Microbiota and Human Reproduction: The Case of Female Infertility

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.

Role of vaginal microbiota in idiopathic infertility: a prospective study

OBJECTIVE

The causes of idiopathic infertility are still not known; however, it may be associated with microbial etiologies. The present study examines the vaginal microbiota of infertile as well as fertile women longitudinally.

METHODOLOGY

The study was presented and accepted by the Institutional Ethical Committee of Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir (India). An observational, prospective, multicenteric investigation was conducted at the Department of Obstetrics and Gynecology, Government Medical College Jammu, and its affiliated hospitals in Jammu and Kashmir (India). In order to examine the microbial composition, a cohort of 80 female individuals were involved in the screening process. The investigation involved sequencing of the V3-V4 region of 16S rRNA gene, which was subsequently analyzed using the Mothur pipeline.

RESULTS

The study revealed that the vaginal microbiota of infertile women differed from that of healthy women who had previously given birth without any complications. Both populations have variations in their alpha as well as beta diversity and taxonomical composition. The microbial profiles in the cases of infertility are characterized by elevated levels of Gardnerella, Prevotella, Atopobium, and Enterococcus whereas a higher level of Lactobacillus iners was observed in case of fertile women.

CONCLUSION

In conclusion, it can be inferred that the composition of the vaginal microbiome potentially exerts a significant influence on females afflicted with idiopathic infertility.

Comparative analysis of reproductive tract microbiomes in modern and slower-growing broiler breeder lines

Introduction

The reproductive tract microbiome in hens is of interest because bacteria in the reproductive tract could potentially affect fertilization and egg production, as well as integrate into the forming egg and vertically transmit to progeny.

Methods

The reproductive tract microbiome of 37-week-old modern commercial Cobb breeding dams was compared with that of dams from a broiler Legacy line which has not undergone selection since 1986. All animals were kept together under the same management protocol from day of hatch to avoid confounders.

Results

In regards to reproductive abilities, Cobb dams' eggs weighed more and the magnum section of their reproductive tract was longer. In regards to microbiome composition, it was found that the reproductive tract microbiomes of the two lines had a lot in common but also that the two breeds have unique reproductive tract microbiomes. Specifically, the order Pseudomonadales was higher in the magnum of Legacy dams, while Verrucomicrobiales was lower. In the infundibulum, Lactobacillales were higher in the Legacy dams while Verrucomicrobiales, Bacteroidales, RF32 and YS2 were lower.

Discussion

our results show that breeding programs have modified not only the physiology of the reproductive tract but also the reproductive tract microbiome. Additional research is required to understand the implications of these changes in the reproductive tract microbiome on the chicken host.

Changes in seminal plasma microecological dynamics and the mechanistic impact of core metabolite hexadecanamide in asthenozoospermia patients

Asthenozoospermia (AZS) is a prevalent contributor to male infertility, characterized by a substantial decline in sperm motility. In recent years, large-scale studies have explored the interplay between the male reproductive system's microecology and its implications for reproductive health. Nevertheless, the direct association between seminal microecology and male infertility pathogenesis remains inconclusive. This study used 16S rDNA sequencing and multi-omics analysis to conduct a comprehensive investigation of the seminal microbial community and metabolites in AZS patients. Patients were categorized into four distinct groups: Normal, mild AZS (AZS-I), moderate AZS (AZS-II), and severe AZS (AZS-III). Microbiome differential abundance analysis revealed significant differences in microbial composition and metabolite profiles within the seminal plasma of these groups. Subsequently, patients were classified into a control group (Normal and AZS-I) and an AZS group (AZS-II and AZS-III). Correlation and cross-reference analyses identified distinct microbial genera and metabolites. Notably, the AZS group exhibited a reduced abundance of bacterial genera such as Pseudomonas, Serratia, and Methylobacterium-Methylorubrum in seminal plasma, positively correlating with core differential metabolite (hexadecanamide). Conversely, the AZS group displayed an increased abundance of bacterial genera such as Uruburuella, Vibrio, and Pseudoalteromonas, with a negative correlation with core differential metabolite (hexadecanamide). In vitro and in vivo experiments validated that hexadecanamide significantly enhanced sperm motility. Using predictive metabolite-targeting gene analysis and single-cell transcriptome sequencing, we profiled the gene expression of candidate target genes PAOX and CA2. Protein immunoblotting techniques validated the upregulation protein levels of PAOX and CA2 in sperm samples after hexadecanamide treatment, enhancing sperm motility. In conclusion, this study uncovered a significant correlation between six microbial genera in seminal plasma and the content of the metabolite hexadecanamide, which is related to AZS. Hexadecanamide notably enhances sperm motility, suggesting its potential integration into clinical strategies for managing AZS, providing a foundational framework for diagnostic and therapeutic advancements.

The role of the endometrial microbiome in embryo implantation and recurrent implantation failure

There is a suggested pathophysiology associated with endometrial microbiota in cases where repeated implantation failure of high-quality embryos is observed. However, there is a suspected association between endometrial microbiota and the pathogenesis of implantation failure. However, there is still a lack of agreement on the fundamental composition of the physiological microbiome within the uterine cavity. This is primarily due to various limitations in the studies conducted, including small sample sizes and variations in experimental designs. As a result, the impact of bacterial communities in the endometrium on human reproduction is still a subject of debate. In this discourse, we undertake a comprehensive examination of the existing body of research pertaining to the uterine microbiota and its intricate interplay with the process of embryo implantation.

Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases

Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.

The role of probiotics in women's health: An update narrative review

Probiotics, live microorganisms that confer health benefits to the host when administered in adequate amounts, have gained considerable attention for their potential role in maintaining women's health. This overview summarizes key clinical findings on the beneficial effects of probiotics in various aspects of women's health. Probiotics, particularly Lactobacillus species, contribute to vaginal health by promoting a balanced vaginal microbiome to prevent infections and maintain an acidic environment. In gynecologic conditions, probiotics show potential in preventing and managing bacterial vaginosis, vulvovaginal candidiasis, and sexually transmitted infections. Probiotic supplementation has also been associated with improvements in metabolic parameters and menstrual irregularities in polycystic ovary syndrome patients. During pregnancy, probiotics may be helpful in reducing the risk of gestational diabetes, maternal group B streptococcal colonization, obstetric anemia, and postpartum mastitis. In recent years, the potential role of probiotics in the prevention and management of gynecologic cancer has gained attention. Further research is needed to better understand the specific mechanisms and determine the optimal Lactobacillus strains and dosages regimens for gynecologic cancer prevention and therapy. In conclusion, probiotics offer a non-invasive and cost-effective approach to support women's health and prevent obstetric and gynecologic complications.

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.

Microbial Dysbiosis and Male Infertility: Understanding the Impact and Exploring Therapeutic Interventions

The human microbiota in the genital tract is pivotal for maintaining fertility, but its disruption can lead to male infertility. This study examines the relationship between microbial dysbiosis and male infertility, underscoring the promise of precision medicine in this field. Through a comprehensive review, this research indicates microbial signatures associated with male infertility, such as altered bacterial diversity, the dominance of pathogenic species, and imbalances in the genital microbiome. Key mechanisms linking microbial dysbiosis to infertility include inflammation, oxidative stress, and sperm structural deterioration. Emerging strategies like targeted antimicrobial therapies, probiotics, prebiotics, and fecal microbiota transplantation have shown potential in adjusting the genital microbiota to enhance male fertility. Notably, the application of precision medicine, which customizes treatments based on individual microbial profiles and specific causes of infertility, emerges as a promising approach to enhance treatment outcomes. Ultimately, microbial dysbiosis is intricately linked to male infertility, and embracing personalized treatment strategies rooted in precision medicine principles could be the way forward in addressing infertility associated with microbial factors.

Exploring Immunome and Microbiome Interplay in Reproductive Health: Current Knowledge, Challenges, and Novel Diagnostic Tools

The dynamic interplay between the immunome and microbiome in reproductive health is a complex and rapidly advancing research field, holding tremendously vast possibilities for the development of reproductive medicine. This immunome-microbiome relationship influences the innate and adaptive immune responses, thereby affecting the onset and progression of reproductive disorders. However, the mechanisms governing these interactions remain elusive and require innovative approaches to gather more understanding. This comprehensive review examines the current knowledge on reproductive microbiomes across various parts of female reproductive tract, with special consideration of bidirectional interactions between microbiomes and the immune system. Additionally, it explores innate and adaptive immunity, focusing on immunoglobulin (Ig) A and IgM antibodies, their regulation, self-antigen tolerance mechanisms, and their roles in immune homeostasis. This review also highlights ongoing technological innovations in microbiota research, emphasizing the need for standardized detection and analysis methods. For instance, we evaluate the clinical utility of innovative technologies such as Phage ImmunoPrecipitation Sequencing (PhIP-Seq) and Microbial Flow Cytometry coupled to Next-Generation Sequencing (mFLOW-Seq). Despite ongoing advancements, we emphasize the need for further exploration in this field, as a deeper understanding of immunome-microbiome interactions holds promise for innovative diagnostic and therapeutic strategies for reproductive health, like infertility treatment and management of pregnancy.

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.

Cycle Biodynamics of Women's Microbiome in the Urinary and Reproductive Systems

The genitourinary microbiome plays a crucial role in the establishment and maintenance of urinary and reproductive health in women throughout their lives. Particularly during the reproductive stage, resident microorganisms contribute to implantation and protect against perinatal complications, including preterm birth, stillbirth, and low birth weight, while also serving as the first line of defense against pathogens that can cause infections, such as urinary tract infections and bacterial vaginosis. This review aimed to elucidate the relationship between a healthy microbiome environment and women's overall health. We examine the variability and dynamics of the microbiome during different developmental stages, ranging from the prepubertal to the postmenopausal stage. Furthermore, we explore the significance of a healthy microbiota in successful implantation and pregnancy development and investigate potential differences between women experiencing infertility. In addition, we analyze the local and systemic inflammatory responses associated with the establishment of a dysbiotic state and compare it to a condition where a healthy microbiome was established. Lastly, we present the most recent evidence regarding preventive measures, such as dietary interventions and the use of probiotics to promote and maintain a healthy microbiome, thereby ensuring comprehensive women's health. By highlighting the importance of the genitourinary microbiome in reproductive health, this review aimed to enhance this microbiome's visibility and significance in the field.

Metagenomics Reveals Specific Microbial Features in Males with Semen Alterations

Infertility incidence is rising worldwide, with male infertility accounting for about 50% of cases. To date, several factors have been associated with male infertility; in particular, it has been suggested that semen microbiota may play a role. Here, we report the NGS-based analyses of 20 semen samples collected from men with (Case) and without (Control) semen alterations. Genomic DNA was extracted from each collected sample, and a specific PCR was carried out to amplify the V4-V6 regions of the 16S rRNA. Sequence reactions were carried out on the MiSeq and analyzed by specific bioinformatic tools. We found a reduced richness and evenness in the Case versus the Control group. Moreover, specific genera, the Mannheimia, the Escherichia_Shigella, and the Varibaculum, were significantly increased in the Case compared to the Control group. Finally, we highlighted a correlation between the microbial profile and semen hyperviscosity. Even if further studies are required on larger groups of subjects to confirm these findings and explore mechanistic hypotheses, our results confirm the correlation between semen features and seminal microbiota. These data, in turn, may open the way to the possible use of semen microbiota as an attractive target for developing novel strategies for infertility management.

The Female Reproductive Tract Microbiota: Friends and Foe

We do not seem to be the only owner of our body; it houses a large population of microorganisms. Through countless years of coevolution, microbes and hosts have developed complex relationships. In the past few years, the impact of microbial communities on their host has received significant attention. Advanced molecular sequencing techniques have revealed a remarkable diversity of the organ-specific microbiota populations, including in the reproductive tract. Currently, the goal of researchers has shifted to generate and perceive the molecular data of those hidden travelers of our body and harness them for the betterment of human health. Recently, microbial communities of the lower and upper reproductive tract and their correlation with the implication in reproductive health and disease have been extensively studied. Many intrinsic and extrinsic factors influences the female reproductive tract microbiota (FRTM) that directly affects the reproductive health. It is now believed that FRTM dominated by Lactobacilli may play an essential role in obstetric health beyond the woman's intimate comfort and well-being. Women with altered microbiota may face numerous health-related issues. Altered microbiota can be manipulated and restored to their original shape to re-establish normal reproductive health. The aim of the present review is to summarize the FRTM functional aspects that influence reproductive health.

Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure

An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.

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.

Microbiota metabolites in the female reproductive system: Focused on the short-chain fatty acids

Several disorders have been linked to modifications in the gut microbial imbalance, intestinal epithelium, and host immune system. In this regard, microbiota derived short-chain fatty acids (SCFAs) play a key function in the regulation of histone deacetylases (HDACs), which affect modulation of immunity and regulation of inflammatory responses in the intestine and other organs. Studies examining the metabolites produced by polymicrobial bacterial vaginosis (BV) states and Lactobacillus-dominated microbiota have noted a dramatic reduction of lactic acid and a shift toward SCFA synthesis. Along with higher levels of SCFAs, acetate is typically the main metabolite in the cervicovaginal fluid of women with symptomatic bacterial vaginosis. The fact that SCFAs made by the vaginal microbiota have been shown to exhibit antibacterial and immune-modulating properties suggests that they may have promise as indicators of disease and/or disease susceptibility. In this review, we overview and summarize the current findings on the detrimental or protective roles of microbiota metabolites especially SCFAs in the health and disease of the female reproductive system.

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.

Biologia Futura: endometrial microbiome affects endometrial receptivity from the perspective of the endometrial immune microenvironment

The existence of Lactobacillus-led colonized bacteria in the endometrium of a healthy human has been reported in recent studies. Unlike the composition of the microbiome in the lower genital tract, that in the endometrium is different and closely associated with the physiological and pathological processes of gynecological diseases. For example, changing the immune microenvironment affects the receptivity of the endometrium, thereby leading to abnormal reproductive outcomes, such as embryo implantation failure and recurrent spontaneous abortion. However, the concrete functions and mechanisms of the endometrial microbiome have not been studied thoroughly. This review elaborates the research progress on the mechanisms by which the endometrial microbiome affects endometrial receptivity from the perspective of endometrial immune microenvironment regulation. Considering the lack of a unified evaluation method for the endometrial microbiome, as well as the lack of an optimal treatment protocol against recurrent spontaneous abortion, we also discussed the application of combining antibiotics with probiotics/prebiotics as precautionary measures.

Human genital tracts microbiota: dysbiosis crucial for infertility

Human body is colonized by trillions of microbes, influenced by several factors, both endogenous, as hormones and circadian regulation, and exogenous as, life-style habits and nutrition. The alteration of such factors can lead to microbial dysbiosis, a phenomenon which, in turn, represents a risk factor in many different pathologies including cancer, diabetes, autoimmune and cardiovascular disease, and infertility. Female microbiota dysbiosis (vaginal, endometrial, placental) and male microbiota dysbiosis (seminal fluid) can influence the fertility, determining a detrimental impact on various conditions, as pre-term birth, neonatal illnesses, and macroscopic sperm parameters impairments. Furthermore, unprotected sexual intercourse creates a bacterial exchange between partners, and, in addition, each partner can influence the microbiota composition of partner's reproductive tracts. This comprehensive overview of the effects of bacterial dysbiosis in both sexes and how partners might influence each other will allow for better personalization of infertility management.

Bacterial infections in cancer: A bilateral relationship

Bacteria share a long commensal relationship with the human body. New findings, however, continue to unravel many complexities associated with this old alliance. In the past decades, the dysbiosis of human microbiome has been linked to tumorigenesis, and more recently to spontaneous colonization of existing tumors. The topic, however, remains open for debate as the claims for causative-prevailing dual characteristics of bacteria are mostly based on epidemiological evidence rather than robust mechanistic models. There are also no reviews linking the collective impact of bacteria in tumor microenvironments to the efficacy of cancer drugs, mechanisms of pathogen-initiated cancer and bacterial colonization, personalized nanomedicine, nanotechnology, and antimicrobial resistance. In this review, we provide a holistic overview of the bilateral relationship between cancer and bacteria covering all these aspects. Our collated evidence from the literature does not merely categorize bacteria as cancer causative or prevailing agents, but also critically highlights the gaps in the literature where more detailed studies may be required to reach such a conclusion. Arguments are made in favor of dual drug therapies that can simultaneously co-target bacteria and cancer cells to overcome drug resistance. Also discussed are the opportunities for leveraging the natural colonization and remission power of bacteria for cancer treatment. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Vaginal Atopobium is Associated with Spontaneous Abortion in the First Trimester: a Prospective Cohort Study in China

Spontaneous abortion (SA) has received more and more attention in light of its increasing incidence. However, the causes and pathogenesis of SA remain largely unknown, especially for those without any pathological features. In this study, we characterized the vaginal microbiota diversity and composition of pregnant women in their first trimester and evaluated the association between the vaginal microbiota and SA before 12 weeks of gestation. Participants' bacterial profiles were analyzed by 16S rRNA gene sequencing in the V3-V4 regions at 5-8 weeks of gestation. A total of 48 patients with SA at 12 weeks of gestation were included as the study group, while 116 women with normal pregnancies (NPs) were included as a control group. The results indicated that the richness of the vaginal microbiome in SA patients was higher (Chao1, P < 0.05) and different in composition relative to that of women with NPs (unweighted UniFrac, R = 0.15, P < 0.01; binary Jaccard, R = 0.15, P < 0.01). Furthermore, the genus Apotobium was significantly enriched in SA patients. An extreme gradient-boosting (XGBoost) analysis was able to classify Atopobium-induced SA more reliably (area under the receiver operating characteristic curve, 0.69; threshold, 0.01%). Moreover, after adjusting for potential confounders, the results showed a robust association between Apotobium and SA (as a categorical variable [<0.01%]; adjusted odds ratio, 2.9; 95% confidence interval, 1.3 to 6.5; P = 0.01). In conclusion, higher vaginal Apotobium levels were associated with SA in the first trimester. IMPORTANCE Spontaneous abortion (SA) is the most common adverse pregnancy outcome in the first trimester. The causal drivers of SA have become a substantial challenge to reveal and overcome. We hypothesize that vaginal microbial dysbiosis is associated with SA, as it was related to several female reproductive disorders in previous studies. In our study, we characterized the vaginal microbiota of patients with SA at 12 weeks of gestation as the study group, and women with normal pregnancies were enrolled as a control group. Generally, significant differences were discovered in the vaginal microbiota between the two groups. Our study also revealed that Apotobium may play an important role in the pathogenesis of SA. To our knowledge, this study is the first detailed elaboration of the vaginal microbiota composition and vaginal Apotobium in association with SA. We believe that our findings will inspire more researchers to consider dynamic changes in the vaginal microbiota as critical features for further studies of nosogenesis not only for SA but also other reproductive diseases.

Bovine Animal Model for Studying the Maternal Microbiome, in utero Microbial Colonization and Their Role in Offspring Development and Fetal Programming

Recent developments call for further research on the timing and mechanisms involved in the initial colonization of the fetal/infant gut by the maternal microbiome and its role in Developmental Origins of Health and Disease (DOHaD). Although progress has been made using primarily preterm infants, ethical and legal constraints hinder research progress in embryo/fetal-related research and understanding the developmental and mechanistic roles of the maternal microbiome in fetal microbial imprinting and its long-term role in early-life microbiome development. Rodent models have proven very good for studying the role of the maternal microbiome in fetal programming. However, some inherent limitations in these animal models make it challenging to study perinatal microbial colonization from a biomedical standpoint. In this review, we discuss the potential use of bovine animals as a biomedical model to study the maternal microbiome, in utero microbial colonization of the fetal gut, and their impact on offspring development and DOHaD.

Microorganisms in the reproductive system and probiotic's regulatory effects on reproductive health

The presence of microbial communities in the reproductive tract has been revealed, and this resident microbiota is involved in the maintenance of health. Intentional modulation via probiotics has been proposed as a possible strategy to enhance reproductive health and reduce the risk of diseases. The male seminal microbiota has been suggested as an important factor that influences a couple’s health, pregnancy outcomes, and offspring health. Probiotics have been reported to play a role in male fertility and to affect the health of mothers and offspring. While the female reproductive microbiota is more complicated and has been identified in both the upper and lower reproductive systems, they together contribute to health maintenance. Probiotics have shown regulatory effects on the female reproductive tract, thereby contributing to homeostasis of the tract and influencing the health of offspring. Further, through transmission of bacteria or through other indirect mechanisms, the parent’s reproductive microbiota and probiotic intervention influence infant gut colonization and immunity development, with potential health consequences. In vitro and in vivo studies have explored the mechanisms underlying the benefits of probiotic administration and intervention, and an array of positive results, such as modulation of microbiota composition, regulation of metabolism, promotion of the epithelial barrier, and improvement of immune function, have been observed. Herein, we review the state of the art in reproductive system microbiota and its role in health and reproduction, as well as the beneficial effects of probiotics on reproductive health and their contributions to the prevention of associated diseases.

The negative impact of most relevant infections on fertility and assisted reproduction technology

Infections may act with variable impact on the physiopathology of the reproductive organs, determining infertility or reducing the outcomes of assisted reproduction technology. The aim of this narrative review is to describe the existing evidence regarding the pathogens with a supposed or recognized role in reproductive medicine. Viral hepatitis, as well as HIV, can reduce sperm quality. Syphilis carries a risk of erectile dysfunction and increased endometrial thickness. Chlamydia is the main cause of pelvic inflammatory disease. In relation to Mycoplasma and Ureaplasma spp., only few species seem to show a correlation with infertility and poor in-vitro fertilization outcomes. There is evidence of a role for bacterial vaginosis in early pregnancy loss. HPV infection in males seems to determine infertility. Herpesviruses are more a risk for fetuses than for fertility itself. Zika virus is responsible for altered early embryo development and waiting to conceive is recommended in suspected or confirmed cases. The impact of SARS-CoV-2 is yet to be elucidated. Rubella and toxoplasmosis can provoke important congenital defects and therefore screening is mandatory before conception; a vaccine for Rubella is recommended. Further and well-designed studies are still needed to better elucidate the role of some infectious agents, to improve fertility and its treatments.

Identifying Predictive Bacterial Markers from Cervical Swab Microbiota on Pregnancy Outcome in Woman Undergoing Assisted Reproductive Technologies

Background and aims: Failure of the embryo to implant causes about three-fourths of lost pregnancies. Female genital tract microbiota has been associated to Assisted Reproductive Technologies (ART) outcomes. The objective of this study was to analyze the microbiota of human cervical swab and to correlate these findings with the ART outcomes. Materials and Methods: In this study, 88 cervical swabs were collected from women undergoing ART cycles, with various causes of infertility, at the beginning of the ART protocols. After microbial DNA extraction, V3–V4 variable regions of the 16S rRNA gene were amplified and sequenced on the Illumina MiSeq platform. PEnalized LOgistic Regression Analysis (PELORA) was performed to identify clusters of bacterial populations with differential abundances between patients with unfavorable and favorable pregnancy outcome groups, respectively. Results: We identified a core of microorganisms at lower taxonomic levels that were predictive of women’s pregnancy outcomes. Statistically significant differences were identified at species levels with Lactobacillus salivarius, Lactobacillus rhamnosus among others. Moreover the abundance of Lactobacillus crispatus and iners, respectively increased and decreased in favorable group as compared to unfavorable group, resulted within the core of microorganisms associated to positive ART outcome. Although the predominance of lactobacilli is generally considered to be advantageous for ART outcome, we found that also the presence of Bifidobacterium (together with the other lactobacilli) was more abundant in the favorable group. Discussion: Cervix is colonized by microorganisms which can play a role in ART outcomes as seen by an overall decrease in embryo attachment rates and pregnancy rates in both fertile and infertile women. If confirmed in a larger cohort, the abundance of these bacteria can be useful not only as a marker of unfavorable pregnancy outcome but also they may open the way to new interventional strategies based on genital tract microbiota manipulation in order to increase the pregnancy rates in woman undergoing assisted reproductive technologies.

The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain

BACKGROUND

Endometriosis is a chronic, burdensome condition that is historically understudied. Consequently, there is a lack of understanding of the etiology of the disease and its associated symptoms, including infertility and chronic pelvic pain (CPP). Endometriosis development is influenced by estrogen metabolism and inflammation, which are modulated by several factors including the microbiome and the estrobolome (the collection of genes encoding estrogen-metabolizing enzymes in the gut microbiome). Therefore, there is increasing interest in understanding the role of microbiota in endometriosis etiology.

OBJECTIVE AND RATIONALE

To date, there is no cure for endometriosis and treatment options often are ineffective. This manuscript will review the potential relationship between the microbiome and endometriosis, infertility and CPP and highlight the available data on the microbiome in relation to endometriosis and its related symptoms. The overarching goal of this manuscript is to inform future microbiome research that will lead to a deeper understanding of the etiology of the disease and possible diagnostic modalities and treatments. The potential impact of the microbiome on estrogen regulation modulated by the estrobolome, as well as inflammation and other endometriosis-promoting mechanisms within the genital tract, will be reviewed. The methodological limitations of microbiome-related studies will be critically assessed to provide improved guidelines for future microbiome and clinical studies.

SEARCH METHODS

PubMed databases were searched using the following keywords: endometriosis AND microbiome, infertility AND microbiome, pelvic pain AND microbiome, IVF (in-vitro fertilization) AND microbiome, endometriosis AND infertility. Clinical and preclinical animal trials that were eligible for review, and related to microbiome and endometriosis, infertility or CPP were included. All available manuscripts were published in 2002-2021.

OUTCOMES

In total, 28 clinical and 6 animal studies were included in the review. In both human and animal studies, bacteria were enriched in endometriosis groups, although there was no clear consensus on specific microbiota compositions that were associated with endometriosis, and no studies included infertility or CPP with endometriosis. However, bacterial vaginosis-associated bacteria and Lactobacillus depletion in the cervicovaginal microbiome were associated with endometriosis and infertility in the majority (23/28) of studies. Interpretation of endometrial studies is limited owing to a variety of methodological factors, discussed in this review. In addition, metadata outlining antibiotic usage, age, race/ethnicity, menopausal status and timing of sample collection in relation to diagnosis of endometriosis was not consistently reported. Animal studies (6/6) support a bidirectional relationship between the gut microbiota and endometriosis onset and progression.

WIDER IMPLICATIONS

There is evidence that a dysbiotic gut or genital microbiota is associated with multiple gynecologic conditions, with mounting data supporting an association between the microbiome and endometriosis and infertility. These microbiomes likely play a role in the gut-brain axis, which further supports a putative association with the spectrum of symptoms associated with endometriosis, including infertility and CPP. Collectively, this review highlights the demand for more rigorous and transparent methodology and controls, consistency across the field, and inclusion of key demographic and clinical characteristics of disease and comparison participants. Rigorous study designs will allow for a better understanding of the potential role of the microbiome in endometriosis etiology and the relationship to other disorders of the female reproductive tract.

The vaginal microbiota composition of women undergoing assisted reproduction: a prospective cohort study

OBJECTIVE

To evaluate the impact of vaginal microbiota on pregnancy outcomes in women undergoing assisted reproduction.

DESIGN

A prospective cohort study.

SETTING

A university-based assisted reproductive technology (ART) centre.

POPULATION

223 women undergoing ART treatment.

METHODS

Prior to embryo transfer, vaginal samples were collected from the posterior fornix. Vaginal microbiota identification was carried out using next-generation sequencing and categorised according to the V3-V4 hypervariable region in the 16S rRNA gene region.

MAIN OUTCOME MEASURES

ART clinical outcomes (implantation, clinical pregnancy rates and live birth rates).

RESULTS

The live birth rate in women with community state type (CST)-I (39%) was higher than that in women with CST-III (21.5%) but the difference was not statistically significant (P = 0.052). The relative abundance of Lactobacillus was lower in women who failed to become pregnant (NP group) (67.71%) than in women who became pregnant (PR group) (79.72%). However, this difference was not statistically significant (P = 0.06). In the NP group, the relative abundance of Streptococcus (7.81%) and Gardnerella (9.40%) was higher than that in the PR group (relative abundance of Streptococcus and Gardnerella was 2.28% and 5.56%, respectively). The abundance of Streptococcus was found to be statistically significantly different between the two study groups (P = 0.014). Linear discriminant analysis (LDA) further validated that Streptococcus had the highest contribution (LDA score >4.0) to the difference between these two groups.

CONCLUSIONS

Streptococcus has the highest contribution to the distinction between the PR and NP groups.

TWEETABLE ABSTRACT

A relatively high abundance of Streptococcus in the vaginal microbiota may be associated with a lower ART success rate.

Mapping the entire functionally active endometrial microbiota

STUDY QUESTION

Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases?

SUMMARY ANSWER

Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle.

WHAT IS KNOWN ALREADY

Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue.

STUDY DESIGN, SIZE, DURATION

RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set.

MAIN RESULTS AND THE ROLE OF CHANCE

With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism.

LARGE SCALE DATA

The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542.

LIMITATIONS, REASONS FOR CAUTION

These pioneering results should be confirmed in a bigger sample size.

WIDER IMPLICATIONS OF THE FINDINGS

Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine.

STUDY FUNDING/COMPETING INTERESTS

This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.

Unraveling the Balance between Genes, Microbes, Lifestyle and the Environment to Improve Healthy Reproduction

Humans’ health is the result of a complex and balanced interplay between genetic factors, environmental stimuli, lifestyle habits, and the microbiota composition. The knowledge about their single contributions, as well as the complex network linking each to the others, is pivotal to understand the mechanisms underlying the onset of many diseases and can provide key information for their prevention, diagnosis and therapy. This applies also to reproduction. Reproduction, involving almost 10% of our genetic code, is one of the most critical human’s functions and is a key element to assess the well-being of a population. The last decades revealed a progressive decline of reproductive outcomes worldwide. As a consequence, there is a growing interest in unveiling the role of the different factors involved in human reproduction and great efforts have been carried out to improve its outcomes. As for many other diseases, it is now clear that the interplay between the underlying genetics, our commensal microbiome, the lifestyle habits and the environment we live in can either exacerbate the outcome or mitigate the adverse effects. Here, we aim to analyze how each of these factors contribute to reproduction highlighting their individual contribution and providing supporting evidence of how to modify their impact and overall contribution to a healthy reproductive status.

Application of Ligilactobacillus salivarius CECT5713 to Achieve Term Pregnancies in Women with Repetitive Abortion or Infertility of Unknown Origin by Microbiological and Immunological Modulation of the Vaginal Ecosystem

In this study, the cervicovaginal environment of women with reproductive failure (repetitive abortion, infertility of unknown origin) was assessed and compared to that of healthy fertile women. Subsequently, the ability of Ligilactobacillus salivarius CECT5713 to increase pregnancy rates in women with reproductive failure was evaluated. Vaginal pH and Nugent score were higher in women with reproductive failure than in fertile women. The opposite was observed regarding the immune factors TGF-β 1, TFG-β 2, and VEFG. Lactobacilli were detected at a higher frequency and concentration in fertile women than in women with repetitive abortion or infertility. The metataxonomic study revealed that vaginal samples from fertile women were characterized by the high abundance of Lactobacillus sequences, while DNA from this genus was practically absent in one third of samples from women with reproductive failure. Daily oral administration of L. salivarius CECT5713 (~9 log₁₀ CFU/day) to women with reproductive failure for a maximum of 6 months resulted in an overall successful pregnancy rate of 56%. The probiotic intervention modified key microbiological, biochemical, and immunological parameters in women who got pregnant. In conclusion, L. salivarius CECT5713 has proved to be a good candidate to improve reproductive success in women with reproductive failure.

One4Two®: An Integrated Molecular Approach to Optimize Infertile Couples' Journey

The current diagnostic path of infertile couples is long lasting and often ineffective. Genetic tests, in particular, appear as a limiting step due to their jeopardized use on one side, and to the limited number of genes evaluated on the other. In this context, the development and diffusion, also in routine diagnostic settings, of next generation sequencing (NGS)-based methods for the analyses of several genes in multiple subjects at a time is improving the diagnostic sensitivity of molecular analyses. Thus, we developed One4Two^®, a custom NGS panel to optimize the diagnostic journey of infertile couples. The panel validation was carried out in three steps analyzing a total of 83 subjects. Interestingly, all the previously identified variants were confirmed, assessing the analytic sensitivity of the method. Moreover, additional pathogenic variants have been identified underlying the diagnostic efficacy of the proposed method. One4Two^® allows the simultaneous analysis of infertility-related genes, disease-genes of common inherited diseases, and of polymorphisms related to therapy outcome. Thus, One4Two^® is able to improve the diagnostic journey of infertile couples by simplifying the whole process not only for patients, but also for laboratories and reproduction specialists moving toward an even more personalized medicine.

Microbiota and Human Reproduction: The Case of Male Infertility

The increasing interest in metagenomics is enhancing our knowledge regarding the composition and role of the microbiota in human physiology and pathology. Indeed, microbes have been reported to play a role in several diseases, including infertility. In particular, the male seminal microbiota has been suggested as an important factor able to influence couple's health and pregnancy outcomes, as well as offspring health. Nevertheless, few studies have been carried out to date to deeper investigate semen microbiome origins and functions, and its correlations with the partner's reproductive tract microbiome. Here, we report the state of the art regarding the male reproductive system microbiome and its alterations in infertility.