregnancy. Today's study focuses on the role of uterine bacteria in pregnancy and embryo implantation. According to our findings, the uterine microbiome influences embryo implantation and pregnancy outcome. Pregnancy is a natural, evolutionarily selected approach to human reproduction. During pregnancy, the microbiota of the reproductive tract changes, facilitating the maintenance of pregnancy, and the human immune system undergoes a series of changes that recognize and adapt to the non-self. From the beginning of pregnancy, a non-self fetus must establish a placenta of embryonic origin to protect itself and promote growth; the VMB tends to be more stable and lactobacillus-dominated in late gestation than in early gestation. Any material that disrupts this connection, such as microbial changes, is associated with a higher risk of poor health and poor pregnancy outcomes in women (eclampsia). The presence of any material that disrupts this connection, such as microbial changes, is associated with a higher risk of poor health and poor pregnancy outcomes (preeclampsia, preterm birth, gestational diabetes, etc.). In this work, we review the last decade of relevant research to improve our understanding of the mechanisms by which the microbiota of the female reproductive tract influences female reproductive health. This work discusses the mechanisms associated with the reproductive tract microbiota and pregnancy immunity, as well as the impact of an abnormal microbiota on adverse pregnancy outcomes. Emphasis is placed on the characteristics and sources of the female vaginal, uterine, and placental microbiota and the importance of a well-stabilized local human microbiota and immune system for embryo implantation, placental development, fetal growth, and pregnancy outcome.

Adverse effect of lactobacilli-depauperate cervicovaginal microbiota on pregnancy outcomes in women undergoing frozen-thawed embryo transfer

Purpose

The cervicovaginal microbiota is essential for maintaining the health of the female reproductive tract. However, whether cervicovaginal microbiota status prior to frozen embryo transfer (FET) associates with pregnancy outcomes is largely unexplored.

Methods

Cervical mucus from 29 women who had undergone FET was collected. Microbial composition was analyzed using 16 S rRNA gene sequence to assess the correlation to the pregnancy outcomes.

Results

CST-categorized Lactobacillus was the most dominant (41.71%) in the pregnant group, while CST-IV-based and BV-related Gardnerella (34.96%) prevailed in the non-pregnant group. The average abundance of Gardnerella compared non-pregnant to pregnant women was the highest (34.96% vs. 4.22%, p = 0.0015) among other CST-IV indicator bacteria. Multivariate analysis revealed that CST-IV-related bacteria have a significantly adverse effect on ongoing pregnancy outcomes (odds ratio, 0.083; 95% confidence index, 0.012-0.589, p = 0.013*).

Conclusions

The study found that the CST-IV microbiota, with significantly increasing Gardnerella and the loss of Lactobacilli as the dominant bacteria, can potentially contribute to pregnancy failure. Therefore, dysbiotic microbiota may be a risk factor in women undergoing FET. Assessing the health of the cervicovaginal microbiota prior to FET would enable couples to make a more thoughtful decision on the timing and might improve pregnancy outcomes.

Effect of vaginal flora on clinical outcome of frozen embryo transfer

Objective

Vaginal microbiota imbalance is a high risk factor for premature birth, and is closely related to female pelvic inflammation and sexually transmitted diseases. The effect of vaginal microbiota on the outcome of assisted reproductive technology is still unclear. In this study, the vaginal microbial composition and the pregnancy outcome of frozen embryo transfer (FET) was investigated.

Methods

From October 2020 to December 2021, 275 FET cycles were selected from the center of reproductive medicine in Affiliated Hospital of Nantong University. Vaginal secretions were collected on the day of endometrium transformation, and smears were Gram stained. According to the Nugent score they were divided into three groups, including normal group, mild dysbiosis group and sever dysbiosis group. The clinical outcomes of each group were compared.

Results

In 275 FET cycles, the embryo implantation rate, clinical pregnancy rate and ongoing pregnancy rate in the normal group (66.9%,84.3% and 83.1%) were significantly higher than those in the mild dysbiosis group (45.5%, 57.3% and 49.3%) and in sever dysbiosis group (29.6%, 34.2% and 27%). The difference was statistically significant (P<0.01). When compared the preclinical pregnancy loss rate and the miscarriage rate, the normal group (1.3% and 1.3%) was significantly lower than those in the mild dysbiosis group (20.4% and 14.0%) and the sever dysbiosis group (25.5% and 21.1%). The difference was statistically significant (P<0.01), but there was no significant difference between the mild dysbiosis group and sever dysbiosis group (P>0.05).

Conclusion

Nugent score is directly related to the clinical outcome of FET. The Lactobacilli-dominant vaginal flora was a favorable factor for the good clinical outcome of FET, while asymptomatic bacterial vaginosis had a negative correlation with the outcome of FET.

Effects of Hydrosalpinx on Endometrial Receptivity and Uterine Microbiome: An Interesting Case of Double Uterus with Unilateral Hydrosalpinx

Endometrial receptivity array (ERA)—an objective tool used in assisted reproductive technology—is used for personalized embryo transfer in in vitro fertilization. Hydrosalpinx affects implantation through various mechanisms. However, its effects on ERA are not well established. In this case report, we present the diagnosis and treatment of a 34-year-old nulligravida woman with infertility for two years, obesity, double uterus with unilateral hydrosalpinx and right kidney deficiency. Based on ERA results, endometrial microbiome metagenomic analysis (EMMA), analysis of infectious chronic endometritis (ALICE), and CD138 immunostaining, the patient was treated with hormonal replacement cycle and amoxicillin/clavulanic acid. After one week of amoxicillin/clavulanic acid administration, the vitirified-warmed 4AA blastocyst was transferred to the left uterus—which was absent of hydrosalpinx and easily accessible to transfer and pregnancy was achieved. To the best of our knowledge, this case study is the first one in which we found that there were no differences between the left and right uterus in ERA, EMMA, ALICE, and CD138 immunostainings. Hence, we suggest that hydrosalpinx does not necessarily cause endometrial changes in all cases. Further research to evaluate the effects of hydrosalpinx on implantation with ERA and EMMA/ALICE is warranted.

Genital Microbiota and Outcome of Assisted Reproductive Treatment-A Systematic Review

The balance between different bacterial species is essential for optimal vaginal health. Microbiome includes the host genome along with microorganism genomes and incorporates the biotic and abiotic factors, reflecting the habitat as a whole. A significant difference exists in the composition and number of the human microbiota in healthy individuals. About one-tenth of the total body microbiota exists in the urogenital tract and these can be identified by microscopy and culture-based methods, quantitative PCR, next generation and whole genome sequencing. The trend of delaying the planning of pregnancy to a later age nowadays has resulted in magnifying the use of assisted reproductive treatment (ART). Hence, genital microbiota and its impact on fertility has generated immense interest in recent years. In this systematic review, we searched the available evidence on the microbiota of the genital tract in women undergoing ART and studied the outcomes of IVF in different microbial compositions. Despite the inconsistency of the studies, it is evident that vaginal, cervical and endometrial microbiota might play a role in predicting ART outcomes. However, there is no clear evidence yet on whether the diversity, richness, quantity, or composition of species in the maternal genital tract significantly affects the outcomes in ARTs.

Seminal and vagino-uterine microbiome and their individual and interactive effects on cattle fertility

Reproductive failure is a major economical drain on cow-calf operations across the globe. It can occur in both males and females and stem from prenatal and postnatal influences. Therefore, the cattle industry has been making efforts to improve fertility and the pregnancy rate in cattle herds as an attempt to maintain sustainability and profitability of cattle production. Despite the advancements made in genetic selection, nutrition, and the implementation of various reproductive technologies, fertility rates have not significantly improved in the past 50 years. This signifies a missing factor or factors in current reproductive management practices that influence successful fertilization and pregnancy. Emerging lines of evidence derived from human and other animals including cattle suggest that the microbial continuum along the male and female reproductive tracts are associated with male and female fertility-that is, fertilization, implantation, and pregnancy success-highlighting the potential for harnessing the male and female reproductive microbiome to improve fertility in cattle. The objective of this narrative review is to provide an overview of the recent studies on the bovine seminal and vagino-uterine microbiome and discuss individual and interactive roles of these microbial communities in defining cattle fertility.

Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples

DNA sequencing assays have been used to characterize the vaginal microbiome and to identify associations with clinical outcomes. The purpose of this study was to evaluate the utility of the NanoString nCounter platform, a more efficient assay compared to sequencing, for the characterization of vaginal microbial communities. A panel of NanoString nCounter probes was designed to detect common vaginal bacteria and viruses with relevance to reproductive health. A defined synthetic community of microbes and 43 clinical samples were interrogated with NanoString nCounter assays and compared to known compositions or metagenomic shotgun sequencing (MSS) results. The NanoString nCounter platform and MSS were able to distinguish closely related microbes. In clinical samples, the relative abundance of bacterial species was similar between the two assays. The assays sometimes disagreed when targets were present at low abundance. More viruses were detected by MSS than by nCounter. However, the nCounter assays are able to provide results in about 30 h with minimal hands-on time, whereas MSS requires at least 138 to 178 h with extensive hands-on time. The reagent cost for the two assays was similar, but the overall cost of the nCounter was lower due to the minimal hands-on time. MSS can be used to inform the design of a targeted multiplex panel for the assessment of vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples for research studies. The sensitivity for low abundance microbes could be improved, possibly by adding additional target amplification cycles before nCounter assessment. This approach has potential as an assay with both research and clinical applications. IMPORTANCE Metagenomic shotgun sequencing can inform the design of a targeted multiplex panel by which the NanoString nCounter platform can assess vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples.

Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events

PURPOSE

The Swedish Maternal Microbiome (SweMaMi) project was initiated to better understand the dynamics of the microbiome in pregnancy, with longitudinal microbiome sampling, shotgun metagenomics, extensive questionnaires and health registry linkage.

PARTICIPANTS

Pregnant women were recruited before the 20th gestational week during 2017-2021 in Sweden. In total, 5439 pregnancies (5193 unique women) were included. For 3973 pregnancies (73%), samples were provided at baseline, and for 3141 (58%) at all three timepoints (second and third trimester and postpartum). In total, 38 591 maternal microbiome samples (vaginal, faecal and saliva) and 3109 infant faecal samples were collected. Questionnaires were used to collect information on general, reproductive and mental health, diet and lifestyle, complemented by linkage to the nationwide health registries, also used to follow up the health of the offspring (up to age 10).

FINDINGS TO DATE

The cohort is fairly representative for the total Swedish pregnant population (data from 2019), with 41% first-time mothers. Women with university level education, born in Sweden, with normal body mass index, not using tobacco-products and aged 30-34 years were slightly over-represented.

FUTURE PLANS

The sample and data collection were finalised in November 2021. The next steps are the characterisation of the microbial DNA and linkage to the health and demographic information from the questionnaires and registries. The role of the microbiome on maternal and neonatal outcomes and early-childhood diseases will be explored (including preterm birth, miscarriage) and the role and interaction of other risk factors and confounders (including endometriosis, polycystic ovarian syndrome, diet, drug use). This is currently among the largest pregnancy cohorts in the world with longitudinal design and detailed and standardised microbiome sampling enabling follow-up of both mothers and children. The findings are expected to contribute greatly to the field of reproductive health focusing on pregnancy and neonatal outcomes.

Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing

PURPOSE

Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis.

METHODS

Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference.

RESULTS

The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing.

CONCLUSIONS

Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.

Characterization of cervical canal and vaginal bacteria in pregnant women with cervical incompetence

Vaginal and cervical canal bacteria are associated with women’s health and pregnancy outcomes. Here, we compared their composition and characteristics in 37 reproductive-aged Chinese women including 24 pregnant women with cervical incompetence (vaginal and cervical canal bacteria formed Groups A and B, respectively) and 13 healthy pregnant women (vaginal and cervical canal bacteria formed Groups C and D, respectively) using high-throughput sequencing of the V4 region of 16S rRNA gene. The results of alpha and beta diversity analysis, respectively, indicated no statistical differences between Groups A and B (p = 0.32, 0.06), nor Groups B and D (p = 0.69, 0.74); however, differences were found between Groups C and D (p = 0.02, 0.01) and between Groups A and C (p = 0.04, 0.02). PLS-DA analysis showed that the individuals from each group were irregularly distributed according to their clade. Lactobacillus, Bifidobacterium and Ureaplasma were the dominant genera in all groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSts) analysis identified 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs associated with the bacterial communities from the four groups, including membrane transport, folding, sorting and degradation, xenobiotics biodegradation and metabolism, and nucleotide metabolism. We further determined relationships between pregnancy outcomes (Apgar scores) and certain bacterial species. A significant positive correlation was found between Apgar scores and Actinomyces neuii and Anoxybacillus flavithermus in the vagina and cervical canal of pregnant women with cervical incompetence while Bacteroides plebeius, Bifidobacterium pseudopodium and Staphylococcus petrasii in the cervical canal displayed negative correlations with Apgar scores. Moreover, Clostridium fimetarium, Methanobacterium congolense, Pseudomonas chlororaphis, and Psychrobacter nivimaris in the vagina were negatively correlated with Apgar scores. These bacteria may serve as potential biomarkers, however, additional research is warranted to verify their role in clinical outcomes.

The relationship between vaginal pH and bacterial vaginosis as diagnosed using qPCR in an asymptomatic subfertile population

PURPOSE

Bacterial vaginosis (BV) is a dysbiosis of the vaginal microbiome and a condition found in 20-30% of all women. Literature describing the possible link between BV and subfertility is increasing. Newer techniques such as quantitative polymerase chain reactions (qPCR) detect BV more accurately than traditional methods but come with high costs. The association between pH and BV as diagnosed using traditional methods is well-established in a symptomatic population. This study is the first to investigate the association between pH and BV diagnosed by qPCR in an asymptomatic subfertile population and to examine the usefulness of pH as a means of cost reduction.

METHODS

Data of 170 pH-qPCR combinations were used from a prospective cohort study examining bacterial vaginosis in a subfertile population. 102 women received a vaginal swab and pH measurement at baseline and subsequent advanced reproductive technology (ART) treatments. The swabs are analysed using the AmpliSens^®Florocenosis/Bacterial vaginosis-FRT qPCR kit.

RESULTS

pH is strongly associated with BV as diagnosed by qPCR (OR 3.06, p = 0.000, CI 1.65-5.68). The cut-off point for pH ≥ 4.7 maximised diagnostic performance [AUC 0.74 (CI 0.66-0.83), sensitivity 76%] and reduced costs by 60%.

CONCLUSION

This study shows that the vaginal pH for a multi-ethnic, asymptomatic population of women attending fertility clinics is strongly associated with BV qPCR outcome. Using the cut-off of pH of 4.7 has a high sensitivity for diagnosis of BV by qPCR and can be achieved at a cost reduction of 60%.

Microbiome Characteristics in Early Threatened Miscarriage Study (MCETMS): a study protocol for a prospective cohort investigation in China

INTRODUCTION

Studies have suggested that the vaginal microbiome and gut microbiome are involved in pregnancy-related diseases, but little exploration of the link with early miscarriage or threatened miscarriage (TM) has been done. Whether the characteristics of the vaginal microbiome and gut microbiome in early pregnancy are related to TM and early pregnancy outcomes remains unclear.

METHODS AND ANALYSIS

The Microbiome Characteristics in Early Threatened Miscarriage Study (MCETMS) is a prospective investigation that will recruit 326 pregnant women with early TM. Pregnant women will be enrolled at 4-8 weeks of gestation, and their vaginal secretions, faecal samples, clinical data and sociodemographic characteristics will be collected prospectively. Pregnant women with TM will be followed up to 12 weeks of gestation to determine the early pregnancy outcomes (ongoing pregnancy or pregnancy loss). DNA will be extracted from the collected samples and will be analysed by 16S rRNA gene sequencing.

ETHICS AND DISSEMINATION

The MCETMS study protocol has been approved by the Ethics Committee of the First Affiliated Hospital of Guangzhou Traditional Chinese Medical University (ZYYECK[2020]051). Dissemination of study findings will occur through peer-reviewed journals, conferences and presentations.

TRIAL REGISTRATION NUMBER

ChiCTR2000041172.