Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality

Asymptomatic bacteriospermia and infertility-what is the connection?

OBJECTIVE

To determine the impact of asymptomatic bacteriospermia on semen quality in subfertile men.

METHODS

We conducted a retrospective, single-centre cohort study in 1300 subfertile men. In those diagnosed with asymptomatic bacteriospermia we performed univariate and multivariate logistic regression models to evaluate the strain-specific association with semen parameters.

RESULTS

Asymptomatic bacteriospermia was diagnosed in 3.2% of patients. The microbiological semen analysis revealed a poly-microbial result in 60%. The most common bacterial species were coagulase-negative Staphylococci species (71.4%), Streptococcus viridans (50.0%) and Enterococcus faecalis (26.2%). Sexually transmitted pathogens were identified in 11.9% of semen samples. The detection of Streptococcus viridians or Haemophilus parainfluenzae correlated with impaired sperm morphology (p < 0.05). The presence of coagulase-negative Staphylococci species or Enterococcus faecalis was associated with pathological low counts of live spermatozoa (p < 0.05). In multivariate analysis only Enterococcus faecalis showed a significant impact on sperm concentration (OR 4.48; 95% CI 1.06-22.10; p = 0.041).

CONCLUSIONS

Asymptomatic bacteriospermia has always been a subject of great controversy. There is still an ongoing debate whether to treat or not to treat. Here, we demonstrate that asymptomatic bacteriospermia is clearly associated with impaired semen quality. Our findings speak in favour of strain-specific interactions with semen parameters. Especially Enterococcus faecalis seriously affects sperm concentration.

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.

Endocrine-Disrupting Chemicals, Gut Microbiota, and Human (In)Fertility-It Is Time to Consider the Triad

The gut microbiota (GM) is a complex and dynamic population of microorganisms living in the human gastrointestinal tract that play an important role in human health and diseases. Recent evidence suggests a strong direct or indirect correlation between GM and both male and female fertility: on the one hand, GM is involved in the regulation of sex hormone levels and in the preservation of the blood-testis barrier integrity; on the other hand, a dysbiotic GM is linked to the onset of pro-inflammatory conditions such as endometriosis or PCOS, which are often associated with infertility. Exposure to endocrine-disrupting chemicals (EDCs) is one of the main causes of GM dysbiosis, with important consequences to the host health and potential transgenerational effects. This perspective article aims to show that the negative effects of EDCs on reproduction are in part due to a dysbiotic GM. We will highlight (i) the link between GM and male and female fertility; (ii) the mechanisms of interaction between EDCs and GM; and (iii) the importance of the maternal-fetal GM axis for offspring growth and development.

Semen dysbiosis—just a male problem?

Seminal microflora is crucial to male fertility. Dysbiosis—disturbance of quantitative ratios of individual bacteria or appearance of pathogenic species—rarely results in symptomatic disease. Inflammation results in decreased sperm production, lower motility, or morphological changes and, in the long term, can cause ejaculatory duct obstruction, leading to infertility. Moreover, it may cause infection of the partner’s female genital tract. Dysbiosis in both partners results in fertility problems, disorders in embryo implantation, or miscarriages. In addition, chronic inflammation of the male genitourinary system may accelerate the appearance of antisperm antibodies. A comprehensive examination of seminal microflora can clarify the causes of infertility or prevent pathological conditions that affect seminal parameters. Seminal microflora as a direct impact on fertility problems as well as a decrease in the effectiveness of assisted reproduction methods, insemination, or in vitro procedures.

Microbiome analysis: An emerging forensic investigative tool

Microbial diversity's potential has been investigated in medical and therapeutic studies throughout the last few decades. However, its usage in forensics is increasing due to its effectiveness in circumstances when traditional approaches fail to provide a decisive opinion or are insufficient in forming a concrete opinion. The application of human microbiome may serve in detecting the type of stains of saliva and vaginal fluid, as well as in attributing the stains to the individual. Similarly, the microbiome makeup of a soil sample may be utilised to establish geographic origin or to associate humans, animals, or things with a specific area, additionally microorganisms influence the decay process which may be used in depicting the Time Since death. Further in detecting the traces of the amount and concentration of alcohol, narcotics, and other forensically relevant compounds in human body or visceral tissues as they also affect the microbial community within human body. Beside these, there is much more scope of microbiomes to be explored in terms of forensic investigation, this review focuses on multidimensional approaches to human microbiomes from a forensic standpoint, implying the potential of microbiomes as an emerging tool for forensic investigations such as individual variability via skin microbiomes, reconstructing crime scene, and linking evidence to individual.

The effects of microbiota on reproductive health: A review

Reproductive issues are becoming an increasing global problem. There is increasing interest in the relationship between microbiota and reproductive health. Stable microbiota communities exist in the gut, reproductive tract, uterus, testes, and semen. Various effects (e.g., epigenetic modifications, nervous system, metabolism) of dysbiosis in the microbiota can impair gamete quality; interfere with zygote formation, embryo implantation, and embryo development; and increase disease susceptibility, thus adversely impacting reproductive capacity and pregnancy. The maintenance of a healthy microbiota can protect the host from pathogens, increase reproductive potential, and reduce the rates of adverse pregnancy outcomes. In conclusion, this review discusses microbiota in the male and female reproductive systems of multiple animal species. It explores the effects and mechanisms of microbiota on reproduction, factors that influence microbiota composition, and applications of microbiota in reproductive disorder treatment and detection. The findings support novel approaches for managing reproductive diseases through microbiota improvement and monitoring. In addition, it will stimulate further systematic explorations of microbiota-mediated effects on reproduction.

Testicular Immunity and Its Connection with the Microbiota. Physiological and Clinical Implications in the Light of Personalized Medicine

Reproduction is a complex process, which is based on the cooperation between the endocrine-immune system and the microbiota. Testicular immunity is characterized by the so-called immune privilege, a mechanism that avoids autoimmune attacks against proteins expressed by spermatozoa. Testicular microbiota is connected with the gut microbiota, the most prevalent site of commensals inthe body. Both microbiotas take part inthe development of the immune system and protection againstpathogen invasion. Dysbiosis is caused by concurrent pathologies, such as obesity, diabetes, infections and trauma. The substitution of beneficial bacteria with pathogens may lead to destruction of spermatozoa directly or indirectly and, ultimately, to male infertility. Novel therapeutic interventions, i.e., nutritional interventions and supplementation of natural products, such as, probiotics, prebiotics, antioxidants and polyphenols, may lead to the restoration of the otherwise-impaired male reproductive potential, even if experimental and clinical results are not always concordant. In this review, the structure and immune function of the testis will be described with special reference to the blood-testisbarrier. The regulatory role of both the gut and testicular microbiota will be illustrated in health and disease, also emphasizing therapeutic attempts with natural products for the correction of male infertility, in the era of personalized medicine.

Bacteriospermia - A formidable player in male subfertility

Bacterial colonization of male reproductive tissues, cells, and fluids, and the subsequent impact of bacteria on the sperm architecture, activity, and fertilizing potential, has recently gained increased attention from the medical and scientific community. Current evidence strongly emphasizes the fact that the presence of bacteria in semen may have dire consequences on the resulting male fertility. Nevertheless, the molecular basis underlying bacteriospermia-associated suboptimal semen quality is sophisticated, multifactorial, and still needs further understanding. Bacterial adhesion and subsequent sperm agglutination and immobilization represent the most direct pathway of sperm-bacterial interactions. Furthermore, the release of bacterial toxins and leukocytic infiltration, associated with a massive outburst of reactive oxygen species, have been repeatedly associated with sperm dysfunction in bacteria-infested semen. This review serves as a summary of the present knowledge on bacteriospermia-associated male subfertility. Furthermore, we strived to outline the currently available methods for assessing bacterial profiles in semen and to outline the most promising strategies for the prevention and/or management of bacteriospermia in practice.

Possible Implications of Bacteriospermia on the Sperm Quality, Oxidative Characteristics, and Seminal Cytokine Network in Normozoospermic Men

This study focused on the identification of bacterial profiles of semen in normozoospermic men and their possible involvement in changes to the sperm structural integrity and functional activity. Furthermore, we studied possible fluctuations of selected cytokines, oxidative markers, and antibacterial proteins as a result of bacterial presence in the ejaculate. Sperm motility was assessed with computer-assisted sperm analysis, while sperm apoptosis, necrosis and acrosome integrity were examined with fluorescent methods. Reactive oxygen species (ROS) generation was quantified via luminometry, sperm DNA fragmentation was evaluated using the TUNEL protocol and chromatin-dispersion test, while the JC-1 assay was applied to evaluate the mitochondrial membrane potential. Cytokine levels were quantified with the biochip assay, whilst selected antibacterial proteins were quantified using the ELISA method. The predominant species identified by the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were Staphylococcus hominis, Staphylococcus capitis and Micrococcus luteus. The results revealed that the sperm quality decreased proportionally to the increasing bacterial load and occurrence of conditionally pathogenic bacteria, including Enterococcus faecalis, Staphylococcus aureus and Escherichia coli. Antimicrobial susceptibility tests revealed a substantial resistance of randomly selected bacterial strains to ampicillin, vancomycin, tobramycin, and tetracycline. Furthermore, an increased bacterial quantity in semen was accompanied by elevated levels of pro-inflammatory cytokines, including interleukin-1, interleukin-2, interleukin-6, tumor necrosis factor alpha as well as ROS overproduction and lipid peroxidation of the sperm membranes. Our results suggest that semen quality may be notably affected by the bacterial quantity as well as quality. It seems that bacteriospermia may be associated with inflammatory processes, oxidative stress, sperm structural deterioration, and a subsequent risk for the development of subfertility, even in normozoospermic males.

Seminal Microbiota of Idiopathic Infertile Patients and Its Relationship With Sperm DNA Integrity

The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was shown to be related to sperm quality parameters, suggesting an effect in human fertility and postulating it as a biomarker candidate. However, its relationship to sperm DNA integrity has not been studied yet. The aim of the present study is to characterize the seminal microbiota of a western Mediterranean population and to evaluate its relationship to sperm chromatin integrity parameters, and oxidative stress. For that purpose, 14 samples from sperm donors and 42 samples from infertile idiopathic patients were obtained and were analyzed to assess the composition of the microbiota through full-length 16S rRNA gene sequencing (Illumina MiSeq platform). Microbial diversity and relative abundances were compared to classic sperm quality parameters (macroscopic semen parameters, motility, morphology and concentration), chromatin integrity (global DNA damage, double-stranded DNA breaks and DNA protamination status) and oxidative stress levels (oxidation-reduction potential). The seminal microbiota observed of these samples belonged to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The most abundant genera were Finegoldia, Peptoniphilus, Anaerococcus, Campylobacter, Streptococcus, Staphylococcus, Moraxella, Prevotella, Ezakiella, Corynebacterium and Lactobacillus. To our knowledge, this is the first detection of Ezakiella genus in seminal samples. Two clusters of microbial profiles were built based on a clustering analysis, and specific genera were found with different frequencies in relation to seminal quality defects. The abundances of several bacteria negatively correlate with the sperm global DNA fragmentation, most notably Moraxella, Brevundimonas and Flavobacterium. The latter two were also associated with higher sperm motility and Brevundimonas additionally with lower oxidative-reduction potential. Actinomycetaceae, Ralstonia and Paenibacillus correlated with reduced chromatin protamination status and increased double-stranded DNA fragmentation. These effects on DNA integrity coincide in many cases with the metabolism or enzymatic activities of these genera. Significant differences between fertile and infertile men were found in the relative presence of the Propionibacteriaceae family and the Cutibacterium, Rhodopseudomonas and Oligotropha genera, which supports its possible involvement in male fertility. Our findings sustain the hypothesis that the seminal microbiome has an effect on male fertility.

Immune infertility in men

Male factors are implicated as the cause of roughly half of cases of infertility, and the presence of antisperm antibodies (ASA) may be responsible for some of these. Their presence is associated with a reduction in natural conception and live birth and impacts the success of assisted reproductive technologies. Interpretation of the data regarding ASAs and fertility is complicated by a lack of standardization in testing methodology and test thresholds and a lack of data on their prevalence in the healthy fertile population. Although their pathogenesis remains elusive, and many cases are idiopathic, a disruption in the immunologic blood-testis barrier (BTB) appears to contribute to the formation of ASA. As delineation of the specific antigen targets of ASA advances, it has been recognized that they may affect almost all aspects of sperm function, and ASA against different targets likely have specific mechanisms of impairing fertility. Intracytoplasmic sperm injection (ICSI) appears to be the most reliable method by which to overcome fertility impairment due to ASA, achieving similar outcomes to ASA-negative patients with regard to fertilization rates, embryonic development, clinical pregnancy rates, and live birth rates. The lack of consistency in testing for and reporting ASA remains a substantial barrier to achieving clarity in describing their role in infertility and the optimal management approach, and future research should use a unified approach to the detection and description of ASA. Determination of the specific antigens targeted by ASA, and their function and clinical relevance, would contribute to improving the understanding of ASA-mediated impacts on fertility and tailoring treatment appropriately to achieve the best outcomes for patients.

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.

Microbiota in Goat Buck Ejaculates Differs Between Breeding and Non-breeding Seasons

Changes in semen microbiota are associated with alterations to sperm quality and fertility. However, the microbiota from most livestock species has not yet been studied. Goats are seasonal breeders, but semen microbiota has never been described in this species, and it is unknown how seasonality affects it. Our study objective is 2-fold: to describe the microbiota in goat buck ejaculates and to determine if it differs between breeding and non-breeding seasons. Semen from six males of the Murciano-Granadina breed was collected during both seasons. Two replicates were performed per male and season on different days. The microbiota was characterized by genomic sequencing technology. Sperm quality was also evaluated. Repetition was not significant for the studied variables. Sperm velocities were higher for the breeding than for the non-breeding season. The ejaculates from both seasons also differed in the proportion of apoptotic spermatozoa. The five dominant phyla were Firmicutes, Proteobacteria, Fusobacteria, Actinobacteria, and Bacteroidetes during the breeding season and Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria during the non-breeding season. The dominant genus during both seasons was Ureaplasma. Differences in microbial community structure (the beta diversity) were found. A decrease in the relative abundance of the genus Faecalibacterium and an increase in the genera Sphingomonas and Halomonas were observed in the ejaculates collected during the breeding season. Sphingomonas and Faecalibacterium abundance favorably and unfavorably correlated with sperm quality, respectively. In conclusion, the semen microbiota from goat bucks varies between breeding and non-breeding seasons, and the microbiota remains stable for 7 days within a season. In addition, the genera Sphingomonas and Faecalibacterium could be possible biomarkers of semen quality in goat bucks. These results contribute to an in-depth understanding of the effects of reproductive seasonality on goat buck ejaculates.

Ligilactobacillus salivarius PS11610 exerts an effect on the microbial and immunological profile of couples suffering unknown infertility

PROBLEM

Unknown or idiopathic infertility has been associated with urogenital tract dysbiosis, reducing pregnancy and delivery ratios during assisted reproductive treatments (ART). The Ligilactobacillus salivarius PS11610 strain has shown extraordinary antimicrobial activity in vitro against urogenital pathogens as well as other probiotic characteristics. Therefore, an intervention study was performed to evaluate the effect of L. salivarius PS11610 on the microbial composition of urogenital tract in infertile couples with bacterial dysbiosis.

METHOD OF STUDY

Seventeen couples undergoing ART diagnosed with unknown infertility were selected. After confirming urogenital dysbiosis, they started a 6-month treatment with L. salivarius PS11610 (1 dose/12 h for female and 1 dose/24 h for male). Vaginal, seminal, glans, uterine and plasma samples were collected for determination of the microbiome and immune profile at the beginning and the end of the treatment.

RESULTS

Supplementation with L. salivarius PS11610 significantly modified the urogenital microbiome composition in male and female samples, solving dysbiosis of 67% of the couples. Pathogens disappeared from the vaginal samples whereas Lactobacilli percentage increased after 3 and 6 months of treatment. Moreover, L. salivarius PS11610 changed the uterine microbiome that could be associated with a change of the uterine immune profile. Additionally, the probiotic intake could be associated with the observed change in the systemic immunological profile of couples. Finally, the pregnant and delivery ratio were improved.

CONCLUSIONS

Probiotic supplementation with L. salivarius PS11610 improved the male and female urogenital tract microbiome, modulating the immune system and increasing pregnancy success in couples undergoing ART.

Paternal periconception metabolic health and offspring programming

The association between maternal metabolic status at the time of conception and subsequent embryogenesis and offspring development has been studied in detail. However, less attention has been given to the significance of paternal nutrition and metabolism in directing offspring health. Despite this disparity, emerging evidence has begun to highlight an important connection between paternal metabolic well-being, semen quality, embryonic development and ultimately adult offspring health. This has established a new component within the Developmental Origins of Health and Disease hypothesis. Building on the decades of understanding and insight derived from the numerous models of maternal programming, attention is now becoming focused on defining the mechanisms underlying the links between paternal well-being, post-fertilisation development and offspring health. Understanding how the health and fitness of the father impact on semen quality is of fundamental importance for providing better information to intending fathers. Furthermore, assisted reproductive practices such as in vitro fertilisation rely on our ability to select the best quality sperm from a diverse and heterogeneous population. With considerable advances in sequencing capabilities, our understanding of the molecular and epigenetic composition of the sperm and seminal plasma, and their association with male metabolic health, has developed dramatically over recent years. This review will summarise our current understanding of how a father's metabolic status at the time of conception can affect sperm quality, post-fertilisation embryonic and fetal development and offspring health.

Perspective on the relationship between reproductive tract microbiota eubiosis and dysbiosis and reproductive function

The role played by microbiota is attracting growing attention within the scientific and medical community, in both human and animal fields, in the last years. Most of the studies have been focused on the intestinal microbiome, whilst little attention has been paid to other systems, like the reproductive tract of both females and males. However, there is a growing body of information showing the interplay between reproductive tract dysbiosis, due to the action of pathogens and/or unhealthy lifestyle, and reproductive disease and disorders in many mammalian species. The present review aims to summarise current knowledge on the biodiversity of the microbiota of the reproductive tract, and the possible relationships between eubiosis or dysbiosis and reproductive health and function in both females and males.

The Microbiome, an Important Factor That Is Easily Overlooked in Male Infertility

Humankind has been interested in reproduction for millennia. Infertility, in which male factors contribute to approximately 50%, is estimated to concern over 72 million people worldwide. Despite advances in the diagnosis, medical treatment, and psychosocial management of male infertility over the past few decades, approximately 30% of male infertility is still thought to be idiopathic. Despite emerging advances in the microbiome associated with male infertility have indicated that the microbiome may be a key factor to the management of male infertility, roles, and mechanisms of the microbiome remain ambiguous. Here, we mainly discussed the association between microbial infection in the genital tract and male infertility, effect of antimicrobial therapy on male reproduction, association between microbial dysbiosis and male infertility, and effect of probiotic intervention on male reproduction. This review made progress toward establishing a relationship between the microbiome and male infertility, and explored the role of the microbiome in male infertility. We call for more high-quality studies to focus on the relationship between microbes and male infertility, and strongly suggest increasing awareness among sterile males with microbial infection and/or microbial dysbiosis when they seek fertility help.

Spermatic Microbiome Characteristics in Infertile Patients: Impact on Sperm Count, Mobility, and Morphology

Through sperm alteration, semen microbiota tend to be recognized as a cause of infertility, but due to the limited number of studies focusing on this ecological niche, this hypothesis remains controversial. This study aimed to characterize and compare the bacterial communities of sperm samples from patients undergoing couple infertility treatment at the time of diagnosis. The study was prospective (September 2019 to March 2020), monocentric, and focused on alterations of spermatic parameters: count, motility, and morphology. After the amplification of the 16S rDNA (V1 to V3), libraries (n = 91, including 53 patients with abnormalities) were sequenced using the MiSeq platform (Illumina). After quality control processing using a homemade pipeline (QIIME2 modules), the main genera were: Prevotella, Finegoldia, Pseudomonas, Peptinophilus, Streptococcus, Anaerococcus and Corynebacterium. Restricted diversity was observed in samples from patients with abnormal sperm morphology (α-diversity, p < 0.05), whereas diversity increased in patients with an abnormal sperm count (β-diversity, p < 0.05). The enrichment of the genus Prevotella and Haemophilus was observed in negative sperm culture samples and samples with abnormal counts, respectively (p < 0.05). Microbiota differed in their composition according to sperm parameters. Finally, this work highlights the need for the optimization of the management of couples undergoing infertility treatment, possibly by modulating the genital microbiome.

Microbiome Transmission During Sexual Intercourse Appears Stochastic and Supports the Red Queen Hypothesis

Microbes inhabit virtually everywhere on and/or in our bodies, including the seminal and vaginal fluids. They have significant importance in maintaining reproductive health and protecting hosts from diseases. The exchange of microbes during sexual intercourse is one of the most direct and significant microbial transmissions between men and women. Nevertheless, the mechanism of this microbial transmission was little known. Is the transmission mode stochastic, passive diffusion similar to the random walk of particles, or driven by some deterministic forces? What is the microbial transmission probability? What are the possible evolutionary implications, particularly from the perspective of sexual reproduction (selection)? We tackle these intriguing questions by leveraging the power of Hubbell's unified neutral theory of biodiversity, specifically implemented as the HDP-MSN (hierarchical Dirichlet process approximated multi-site neutral model), which allows for constructing truly multi-site metacommunity models, simultaneously including vaginal and semen microbiomes. By reanalyzing the microbiome datasets of seminal and vaginal fluids from 23 couples both before and after sexual intercourses originally reported by Mändar and colleagues, we found that the microbial transmission between seminal and vaginal fluids is a stochastic, passive diffusion similar to the random walk of particles in physics, rather than driven by deterministic forces. The transmission probability through sexual intercourse seems to be approximately 0.05. Inspired by the results from the HDP-MSN model, we further conjecture that the stochastic drifts of microbiome transmissions during sexual intercourses can be responsible for the homogeneity between semen and vaginal microbiomes first identified in a previous study, which should be helpful for sexual reproduction by facilitating the sperm movement/survival and/or egg fertilization. This inference seems to be consistent with the classic Red Queen hypothesis, which, when extended to the co-evolutionary interactions between humans and their symbiotic microbiomes, would predict that the reproductive system microbiomes should support sexual reproduction.

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.

Cultivable vaginal Lactobacillus is not associated with fecundability in Kenyan women attempting to conceive

OBJECTIVE

To examine the association between cultivable vaginal Lactobacillus and fecundability in Kenyan women attempting nonmedically assisted conception.

DESIGN

Prospective preconception cohort.

SETTING

Nairobi and Mombasa, Kenya.

PATIENT(S)

Women trying to conceive who reported ≤3 months of pre-enrollment conception attempt time.

INTERVENTION(S)

Cultivable Lactobacillus (primary), Lactobacillus morphotypes on Gram stain (secondary).

MAIN OUTCOME MEASURE(S)

Participants reported the first day of their last menstrual period and recent sexual behavior, underwent pregnancy testing, and provided vaginal specimen samples for Lactobacillus culture and Gram stain at ≤6 monthly preconception visits. The outcome was fecundability-the per-menstrual cycle probability of pregnancy. Associations between cultivable Lactobacillus and Lactobacillus morphotypes on Gram stain at the visit before each pregnancy test and fecundability were estimated using proportional probabilities models to generate fecundability ratios (FRs).

RESULT(S)

A total of 458 women contributed 1,376 menstrual cycles. At enrollment, 65.3% (n = 299) of participants had cultivable Lactobacillus, 47.4% (n = 217) had cultivable hydrogen peroxide producing Lactobacillus, and 64.6% (n = 296) had Lactobacillus detected on Gram stain. In unadjusted analysis, there was no association between cultivable Lactobacillus at the prior visit and fecundability (FR, 0.92; 95% CI, 0.73-1.16); results were similar after adjustment for age, frequency of condomless sex, and study site (adjusted FR, 0.92; 95% CI, 0.72-1.18). Lactobacillus on Gram stain at the visit prior was associated with modestly higher fecundability (adjusted FR, 1.18; 95% CI, 0.92-1.51).

CONCLUSION(S)

Cultivable Lactobacillus was not associated with fecundability, although Lactobacillus morphotypes detected on Gram stain were somewhat associated with increased fecundability. The relationship between vaginal Lactobacillus and fecundity may be species-specific.

The Semen Microbiome and Semen Parameters in Healthy Stallions

Simple Summary

Stallion infertility is a major cause of concern in the horse industry. Despite zootechnics advances, sub- or infertile animals appear in stud farms without a toxic, genetic, or nutritional reason. Recent research in human andrology has opened the door for a new, plausible factor that affects sperm quality: seminal microflora. In recent years, there has been an increasing amount of evidence regarding the relationship between different seminal flora compositions and male fertility. However, little has been studied in veterinary science, including horses. Therefore, the objective of this study was to examine associations with the presence of bacteria families in horse semen with five sperm quality parameters: concentration, total number of spermatozoa, total and progressive sperm motility, and DNA fragmentation. Our study detected a correlation between the presence of the Peptoniphilaceae family and higher total motility and the presence of Clostridiales Incertae Sedis XI and lower progressive motility. These changes in seminal flora may contribute to the idiopathically poorer sperm quality in certain animals. Although further mechanisms behind bacteria–spermatozoa interactions are unknown, these associations are already leading to a new therapeutic approach to infertility: the use of prebiotics, which has already yielded promising results in human andrology.

Abstract

Despite the advances in reproductive technology, there is still a considerable number of low sperm quality cases in stallions. Recent studies in humans have detected several seminal microflora–spermatozoa associations behind some idiopathic infertility cases. However, no studies are available on horses, and there is limited information on the microflora present in stallion ejaculates. Accordingly, the objective of this study was to examine associations to the presence of bacteria families with five sperm quality parameters: concentration, total number of spermatozoa, total and progressive motility, and DNA fragmentation. Samples were cryopreserved after their extraction. High-speed homogenization using grinding media was performed for cell disruption. Family identification was performed via 16S rRNA sequencing. Bacterial families were only considered if the relative abundance was higher than 1%. Only two families appeared to have a correlation with two sperm quality parameters. Peptoniphilaceae correlated positively with total sperm motility, whereas Clostridiales Incertae Sedis XI correlated negatively with progressive motility. No significant differences were found for the rest of the parameters. In conclusion, the seminal microbiome may affect spermatozoa activity. Our findings are based on statistical associations; thus, further studies are needed to understand the internal interactions between seminal flora and cells.

Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird

The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.

Characterization of the Gastrointestinal and Reproductive Tract Microbiota in Fertile and Infertile Pakistani Couples

Simple Summary

We describe microbial taxa associated with the gastrointestinal and reproductive tracts of married Pakistani couples. We highlight differences in microbial composition and diversity that are associated with fertile and infertile couples and provide a baseline for future in-depth studies to target the association of the human microbiome with infertility.

Abstract

The human microbiota is recognized as a vital “virtual” organ of the human body that influences human health, metabolism, and physiology. While the microbiomes of the gut, oral cavity, and skin have been extensively studied in the literature, relatively little work has been done on characterizing the microbiota of the human reproductive tract organs, and specifically on investigating its association to fertility. Here, we implemented a 16S ribosomal RNA (rRNA) amplicon sequencing approach to sequence and characterize the gut and genital tract microbiomes from several married Pakistani couples. The recruited individuals included 31 fertile and 35 infertile individuals, with ages ranging from 19–45 years. We identified several fluctuations in the diversity and composition of the gut and genital microbiota among fertile and infertile samples. For example, measures of α-diversity varied significantly between the genital samples donated by fertile and infertile men and there was overall greater between-sample variability in genital samples regardless of gender. In terms of taxonomic composition, Actinobacteria, Bacteroidetes, and Firmicutes fluctuated significantly between the gut microbiomes of fertile and infertile samples. Finally, biomarker analyses identified features (genera and molecular functions and pathways) that differed significantly between the fertile and infertile samples and in the past have been associated with bacterial vaginosis. However, we emphasize that 16S amplicon data alone has no bearing on individual health and is merely representative of microbial taxonomic differences that could also arise due to multiple other factors. Our findings, however, represent the first effort to characterize the microbiome associated with fertile and infertile couples in Pakistan and will hopefully pave the way for more comprehensive and broad-scale investigations in the future.

Interactions between reproductive biology and microbiomes in wild animal species

Many parts of the animal body harbor microbial communities, known as animal-associated microbiomes, that affect the regulation of physiological functions. Studies in human and animal models have demonstrated that the reproductive biology and such microbiomes also interact. However, this concept is poorly studied in wild animal species and little is known about the implications to fertility, parental/offspring health, and survival in natural habitats. The objective of this review is to (1) specify the interactions between animals' reproductive biology, including reproductive signaling, pregnancy, and offspring development, and their microbiomes, with an emphasis on wild species and (2) identify important research gaps as well as areas for further studies. While microbiomes present in the reproductive tract play the most direct role, other bodily microbiomes may also contribute to facilitating reproduction. In fish, amphibians, reptiles, birds, and mammals, endogenous processes related to the host physiology and behavior (visual and olfactory reproductive signals, copulation) can both influence and be influenced by the structure and function of microbial communities. In addition, exposures to maternal microbiomes in mammals (through vagina, skin, and milk) shape the offspring microbiomes, which, in turn, affects health later in life. Importantly, for all wild animal species, host-associated microbiomes are also influenced by environmental variations. There is still limited literature on wild animals compared to the large body of research on model species and humans. However, the few studies in wild species clearly highlight the necessity of increased research in rare and endangered animals to optimize conservation efforts in situ and ex situ. Thus, the link between microbiomes and reproduction is an emerging and critical component in wild animal conservation.

Association between the presence of Mycoplasma spp. and male infertility

While male infertility has been associated with Mycoplasma infections, few studies have investigated the association between Mycoplasma infection and male infertility. Therefore, this study aimed at addressing this issue. Semen samples were collected from 136 patients (68 infertile men and 68 fertile men) in the Central Laboratory of Yazd, Iran. Of semen samples collected from 68 infertile and 68 fertile men, 13 (19.12%) and 2 (2.94%) cases were positive for Mycoplasma spp. using PCR, respectively. Among Mycoplasma-infected infertile men, 10 and 6 men showed abnormal sperm morphology and motility, respectively. None of the positive samples for Mycoplasma spp. was positive for M. hominis and one of the positive samples for Mycoplasma spp. belonged to Mycoplasma hyorhinis (strain NBRC 14858). The presence of Mycoplasma spp. was significantly higher in infertile men (p = .003). Mycoplasma infection was relatively high in infertile men. The surprising issue was the absence of M. hominis and the presence of M. hyorhinis strain NBRC 14858 in the semen of infertile men. Therefore, investigating reproductive tract infections caused by other Mycoplasma spp. should be taken into consideration in male infertility.Impact statementWhat is already known on this subject? Mycoplasma hyorhinis has been mostly reported as a cause of animal respiratory tract infections and the development of various cancers. Information on the association of M. hyorhinis with male infertility is not yet available.What do the results of this study add? This study shows that the presence of M. hyorhinis in the semen of infertile men may be associated with infertility. This study shows that the investigation of unpredictable species of genus Mycoplasma such as M. hyorhinis in the semen of infertile men is essential.What are the implications of these findings for clinical practice and/or further research? The results of the present study indicate that in addition to M. genitalium and M. hominis, studies on the role of M. hyorhinis in reproductive tract infections and infertility should be expanded.

Seminal and testicular microbiome and male fertility: A systematic review

Supplemental Digital Content is available in the text

Microbiome is of upmost importance for the well-being of the human body. Based on culture and PCR methods, seminal flora has been pointed as a potential cause for some of the unexplained male infertility.

This is a systematic review about the effect of seminal microbiota studied by Next Generation Sequencing techniques on sperm quality and male fertility, performed according to PRISMA statement.

Nine articles were included. Results of different studies are diverse. It seems that microbiota may a play a role in seminal quality and further male fertility, but the way this effect is modulated is still to be unknown. Lactobacillus spp seemed to play a beneficial role in semen quality, but the role of the remaining bacteria is unclear.

Due to the lack of research and the incongruence of the results so far, the effect of microbiota on seminal quality is still unclear.

Semen microbiota in normal and leukocytospermic males

Large numbers of microbes can be present in seminal fluid, and there are differences in the semen microbiota between normal and abnormal semen samples. To evaluate the semen microbiota in patients with leukocytospermia, 87 seminal fluid samples, including 33 samples with a normal seminal leukocyte count and 54 samples with leukocytospermia, were obtained for a cross-sectional analysis. Twenty samples with a normal seminal leukocyte count had normal sperm parameters (Control group), and 13 samples with a normal seminal leukocyte count were from asthenozoospermia patients (Ast group). However, 32 samples with leukocytospermia were from asthenozoospermia patients (LA group), and only 22 samples with leukocytospermia had normal sperm parameters (Leu group). The 16S ribosomal RNA (rRNA) gene sequencing method was used to sequence the microbiota in the seminal fluid, and multiple bioinformatics methods were utilized to analyze the data. Finally, the results showed that the worse sperm parameters were observed in the leukocytospermia-related groups. Semen microbiota analysis found that there was increased alpha diversity in the leukocytospermia-related groups. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the primary phyla in the seminal fluid. Two microbiota profiles, namely, Lactobacillus-enriched and Streptococcus-enriched groups, were identified in this study. The majority of the samples in the groups with a normal seminal leukocyte count could be categorized as Lactobacillus-enriched, whereas the majority of the leukocytospermia samples could be categorized as Streptococcus-enriched. Our study indicated that males with leukocytospermia have worse sperm parameters and a different semen microbiota composition compared to males with a normal seminal leukocyte count.

Core Microbiome of Slovak Holstein Friesian Breeding Bulls' Semen

Simple Summary

The aim of this study was to characterize the bacterial profile of semen collected from Holstein Friesian breeding bulls via a high-throughput sequencing approach for a 16S rRNA gene variability analysis. A total of 55 fresh semen samples of sexually mature breeding bulls were used in the study. They were gathered from Holstein Friesian breeding bulls at Slovak Biological Services in Nitra, Slovak Republic. To amplify the V4 region of the 16S rRNA bacterial gene, universal primers 515F and 806R enhanced by a 6 bp barcode identification sequence were used. The 16S rRNA high-throughput sequencing strategy was used. Two microbial clusters were identified among the analyzed samples—the first cluster was based on Actinobacteria and Firmicutes, while the second cluster contained a high prevalence of Fusobacteria.

Abstract

Bacterial contamination of semen is an important factor connected to the health status of bulls that may significantly affect semen quality for artificial insemination. Moreover, some important bovine diseases may be transmitted through semen. Up to now, only a very limited number of complex studies describing the semen microbiome of bulls have been published, as many bacteria are hard to cultivate using traditional techniques. The 16S rRNA high-throughput sequencing strategy allows for the reliable identification of bacterial profiles of bovine semen together with the detection of noncultivable bacterial species. Fresh samples from Holstein Friesian breeding bulls (n = 55) were examined for the natural variability in the present bacteria. Semen doses were selected randomly from Slovak Biological Services in Nitra, Slovak Republic. The most predominant phyla within the whole dataset were Firmicutes (31%), Proteobacteria (22%), Fusobacteria (18%), Actinobacteria (13%) and Bacteroidetes (12%). Samples of semen were divided into two separate clusters according to their microbiome compositions using a cording partition around a medoids analysis. Microbiomes of the first cluster (CL1) of samples (n = 20) were based on Actinobacteria (CL1 average = 25%; CL = 28%) and Firmicutes (CL1 = 38%; CL2 = 27%), while the second cluster (CL2; n = 35) contained samples characterized by a high prevalence of Fusobacteria (CL1 = 4%; CL2 = 26%). Some important indicator microbial groups were differentially distributed between the clusters.

Semen microbiota and cytokines of healthy and infertile men

In this study, we determined the levels of cytokine secretory inhibitors and the microbiota biofilms of semen from healthy and infertile subjects. A total of 118 clinical bacterial isolates were isolated and tested. Cytokine secretory inhibitors were determined based on the difference in cytokine content between the control and experimental samples of cell-free supernatants of isolated microorganisms. Biofilm formation was studied by determining the adhesion of microorganisms to the surface of a 96-well sterile plate and expressed as the optical density at 630 nm (OD₆₃₀). Cell-free supernatants of Staphylococcus contained higher levels of secretory inhibitor of cytokines in conditionally healthy than in infertile patients. In contrast, in infertile men, the ability to reduce cytokine levels was more characteristic of Enterococcus and Corynebacterium. Seminal Staphylococcus, Corynebacterium, and Enterococcus isolated from infertile subjects showed a greater ability to form biofilms than the same bacteria isolated from healthy men. Further research is needed on this topic, since it is necessary to determine the relationships between decreased secretory inhibitors of cytokines, production of biofilms by bacteria in semen, and infertility. It is likely that the ability of microorganisms to change the concentration of cytokines and increase the level of biofilm formation in semen may be associated with minimal impairments of fertilizing ability, which are not detected using other methods.

Microbiota of semen samples with normozoospermia: analysis of real-time PCR data

The analysis of semen microbiota is difficult due to the lack of established criteria for interpretation of microbiological tests. The aim of the study was to determine the stable clusters of semen microbiota analyzed by real-time PCR in samples with normozoospermia. Semen samples of 227 men with normal spermiograms were included in the study. The quantity of total bacterial DNA and at least one group of microorganisms was more than 103 GE/ml in 107 (41.7%) samples. Four stable microbiota clusters with the prevalence of a specific microorganism group were distinguished in these samples: obligate anaerobes (OA) cluster (proportion in the centroid — 81.1%); Lactobacillus spp. cluster (proportion in the centroid — 64.3%); gram-positive facultative anaerobes (GPFA) cluster (proportion in the centroid — 92.5%); Enterobacteriaceae/Enterococcoccus (EE) cluster (proportion in the centroid — 80.8%). The clusters were ranked by frequency of occurrence: OA cluster was the most prevalent (43 (40.2%) of 107), second-most frequent were GPFA-cluster (27 (25.2%)) and Lactobacillus-cluster (22 (20.6%)). EE-dominated cluster was found in 15 (14.0%) cases.

Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes?

Background

Bacterial infections are usually suspected in infertile couples seeking IVF with no clear understanding of the microbial compositions present in the seminal fluids and vaginal niche of the patients. We used next-generation sequencing technology to correlate microbiota compositions with IVF clinical outcomes.

Methods

Thirty-six couples were recruited to provide seminal fluids and vaginal swabs. Bacterial DNA was extracted, and V4 region of the 16S rRNA was amplified and sequenced in a pair-end configuration on the Illumina MiSeq platform rendering 2 × 150 bp sequences. Microbial taxonomy to species level was generated using the Greengenes database. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biologically and statistically significant differences in relative abundance.

Results

Seminal fluid microbiota compositions had lower bacterial concentrations compared with the vagina, but species diversity was significantly higher in seminal fluid samples. Azoospermic subjects had more relative abundance of Mycoplasma and Ureaplasma. In Normospermic semen, Lactobacillus (43.86%) was the most abundant, followed by Gardnerella (25.45%), while the corresponding vaginal samples, Lactobacillus (61.74%) was the most abundant, followed by Prevotella (6.07%) and Gardnerella (5.86%).

Conclusions

Semen samples with positive IVF were significantly colonized by Lactobacillus jensenii (P=0.002), Faecalibacterium (P=0.042) and significantly less colonized by Proteobacteria, Prevotella, Bacteroides, and lower Firmicutes/Bacteroidetes ratio compared with semen samples with negative IVF. Vaginal samples with positive IVF clinical outcome were significantly colonized by Lactobacillus gasseri, less colonized by Bacteroides and Lactobacillus iners. This study has opened a window of possibility for Lactobacillus replenishments in men and women before IVF treatment.

Effects of common Gram-negative pathogens causing male genitourinary-tract infections on human sperm functions

Male genitourinary tract (MGT) bacterial infections are considered responsible for 15% of male infertility, but the mechanisms underlying decreased semen quality are poorly known. We evaluated in vitro the effect of strains of Gram-negative uropathogenic species (two E.coli strains, three K. pneumoniae strains, P. aeruginosa and E. cloacae) on motility, viability, mitochondrial oxidative status, DNA fragmentation and caspase activity of human spermatozoa. All strains, except P. aeruginosa, reduced significantly sperm motility, with variable effects. Sperm Immobilizing Factor (SIF) was largely responsible for deteriorating effects on sperm motility of E. coli strains since they were completely reverted by knockout of SIF coding recX gene. Sequence alignment for RecX showed the presence of high homologous sequences in K. pneumoniae and E. cloacae but not in P. aeruginosa. These results suggest that, in addition to E.coli, other common uropathogenic Gram-negative bacteria affect sperm motility through RecX products. In addition to sperm motility, the E. coli strain ATCC 35218 also affected sperm viability, and induced caspase activity, oxidative stress and DNA fragmentation suggesting an interspecies variability in the amount and/or type of the produced spermatotoxic factors. In general, our results highlight the need for a careful evaluation of semen infections in the diagnostic process of the infertile man.

Metatranscriptomic Analysis of Human Lung Metagenomes from Patients with Lung Cancer

This study was designed to characterize the microbiomes of the lung tissues of lung cancer patients. RNA-sequencing was performed on lung tumor samples from 49 patients with lung cancer. Metatranscriptomics data were analyzed using SAMSA2 and Kraken2 software. 16S rRNA sequencing was also performed. The heterogeneous cellular landscape and immune repertoires of the lung samples were examined using xCell and TRUST4, respectively. We found that nine bacteria were significantly enriched in the lung tissues of cancer patients, and associated with reduced overall survival (OS). We also found that subjects with mutations in the epidermal growth factor receptor gene were less likely to experience the presence of Pseudomonas. aeruginosa. We found that the presence of CD8+ T-cells, CD4+ naive T-cells, dendritic cells, and CD4+ central memory T cells were associated with a good prognosis, while the presence of pro B-cells was associated with a poor prognosis. Furthermore, high clone numbers were associated with a high ImmuneScore for all immune receptor repertoires. Clone numbers and diversity were significantly higher in unpresented subjects compared to presented subjects. Our results provide insight into the microbiota of human lung cancer, and how its composition is linked to the tumor immune microenvironment, immune receptor repertoires, and OS.

The relationship between sexually transmitted bacteria, microbiota and seminal quality in asymptomatic men

Objective

To detect DNA of different microorganisms, in semen samples from apparently healthy men and correlate their presence with seminal quality.

Methods

Semen samples from 81 healthy volunteers were collected, and semen parameters were analyzed. DNA extraction was performed using the phenol-chloroform technique, and the microorganisms were detected by the amplification of specific primers using polymerase chain reaction.

Results

DNA from at least one of the microorganisms was detected in 78 samples. The most frequent microorganism found in semen were: Lactobacillus spp. (70%), Neisseria gonorrhoeae (N. gonorrhoeae) (36%), Streptococcus epidermidis (64%), Klebsiella pneumoniae (56%), Staphylococcus aureus (32%), Chlamydia trachomatis (C. trachomatis) (28%), Pseudomonas aeruginosa (27%). The seminal parameters of all semen samples were over the lower reference values for normal semen analysis. To compare with negative samples, seminal volume was higher for the Escherichia coli positive samples and lower for Pseudomonas aeruginosa positive samples. Semen samples positive for Staphylococcus aureus had worse sperm morphology. The frequency of progressive motility was higher in positive samples for N. gonorrhoeae and C. trachomatis. Positive semen samples for C. trachomatis had a higher concentration per milliliter.

Conclusion

It is common to find microorganisms in semen of asymptomatic men, including those responsible for sexually transmitted infections. Antimicrobial treatment is recommended only in those individuals with a sexually transmitted infection (C. trachomatis and N. gonorrhoeae) and always promote condom use.

Characterization of the seminal bacterial microbiome of healthy, fertile stallions using next-generation sequencing

High-throughput sequencing studies have shown the important role microbial communities play in the male reproductive tract, indicating differences in the semen microbial composition between fertile and infertile males. Most of these studies were made on human beings but little is known regarding domestic animals. Seminal bacteria studies made in stallions mostly focus on pathogenic bacteria and on their impact on reproductive technology. However, little is known about stallion commensal seminal microflora. That ultimately hinders our capacity to associate specific bacteria to conditions or seminal quality. Therefore, the aim of this study was to characterize the seminal microbial composition of 12 healthy, fertile stallion using next-generation sequencing. Hypervariable region V3 was chosen for bacterial identification. A total of nine phyla was detected. The most abundant ones were Bacteroidetes (46.50%), Firmicutes (29.92%) and Actinobacteria (13.58%). At family level, we found 69 bacterial families, but only nine are common in all samples. Porphyromonadaceae (33.18%), Peptoniphilaceae (14.09%), Corynebacteriaceae (11.32%) and Prevotellaceae (9.05%) were the most representative ones, while the Firmicutes phylum displayed the highest number of families (23, a third of the total). Samples showed high inter-subject variability. Findings previously described in other species notably differ from our findings. Families found in human such as Lactobacillaceae, Staphylococcaceae and Streptococcaceae only represented a 0.00%, 0.17% and 0.22% abundance in our samples, respectively. In conclusion, Porphyromonadaceae, Prevotellaceae, Peptoniphilaceae and Corynebacteriaceae families are highly represented in the seminal microbiome of healthy, fertile stallions. A high variation among individuals is also observed.

Assessing the testicular sperm microbiome: a low-biomass site with abundant contamination

RESEARCH QUESTION

The semen harbours a diverse range of microorganisms. The origin of the seminal microbes, however, has not yet been established. Do testicular spermatozoa harbour microbes and could they potentially contribute to the seminal microbiome composition?

DESIGN

The study included 24 samples, comprising a total of 307 testicular maturing spermatozoa. A high-throughput sequencing method targeting V3 and V4 regions of 16S rRNA gene was applied. A series of negative controls together with stringent in-silico decontamination methods were analysed.

RESULTS

Between 50 and 70% of all the detected bacterial reads accounted for contamination in the testicular sperm samples. After stringent decontamination, Blautia (P = 0.04), Cellulosibacter (P = 0.02), Clostridium XIVa (P = 0.01), Clostridium XIVb (P = 0.04), Clostridium XVIII (P = 0.02), Collinsella (P = 0.005), Prevotella (P = 0.04), Prolixibacter (P = 0.02), Robinsoniella (P = 0.04), and Wandonia (P = 0.04) genera demonstrated statistically significant abundance among immature spermatozoa.

CONCLUSIONS

Our results indicate that the human testicle harbours potential bacterial signature, though in a low-biomass, and could contribute to the seminal microbiome composition. Further, applying stringent decontamination methods is crucial for analysing microbiome in low-biomass site.

Obesity Causes Abrupt Changes in the Testicular Microbiota and Sperm Motility of Zebrafish

Background

Obesity is a recognized risk factor for low fertility and is becoming increasingly prevalent in many countries around the world. Obesity changes intestinal microbiota composition, causes inflammation of various organs, and also reduces sperm quality. Several microorganisms are present in the testis. However, whether obesity affects the changes of testicular microbiota and whether these changes are related to reduced fertility in obese men remain to be elucidated.

Methods

In the present study, a zebrafish obesity model was established by feeding with egg yolk powder. Sperm motility was measured by the Computer Assisted Sperm Analysis system, testicular microbial communities was assessed via 16s RNA sequencing, the immune response in zebrafish testis was quantified by quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay, and the testicular tissue structure was detected by electron microscopy and hematoxylin–eosin staining.

Results

Compared with the control group, zebrafish sperm motility was dramatically reduced, the expression of testicular proinflammatory cytokines in the testes was upregulated, and the blood–testis barrier structure was disrupted in the obese group. In addition, testicular microbiome composition was clearly altered in the obese group.

Conclusion

Obesity alters testicular microbiota composition, and the reason behind the decreased sperm motility in obese zebrafish may be related to changes in the testicular microbial communities.

Bacterial Vaginosis: Effects on reproduction and its therapeutics

Bacterial Vaginosis (BV) is the most common vaginal infection. A large amount of evidence shows that the anatomical scope of BV's pathogenic effect is far beyond the lower reproductive tract. BV is closely related to adverse reproductive outcomes, which may be due to the infection of the vaginal flora ascending to the upper genital tract. In addition, the incidence of BV is relatively high in infertile women. The vaginal microbiome also plays an important role in women's health and diseases. For most women, the normal vaginal microbiota is dominated by Lactobacillus, which can maintain a healthy vaginal environment by producing lactic acid, H₂O₂ and bacteriocin, etc. BV is characterized by the imbalanced vaginal flora. It changes the acidic environment that is normally dominated by Lactobacillus, and causes an overgrowth of anaerobic and facultative anaerobic bacteria such as Gardnerella vaginalis and Atopobium vaginae. Studies have shown that bacterial infections in the vagina can spread to upper genital tract and cause adverse fertility outcome. Therefore, early diagnosis and therapeutics of symptomatic BV is helpful to improve the outcome of poor fertility.

HPV infection and bacterial microbiota in the semen from healthy men

BACKGROUND

Aberrant microbiota composition has been linked to disease development at numerous anatomical sites. Microbiota changes in reaction to viral infections, such as human papillomavirus (HPV), have been investigated almost exclusively in the female reproductive tract. However, HPV infection may also affect male health by reducing semen quality and fertility. The aim of this study was to investigate whether present HPV DNA is associated with detectable changes in semen bacterial microbiota composition and diversity.

METHODS

This study relied on stored semen samples from 31 fertile healthy men who participated in the Finnish family HPV Study during the years 1998-2001. DNA was extracted from semen with PCR template preparation kit. HPV was genotyped using Luminex-based Multimetrix® assay. Microbiota was analyzed from the V3-V4 region of 16S rDNA gene following sequencing on an Illumina MiSeq platform. All statistical analyses were performed with Calypso software version 8.84.

RESULTS

HPV DNA was detected in 19.4% (6/31) of the semen samples. HPV status in the semen did not impact the α-diversity estimations, as measured by Chao1 and Shannon indices, nor ß-diversity. Nevertheless, HPV-positive semen samples exhibited differences in the taxonomic composition of the bacterial microbiota including higher abundances of Moraxellaceae (p = 0.028), Streptococcus (p = 0.0058) and Peptostreptococcus (p = 0.012) compared to HPV-negative semen samples.

CONCLUSION

HPV infection is associated with altered bacterial microbiota composition in semen, and this might have in impact to male health in general. As of present, it is unclear whether these changes result from HPV infection or whether altered bacterial microbiota increases susceptibility to HPV infection. More research is needed on viral-bacterial interactions in the male reproductive system.

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.

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques

BACKGROUND

An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples.

RESULTS

Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes.

CONCLUSIONS

Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.

Functional and Taxonomic Dysbiosis of the Gut, Urine, and Semen Microbiomes in Male Infertility

BACKGROUND

Little is known about the role of the genitourinary and gastrointestinal microbiota in the pathogenesis of male infertility.

OBJECTIVE

To compare the taxonomic and functional profiles of the gut, semen, and urine microbiomes of infertile and fertile men.

DESIGN, SETTING, AND PARTICIPANTS

We prospectively enrolled 25 men with primary idiopathic infertility and 12 healthy men with proven paternity, and we collected rectal swabs, semen samples, midstream urine specimens, and experimental controls.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

We performed comprehensive semen analysis, 16S rRNA sequencing for quantitative high-resolution taxonomy, and shotgun metagenomics with a median of 140 million reads per sample for functional metabolic pathway profiling.

RESULTS AND LIMITATIONS

We identified a diverse semen microbiome with modest similarity to the urinary microbiome. Infertile men harbored increased seminal α-diversity and distinct β-diversity, increased seminal Aerococcus, and decreased rectal Anaerococcus. Prevotella abundance was inversely associated with sperm concentration, and Pseudomonas was directly associated with total motile sperm count. Vasectomy appeared to alter the seminal microbiome, suggesting a testicular or epididymal contribution. Anaerobes were highly over-represented in the semen of infertile men with a varicocele, but oxidative stress and leukocytospermia were associated with only subtle differences. Metagenomics data identified significant alterations in the S-adenosyl-L-methionine cycle, which may play a multifaceted role in the pathogenesis of infertility via DNA methylation, oxidative stress, and/or polyamine synthesis.

CONCLUSIONS

This pilot study represents the first comprehensive investigation into the microbiome in male infertility. These findings provide the foundation for future investigations to explore causality and identify novel microbiome-based diagnostics and therapeutics for men with this complex and emotionally devastating disease.

PATIENT SUMMARY

We explored the resident populations of bacteria living in the gut, semen, and urine of infertile and fertile men. We found several important bacterial and metabolic pathway differences with the potential to aid in diagnosing and treating male infertility in the future.

Flujo vaginal y semen: La microbiota de las relaciones sexuales

Durante las relaciones sexuales, se da el intercambio de especies bacterianas entre las parejas, siendo las relaciones sexuales un factor crucial en la modificación de la microbiota genital. En el presente artículo de reflexión, se analizó el efecto de las relaciones sexuales sobre el intercambio de la microbiota vaginal y seminal. Las parejas que sostienen relaciones sexuales sin protección comparten especies bacterianas que podrían influir negativamente o positivamente sobre los parámetros seminales, como los Lactobacillus con potencial probiótico para el mantenimiento de la calidad del semen.

Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants

Early childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.

Role of Lactobacillus in Female Infertility Via Modulating Sperm Agglutination and Immobilization

Infertility has become a common problem in recent decades. The pathogenesis of infertility is variable, but microbiological factors account for a large proportion of it. Dysbiosis of vaginal microbiota is reportedly associated with female infertility, but the influence of normal vaginal microbiota on infertility is unclear. In this review, we summarize the physiological characteristics of the vaginal tract and vaginal microbiota communities. We mainly focus on the bacterial adherence of vaginal Lactobacillus species. Given that the adherent effect plays a crucial role in the colonization of bacteria, we hypothesize that the adherent effect of vaginal Lactobacillus may also influence the fertility of the host. We also analyze the agglutination and immobilization effects of other bacteria, especially Escherichia coli, on ejaculated spermatozoa, and speculate on the possible effects of normal vaginal microbiota on female fertility.

Pyospermia: background and controversies

Pyospermia (or leukocytospermia) is suspected based on the presence of >1 × 10⁶ round cells/mL of ejaculate and diagnosed using peroxidase stain revealing >1 × 10⁶ white blood cells/mL. The presence of white blood cells is a concern for overt infections or excessive inflammation, both of which have been postulated to negatively impact bulk semen parameters and fertilization capability. The threshold for pyospermia has been debated upon in the literature, as has the optimal treatment method. In the absence of clinical infectious symptoms, it appears that antibiotics, anti-inflammatory agents, and/or frequent ejaculation may improve bulk semen parameters in men with pyospermia. Further research is needed to adequately assess the effect of these methods on pregnancy and live birth outcomes, especially among couples attempting natural conception compared to those attempting intrauterine insemination or in vitro fertilization.

The microbiome of the infertile male

PURPOSE OF REVIEW

Contrary to historic dogma, many tissues and organs in the human body contain a resident population of bacteria, fungi, and viruses collectively known as the microbiome. The microbiome plays a role in both homeostatic symbiosis and also pathogenic dysbiosis in a wide array of diseases. Our understanding of the relationship between the microbiome and male factor infertility is in its infancy but is slowly evolving.

RECENT FINDINGS

Recent literature indicates that semen (and likely the testis) is not sterile and contains a distinct microbiome, and these changes in its composition are associated with alterations in semen quality and fertility status. Preliminary investigation indicates that manipulating the human microbiome may have implications in improving semen parameters and fertility.

SUMMARY

In this review, we describe relationships between the microbiome and the genitourinary system, discuss the prior work on the relationship among bacteriospermia, leukocytospermia and male factor infertility, and summarize the current literature utilizing 16s rRNA-based next-generation sequencing on the seminal and testicular microbiome. We explore the specific microbial taxa implicated in various aspects of spermatic dysfunction and introduce preliminary evidence for therapeutic approaches to alter the microbiome and improve fertility status.

Selfish genetic elements and male fertility

Selfish genetic elements (SGEs) are diverse and near ubiquitous in Eukaryotes and can be potent drivers of evolution. Here, we discuss SGEs that specifically act on sperm to gain a transmission advantage to the next generation. The diverse SGEs that affect sperm often impose costs on carrier males, including damaging ejaculates, skewing offspring sex ratios and in particular reducing sperm-competitive success of SGE-carrying males. How males and females tolerate and mitigate against these costs is a dynamic and expanding area of research. The intense intra-genomic conflict that these selfish elements generate could also have implications for male fertility and spermatogenesis more widely. This article is part of the theme issue 'Fifty years of sperm competition'.