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

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'.

The semen microbiome and its impact on sperm function and male fertility: A systematic review and meta-analysis

BACKGROUND

Male factor is attributable in up to 50% of cases of infertility. In vitro studies demonstrate that bacteria can negatively impact sperm function. The use of next-generation sequencing techniques has provided a better understanding of the human microbiome, and dysbiosis has been reported to impact health. Evidence regarding the impact of the semen microbiome on sperm function and fertility remains conflicting.

MATERIALS AND METHODS

A systematic search was conducted in accordance with the Preferred Reporting Items for Reviews and Meta-analysis (PRISMA) statement. The databases MEDLINE, OVID and PubMed were searched to identify English language studies related to the identification of bacteria in the semen of infertile and fertile men, between 1992 and 2019. Fifty-five observational studies were included, with 51 299 subjects. We included studies identifying bacteria using next-generation sequencing, culture or polymerase chain reaction.

RESULTS

The semen microbiome was rich and diverse in both fertile and infertile men. Three NGS studies reported clustering of the seminal microbiome with a predominant species. Lactobacillus and Prevotella were dominant in respective clusters. Lactobacillus was associated with improvements in semen parameters. Prevotella appeared to exert a negative effect on sperm quality. Bacteriospermia negatively impacted sperm concentration and progressive motility, and DNA fragmentation index (DFI; MD: 3.518, 95% CI: 0.907 to 6.129, P = .008). There was an increased prevalence of ureaplasma urealyticum in infertile men (OR: 2.25, 95% CI: 1.47-3.46). Ureaplasma urealyticum negatively impacted concentration and morphology. There was no difference in the prevalence of chlamydia trachomatis between fertile and infertile men and no significant impact on semen parameters. Enterococcus faecalis negatively impacted total motility, and Mycoplasma hominis negatively impacted concentration, PM and morphology.

DISCUSSION AND CONCLUSIONS

Ureaplasma urealyticum, Enterococcus faecalis, Mycoplasma hominis and Prevotella negatively impact semen parameters, whereas Lactobacillus appears to protect sperm quality. These findings may facilitate the development of novel therapies (eg probiotics), although the evidence regarding the impact of the seminal microbiome on fertility is inconclusive and further studies are needed to investigate this association.

Semen microbiota: cluster analysis of real-time PCR data

To this day semen microbiota is still poorly understood, and clinical significance of detecting specific microorganism groups has not been clearly determined. The aim of this work was to conduct cluster analysis of semen microbiota detected using real-time PCR. 634 semen samples of reproductive age men were analyzed using the Androflor kit. Microbial DNA in the quantity of no less than 103 GE/ml was detected in 460 samples (72.5%). From 1 to 14 microorganism groups were detected in 350 samples (55.2%) in the quantities that exceeded the threshold values (the detection rate of specific groups: 3.3–21.0%). In these 350 samples 4 stable microbiota clusters were determined. Each of the clusters was characterized by the prevalence of a specific microorganism group: obligate anaerobes (cluster 1; n = 172; detection rate — 49.1%), Lactobacillus spp. (cluster 2; n = 78; detection rate — 22.3%), gram-positive facultative anaerobes (cluster 3; n = 62; detection rate — 17.7%), Enterobacteriaceae / Enterococcoccus (cluster 4; n = 62; detection rate — 10.9%). Cluster 1 was less stable and was characterized by the larger species diversity compared to other clusters.

Roles of host genetics and sperm microbiota in reproductive success in healthy rabbit

Although the effects of sperm microbiota and sperm quality have been described previously, recent studies provide evidence that female genital modifications triggered by seminal components could be of significant importance to identify some disturbances associated with fertility. So, sperm microbiota could play a key role in sperm quality, contributing to fertilisation. To understand how sperm microbiota diversity is influenced by the host genetics, the symbiotic bacteria in four inbred lines raised in the same animal facility and their effects on sperm quality and fertility were analysed. Forty healthy rabbits from four selected Spanish commercial lines were used in this research (three based on litter performance, designated A, V and LP, and one selected for daily body weight gain, called R). Significant variations in the seminal concentration, morphology and some motion parameters were found among inbred lines, but sperm motility and viability were similar among inbred lines. After mating, inbred lines selected for litter size had the same fertility rate, significantly higher than inbred line selected for body weight (82 ± 3.3%, 79 ± 3.5% and 89 ± 4.5% versus 61 ± 3.7%, for the A, V and LP vs R lines, respectively, p < 0.05). Bacteria belonging to Proteobacteria, Firmicutes, Fusobacteria and Bacteroidetes were identified in sperm microbiota. At genus level, the bacterial community composition in the sperm microbiota was influenced by host genetics. A total of 35, 16, 34, and 51 genera were accurately detected in the A, V, LP, and R lines, respectively. Moreover, Enhydrobacter, Ferruginibacter, Myroides Paracoccus, Rheinheimera, Tepidiphilus, Tetradesmus obliquus and Thauera genera were present only in the inbred lines selected for litter size. Moreover, the discriminant analysis revealed Lysinibacillus and Flavobacterium genera as potential biomarkers for fertility. Thus, these two genera may play a key role in fertility. Our results demonstrated the existence of a rabbit inbred line-specific variation in bacterial occurrence in sperm microbiota. Moreover, fertility differentials among inbred lines that were not predicted by routine semen analysis could be partly explained by the symbiotic state of the semen microbiota.

Molecular detection of important abortion-causing microorganisms in preputial swab of breeding bucks using PCR-based assays

Infectious diseases and aetiological agents related to female reproductive systems were extensively covered compared to its male counterpart. There needs a proper study to bridge this gap, where microflora and infectious agents of both male and female reproductive are mutually intelligible. With this study, we aimed to evaluate the microbial contamination of the preputial cavity and also screened for abortion-causing agents which are zoonotic as well. In goats, such types of abortions are caused by Brucella melitensis, Chlamydophila, Campylobacter and Coxiella etc. One of the major sources of contamination of semen is the preputial cavity, which is exposed to the external environment leading to spread of infection into the female via semen straws or by natural service. In the current study, good quality bucks (n = 32, Barbari = 12, Jamunapari = 10, Jakhrana = 10) which were routinely used for semen collection were screened for their preputial swabs, for the presence of the above pathogens. For detection of Brucella melitensis, OMP31 based TaqMan® probe real-time PCR assay was used, and for Chlamydia, 16srRNA gene based SYBR® green real-time PCR assay was employed for detection of Chlamydophila abortus. While for Campylobacter spp. and Coxiella burnetii, 16srRNA gene based conventional PCR and Trans-PCR were used, respectively. In the current study, of the screened preputial swabs, none of them showed positive for Brucella and Coxiella, but of the screened 32 samples 17 showed positive for Chlamydia (53.13%) and two (6.25%) showed positive for Campylobacter spp. The current study emphasizes on the farms and laboratories which were regularly involved in screening of brucellosis also often overlook the other potential non-brucella pathogens, causing abortions eventually incurring severe economic losses to the goat keepers.

A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput characterization of the swine sperm microbiome remains scarce. We carried RNA-seq on 40 ejaculates each from a different Pietrain boar and found that a proportion of the sequencing reads did not map to the Sus scrofa genome. The current study aimed at using these reads not belonging to pig to carry a pilot study to profile the boar sperm bacterial population and its relation with 7 semen quality traits. We found that the boar sperm contains a broad population of bacteria. The most abundant phyla were Proteobacteria (39.1%), Firmicutes (27.5%), Actinobacteria (14.9%) and Bacteroidetes (5.7%). The predominant species contaminated sperm after ejaculation from soil, faeces and water sources (Bacillus megaterium, Brachybacterium faecium, Bacillus coagulans). Some potential pathogens were also found but at relatively low levels (Escherichia coli, Clostridioides difficile, Clostridium perfringens, Clostridium botulinum and Mycobacterium tuberculosis). We also identified 3 potential antibiotic resistant genes from E. coli against chloramphenicol, Neisseria meningitidis against spectinomycin and Staphylococcus aureus against linezolid. None of these genes were highly abundant. Finally, we classified the ejaculates into categories according to their bacterial features and semen quality parameters and identified two categories that significantly differed for 5 semen quality traits and 13 bacterial features including the genera Acinetobacter, Stenotrophomonas and Rhodobacter. Our results show that boar semen contains a bacterial community, including potential pathogens and putative antibiotic resistance genes, and that these bacteria may affect its reproductive performance.

Genomic Sequencing Reveals the Diversity of Seminal Bacteria and Relationships to Reproductive Potential in Boar Sperm

A number of emerging studies suggest that pathogenic microorganisms in semen may cause a decline in the reproductive potential of spermatozoa, and the bacterial diversity and profile of ejaculated boar semen in different seasons are currently unknown. To explore the bacterial composition and changes in ejaculated boar semen from winter and summer, and the underlying mechanism of decline in sperm quality and fertility capacity in summer, 120 ejaculated semen samples were examined for bacterial communities using genomic sequencing technology, and the associations between microbial composition and sperm reproductive potential were investigated. The results showed that Proteobacteria (57.53%), Firmicutes (31.17%), Bacteroidetes (4.24%), and Actinobacteria (3.41%) are the dominant phyla in the ejaculated semen, and the dominant genera were Pseudomonas (34.41%) and Lactobacillus (19.93%), which belong to the phyla of Proteobacteria and Firmicutes, respectively. Interestingly, the higher diversity of bacteria in ejaculated semen of winter differs from that of summer semen, potentially due to seasonal changes related to changes in semen quality and sperm fertilizing capacity. Furthermore, the highly abundant Lactobacillus in winter samples were positively associated with sperm quality and reproductive performance obtained from sows inseminated with such semen samples, while in contrast, the highly abundant Pseudomonas in summer samples was negatively associated with sperm quality and reproductive potential. Additionally, our results strongly indicated that Lactobacillus is not only a potential probiotic for semen quality and fertility potential but also beneficial for restraining the negative influence of Pseudomonas. Overall, our findings significantly contribute to the current understanding of the phenotypes and etiology of male "summer infertility," and may represent a frontier in male reproductive disorders and possible early prevention against pathogenic bacteria.

Bacterial infection of the male reproductive system causing infertility

Bacterial infections play a disruptive and hidden role in male reproductive failure. Different kinds of bacteria are often able to interfere with reproductive function in both sexes and lead to infertility. In this study, to further evaluate the role of bacterial infections in male reproduction we provided an extensive overview of so far researches investigating the effects of bacterial infections on male fertility. We searched Medline, PubMed, Scopus and Google scholar databases to identify the potentially relevant studies on bacterial infections and their implications in male infertility. All the bacteria included in this article have negative effects on the male reproductive function; however, there is ample evidence to blame bacteria such as Escherichia coli, Chlamydia trachomatis, Ureaplasma, Mycoplasma and Staphylococcus aureus for reduced fertility and deterioration of sperm parameters. More studies are needed to clarify the molecular mechanisms by which different bacteria exert their detrimental effects on male reproductive system. Getting more insight into probable mechanisms, would significantly facilitate the production of new, advanced, and effective remedies in the future. In view of all evidence, we strongly suggest increasing awareness among people and considering screening programs for patients seeking fertility both to avoid transmission and to improve fertility outcomes among them.

The Seminal Microbiome and Male Factor Infertility

Purpose of Review

Focusing on studies published within the last decade, we review the literature on the seminal microbiome and male factor infertility. We highlight potential mechanisms by which microbes may impact fertility and underscore key limitations and clinical implications of these studies.

Recent Findings

The seminal microbiome encompasses a metabolically and phylogenetically diverse group of microorganisms. Lactobacillus was consistently associated with normal semen analysis parameters and fertility; Anaerococcus was negatively associated with semen quality. These microbes may participate in a complex cross-talk with the host immune system, thereby modulating local and perhaps systemic inflammatory responses, impacting semen quality.

Summary

Research investigating the intersection between the seminal microbiome and male fertility is still in its infancy. Recent investigations have been exclusively cross-sectional, correlational studies, limiting the clinical applicability of published research. Prospective studies with more sophisticated methodologies are necessary.

Influence of the Ovine Genital Tract Microbiota on the Species Artificial Insemination Outcome. A Pilot Study in Commercial Sheep Farms

To date, there is a lack of research into the vaginal and sperm microbiome and its bearing on artificial insemination (AI) success in the ovine species. Using hypervariable regions V3-V4 of the 16S rRNA, we describe, for the first time, the combined effect of the ovine microbiome of both females (50 ewes belonging to five herds) and males (five AI rams from an AI center) on AI outcome. Differences in microbiota abundance between pregnant and non-pregnant ewes and between ewes carrying progesterone-releasing intravaginal devices (PRID) with or without antibiotic were tested at different taxonomic levels. The antibiotic treatment applied with the PRID only altered Streptobacillus genus abundance, which was significantly lower in ewes carrying PRID with antibiotic. Mageebacillus, Histophilus, Actinobacilllus and Sneathia genera were significantly less abundant in pregnant ewes. In addition, these genera were more abundant in two farms with higher AI failure. Species of these genera such as Actinobacillus seminis and Histophilus somni have been associated with reproductive disorders in the ovine species. These genera were not present in the sperm samples of AI rams, but were found in the foreskin samples of rams belonging to herd 2 (with high AI failure rate) indicating that their presence in ewes' vagina could be due to prior transmission by natural mating with rams reared in the herd.

Diagnostic significance of Lactobacillus spp. identification in ejaculate

Popularization of the real-time polymerase chain reaction method (RT-PCR), which is a trend of the recent years, allowed to significantly expand of the range of microorganisms that can be detected in the genitourinary tract of men. Moreover, the available picture of the microbiome's bacterial component structure became more detailed. Lactobacillus spp. remains one of the least studied groups of microorganisms. Treating patients with reproductive disorders, the authors have accumulated clinical experience demonstrating the possible relationship between presence of Lactobacillus spp. in the ejaculate and changes in the level of sex hormones and the key values registered with a spermogram. This study aimed to compare the levels of luteinizing hormone, follicle-stimulating hormone, testosterone, estradiol, prolactin, progesterone, and sex hormone binding globulin (SHBG) in blood serum and changes in spermogram values in 210 men with and without Lactobacillus spp. detected in their ejaculate. The treatment group included 105 men whose ejaculate had Lactobacillus spp. in the amount of (Lg) ≥ 103, as detected by RT-PCR. The control group included 105 men whose ejaculate did not have Lactobacillus spp. detected; the microbiome's bacterial component structure of their ejaculate was normal. Compared to the control group, treatment group had hormonal disorders registered more often: abnormal levels of three or more hormones (p = 0.04), hyperestradiolemia (p = 0.05), increased level of SHBG (p = 0.01). It was established that the presence of Lactobacillus spp. in the ejaculate of treatment group participants is associated with oligoastenoteratozoospermia (p < 0.01), decreased concentration of spermatozoa (p = 0.01), their decreased motility (p < 0.01) morphology abnormalities (p < 0.01). Thus, the presence of Lactobacillus spp. in the ejaculate can be interpreted as an additional marker of hormonal imbalance and fertility dysfunction in men.

Identification and evaluation of the microbiome in the female and male reproductive tracts

BACKGROUND

The existence of an extensive microbiome in and on the human body has increasingly dominated the scientific literature during the last decade. A shift from culture-dependent to culture-independent identification of microbes has occurred since the emergence of next-generation sequencing (NGS) techniques, whole genome shotgun and metagenomic sequencing. These sequencing analyses have revealed the presence of a rich diversity of microbes in most exposed surfaces of the human body, such as throughout the reproductive tract. The results of microbiota analyses are influenced by the technical specifications of the applied methods of analyses. Therefore, it is difficult to correctly compare and interpret the results of different studies of the same anatomical niche.

OBJECTIVES AND RATIONALE

The aim of this narrative review is to provide an overview of the currently used techniques and the reported microbiota compositions in the different anatomical parts of the female and male reproductive tracts since the introduction of NGS in 2005. This is crucial to understand and determine the interactions and roles of the different microbes necessary for successful reproduction.

SEARCH METHODS

A search in Embase, Medline Ovid, Web of science, Cochrane and Google scholar was conducted. The search was limited to English language and studies published between January 2005 and April 2018. Included articles needed to be original microbiome research related to the reproductive tracts.

OUTCOMES

The review provides an extensive up-to-date overview of current microbiome research in the field of human reproductive medicine. The possibility of drawing general conclusions is limited due to diversity in the execution of analytical steps in microbiome research, such as local protocols, sampling methods, primers used, sequencing techniques and bioinformatic pipelines, making it difficult to compare and interpret results of the available studies. Although some microbiota are associated with reproductive success and a good pregnancy outcome, it is still unknown whether a causal link exists. More research is needed to further explore the possible clinical implications and therapeutic interventions.

WIDER IMPLICATIONS

For the field of reproductive medicine, determination of what is a favourable reproductive tract microbiome will provide insight into the mechanisms of both unsuccessful and successful human reproduction. To increase pregnancy chances with live birth and to reduce reproduction-related health costs, future research could focus on postponing treatment or conception in case of the presence of unfavourable microbiota and on the development of therapeutic interventions, such as microbial therapeutics and lifestyle adaptations.

Potential Pathogenic Bacteria in Seminal Microbiota of Patients with Different Types of Dysspermatism

Human microbiota play an important role in the health of their human hosts. Recent studies have demonstrated that microbiota exist in seminal plasma. The current study aims to elucidate whether seminal microbiota exist in patients with different types of dysspermatism and whether bacterial biomarkers can be identified for them. A total of 159 study participants were recruited, including 22 patients with oligoasthenospermia, 58 patients with asthenospermia, 8 patients with azoospermia, 13 patients with oligospermia, and 58 matched healthy controls. Seminal microbiota composition was analyzed using 16S rRNA gene-based sequencing. The results showed that the composition of seminal microbiota of patients with dysspermatism differed from those of healthy controls. Comparison of the microbiota composition in semen samples from patients with different types of dysspermatism showed that microbiota in patients with asthenospermia and oligoasthenospermia were distinct from healthy controls in beta diversity (P < 0.05). Characteristic biomarkers, including Ureaplasma, Bacteroides, Anaerococcus, Finegoldia, Lactobacillus and Acinetobacter lwoffii, were identified based on LEfSe analysis. Inferred functional analysis based on seminal microbiome data further indicated the presence of potential pathogenic biomarkers in patients with asthenospermia and oligoasthenospermia. These results provided profiles of seminal microbiota exhibited in different types of dysspermatism, thus providing new insights into their pathogenesis.

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.

Inflammatory and antimicrobial properties differ between vaginal Lactobacillus isolates from South African women with non-optimal versus optimal microbiota

Female genital tract (FGT) inflammation increases HIV infection susceptibility. Non-optimal cervicovaginal microbiota, characterized by depletion of Lactobacillus species and increased bacterial diversity, is associated with increased FGT cytokine production. Lactobacillus species may protect against HIV partly by reducing FGT inflammation. We isolated 80 lactobacilli from South African women with non-optimal (Nugent 4–10; n = 18) and optimal microbiota (Nugent 0–3; n = 14). Cytokine production by vaginal epithelial cells in response to lactobacilli in the presence and absence of Gardnerella vaginalis was measured using Luminex. Adhesion to vaginal epithelial cells, pH, D/L-lactate production and lactate dehydrogenase relative abundance were assessed. Lactobacilli from women with non-optimal produced less lactic acid and induced greater inflammatory cytokine production than those from women with optimal microbiota, with IL-6, IL-8, IL-1α, IL-1β and MIP-1α/β production significantly elevated. Overall, lactobacilli suppressed IL-6 (adjusted p < 0.001) and IL-8 (adjusted p = 0.0170) responses to G. vaginalis. Cytokine responses to the lactobacilli were inversely associated with lactobacilli adhesion to epithelial cells and D-lactate dehydrogenase relative abundance. Thus, while cervicovaginal lactobacilli reduced the production of the majority of inflammatory cytokines in response to G. vaginalis, isolates from women with non-optimal microbiota were more inflammatory and produced less lactic acid than isolates from women with optimal microbiota.

The microbiome and gynaecological cancer development, prevention and therapy

The female reproductive tract (FRT), similar to other mucosal sites, harbours a site-specific microbiome, which has an essential role in maintaining health and homeostasis. In the majority of women of reproductive age, the microbiota of the lower FRT (vagina and cervix) microenvironment is dominated by Lactobacillus species, which benefit the host through symbiotic relationships. By contrast, the upper FRT (uterus, Fallopian tubes and ovaries) might be sterile in healthy individuals or contain a low-biomass microbiome with a diverse mixture of microorganisms. When dysbiosis occurs, altered immune and metabolic signalling can affect hallmarks of cancer, including chronic inflammation, epithelial barrier breach, changes in cellular proliferation and apoptosis, genome instability, angiogenesis and metabolic dysregulation. These pathophysiological changes might lead to gynaecological cancer. Emerging evidence shows that genital dysbiosis and/or specific bacteria might have an active role in the development and/or progression and metastasis of gynaecological malignancies, such as cervical, endometrial and ovarian cancers, through direct and indirect mechanisms, including modulation of oestrogen metabolism. Cancer therapies might also alter microbiota at sites throughout the body. Reciprocally, microbiota composition can influence the efficacy and toxic effects of cancer therapies, as well as quality of life following cancer treatment. Modulation of the microbiome via probiotics or microbiota transplant might prove useful in improving responsiveness to cancer treatment and quality of life. Elucidating these complex host-microbiome interactions, including the crosstalk between distal and local sites, will translate into interventions for prevention, therapeutic efficacy and toxic effects to enhance health outcomes for women with gynaecological cancers.

What human sperm RNA-Seq tells us about the microbiome

PURPOSE

The study was designed to assess the capacity of human sperm RNA-seq data to gauge the diversity of the associated microbiome within the ejaculate.

METHODS

Semen samples were collected, and semen parameters evaluated at time of collection. Sperm RNA was isolated and subjected to RNA-seq. Microbial composition was determined by aligning sequencing reads not mapped to the human genome to the NCBI RefSeq bacterial, viral and archaeal genomes following RNA-Seq. Analysis of microbial assignments utilized phyloseq and vegan.

RESULTS

Microbial composition within each sample was characterized as a function of microbial associated RNAs. Bacteria known to be associated with the male reproductive tract were present at similar levels in all samples representing 11 genera from four phyla with one exception, an outlier. Shannon diversity index (p < 0.001) and beta diversity (unweighted UniFrac distances, p = 9.99e-4; beta dispersion, p = 0.006) indicated the outlier was significantly different from all other samples. The outlier sample exhibited a dramatic increase in Streptococcus. Multiple testing indicated two operational taxonomic units, S. agalactiae and S. dysgalactiae (p = 0.009), were present.

CONCLUSION

These results provide a first look at the microbiome as a component of human sperm RNA sequencing that has sufficient sensitivity to identify contamination or potential pathogenic bacterial colonization at least among the known contributors.

The complex microbiome from native semen to embryo culture environment in human in vitro fertilization procedure

BACKGROUND

Only a few microbial studies have conducted in IVF (in vitro fertilization), showing the high-variety bacterial contamination of IVF culture media to cause damage to or even loss of cultured oocytes and embryos. We aimed to determine the prevalence and counts of bacteria in IVF samples, and to associate them with clinical outcome.

METHODS

The studied samples from 50 infertile couples included: raw (n = 48), processed (n = 49) and incubated (n = 50) sperm samples, and IVF culture media (n = 50). The full microbiome was analyzed by 454 pyrosequencing and quantitative analysis by real-time quantitative PCR. Descriptive statistics, t-, Mann-Whitney tests and Spearman's correlation were used for comparison of studied groups.

RESULTS

The study involved normozoospermic men. Normal vaginal microbiota was present in 72.0% of female partners, while intermediate microbiota and bacterial vaginosis were diagnosed in 12.0 and 16.0%, respectively. The decreasing bacterial loads were found in raw (35.5%), processed (12.0%) and sperm samples used for oocyte insemination (4.0%), and in 8.0% of IVF culture media. The most abundant genera of bacteria in native semen and IVF culture media were Lactobacillus, while in other samples Alphaproteobacteria prevailed. Staphylococcus sp. was found only in semen from patients with inflammation. Phylum Bacteroidetes was in negative correlation with sperm motility and Alphaproteobacteria with high-quality IVF embryos.

CONCLUSION

Our study demonstrates that IVF does not occur in a sterile environment. The prevalent bacteria include classes Bacilli in raw semen and IVF culture media, Clostridia in processed and Bacteroidia in sperm samples used for insemination. The presence of Staphylococcus sp. and Alphaproteobacteria associated with clinical outcomes, like sperm and embryo quality.

Microorganisms in the reproductive tissues of arthropods

Microorganisms that reside within or transmit through arthropod reproductive tissues have profound impacts on host reproduction, health and evolution. In this Review, we discuss select principles of the biology of microorganisms in arthropod reproductive tissues, including bacteria, viruses, protists and fungi. We review models of specific symbionts, routes of transmission, and the physiological and evolutionary outcomes for both hosts and microorganisms. We also identify areas in need of continuing research, to answer the fundamental questions that remain in fields within and beyond arthropod-microorganism associations. New opportunities for research in this area will drive a broader understanding of major concepts as well as the biodiversity, mechanisms and translational applications of microorganisms that interact with host reproductive tissues.

Differential Composition of Vaginal Microbiome, but Not of Seminal Microbiome, Is Associated With Successful Intrauterine Insemination in Couples With Idiopathic Infertility: A Prospective Observational Study

Background

Vaginal and seminal microbiomes have gained increasing interest for their involvement in reproductive health and fertility. However, their role in reproductive outcome is not fully understood yet. In this study, we aimed to correlate the vaginal and the seminal microbiome of 23 couples with idiopathic infertility to the clinical pregnancy rate after intrauterine insemination (IUI).

Methods

Vaginal swabs and seminal fluids were collected on the day of IUI procedure and analyzed through polymerase chain reaction amplification of variable regions 3 and 4 (V3–V4) of 16S ribosomal ribonucleic acid genes and Illumina MiSeq sequencing. The taxonomic data were then correlated to IUI success.

Results

Idiopathic infertile women showed a different average composition of vaginal microbiome compared with control sequences, whereas for seminal counterpart no relevant differences were observed. Furthermore, among idiopathic infertile women, different patterns of Lactobacillus species dominations were observed, with a predominance either of Lactobacillus crispatus, a marker of a healthy vaginal ecosystem, or of Lactobacillus iners and Lactobacillus gasseri, associated with a more dysbiosis-prone environment. More important, considering all investigated variables, vaginal L crispatus domination was the only factor strongly associated to IUI success (P = .0002).

Conclusions

Our results strengthen the potential role of L crispatus in promoting a favorable environment for pregnancy and suggest that microbiome characterization could be useful, together with standard clinical and laboratory assessments, in the pre-IUI evaluation of infertile couples.

Composition and diversity of the preputial microbiota in healthy bulls

Characterization of microbial communities inhabiting the reproductive tracts of cattle may lead to a better comprehension of bovine physiology and reproductive health. To date, reported studies have utilized culture-independent 16S ribosomal RNA (rRNA) for the classification of microbiota in the vaginal tract of cows but no studies have looked at the microbiota of the prepuce or penis of the bull. The aim of this study was to elucidate the microbiota present on the epithelial surface of the penis and prepuce of the post-pubertal bull using 16S rRNA gene sequencing. Ninety-two healthy bulls of a variety of ages and breeding history, presented for routine breeding soundness examinations, were utilized in this investigation. Bacteria belonging to Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria were identified in the prepuce. From all the bulls, two major community types were found, those with low or high bacterial species richness (up to 400 operational taxonomic units in one sample). There was no animal characteristic (breed or age) or management practice (feed type, antibiotic use, co-housing, breeding history) that was correlated with the bull penile microbial community composition. However, Bradyrhizobium was a distinguishing genus only found in the low diversity samples. The bull penile microbial community includes members of genera that are common in soil, cow vagina, respiratory tract, and feces. The baseline preputial microbial community in healthy bulls is described in the current study. This knowledge can be used later when investigating the interactions between disease and the male urogenital tract microbial community.

Uterine Immunity and Microbiota: A Shifting Paradigm

The female reproductive tract harbors distinct microbial communities, as in the vagina, cervical canal, uterus, and fallopian tubes. The nature of the vaginal microbiota is well-known; in contrast, the upper reproductive tract remains largely unexplored. Alteration in the uterine microbiota, which is dependent on the nutrients and hormones available to the uterus, is likely to play an important role in uterine-related diseases such as hysteromyoma, adenomyosis, and endometriosis. Uterine mucosa is an important tissue barrier whose main function is to offer protection against pathogens and other toxic factors, while maintaining a symbiotic relationship with commensal microbes. These characteristics are shared by all the mucosal tissues; however, the uterine mucosa is unique since it changes cyclically during the menstrual cycle as well as pregnancy. The immune system, besides its role in the defense process, plays crucial roles in reproduction as it ensures local immune tolerance to fetal/paternal antigens, trophoblast invasion, and vascular remodeling. The human endometrium contains a conspicuous number of immune cells, mainly Natural Killers (NK) cells, which are phenotypically distinct from peripheral cytotoxic NK, cells and macrophages. The endometrium also contains few lymphoid aggregates comprising B cell and CD8⁺ T cells. The number and the phenotype of these cells change during the menstrual cycle. It has become evident in recent years that the immune cell phenotype and function can be influenced by microbiota. Immune cells can sense the presence of microbes through their pattern recognition receptors, setting up host-microbe interaction. The microbiota exerts an appropriately controlled defense mechanism by competing for nutrients and mucosal space with pathogens. It has recently been considered that uterus is a non-sterile compartment since it seems to possess its own microbiota. There has been an increasing interest in characterizing the nature of microbial colonization within the uterus and its apparent impact on fertility and pregnancy. This review will examine the potential relationship between the uterine microbiota and the immune cells present in the local environment.

CASA-Mot in mammals: an update

Sperm motility is one of the most widely used parameters of sperm quality. Computer-aided sperm motility analysis (CASA-Mot) systems were developed to reduce the subjectivity of sperm motility assessment, and have had broad scientific and practical acceptance. In this review, the sources of variation and current applications of this technology and its relationships with other sperm quality tests are described in detail. Despite remarkable advances in the technique, there is still great need for standardisation in many species, and the numerous factors that affect the results make it difficult to provide universally accepted criteria for classifying semen samples based on sperm motility characteristics. The main fields for CASA-Mot include the study of male fertility and pathologies, evaluation of the effects of physical and chemical agents, improvement of epidemiological survey studies, more precise calculation of seminal doses for farm animals, realisation of basic studies about sperm function, improvement of sperm technologies such as cryopreservation and quality control analysis. Numerous relationships have been established between CASA-Mot and other sperm quality tests, although most of these parameters are complementary. Future CASA-Mot systems will probably be able to integrate several sperm quality parameters with motility.

High prevalence of urogenital infection/inflammation in patients with azoospermia does not impede surgical sperm retrieval

Considering infection/inflammation to be an important risk factor in male infertility, the aim of this study was to make a comprehensive evaluation of the prevalence of urogenital tract infection/inflammation and its potential impact on sperm retrieval in azoospermic patients. In this prospective study, 71 patients with azoospermia were subjected to an extensive andrological workup including comprehensive microbiological diagnostics (2-glass test, semen, testicular swab and testicular tissue analysis) and testicular biopsy/testicular sperm extraction (TESE). Medical history suggested urogenital tract infection/inflammation in 7% of patients, 11% harboured STIs, 14% showed significant bacteriospermia, 15% had seminal inflammation, 17% fulfilled the MAGI definition, and 27% had relevant pathogens. At the testicular level, 1 patient had a swab positive for bacteria, no viruses were detected, tissue specimens never indicated pathogens, whereas histopathology revealed focal immune cell infiltrates in 23% of samples. Testicular sperm retrieval rate was 100% in obstructive and 46% in nonobstructive azoospermia. None of the infection/inflammation-related variables was associated with the success of sperm retrieval or inflammatory lesions in the testis. The high prevalence of urogenital infection/inflammation among azoospermic men underpins their role as significant aetiologic factors in male infertility. However, this observation does not refer to the chances of sperm retrieval at the time of surgery/TESE.

Diet Supplemented with Antioxidant and Anti-Inflammatory Probiotics Improves Sperm Quality after Only One Spermatogenic Cycle in Zebrafish Model

Infertility is a medical concern worldwide and could also have economic consequences in farmed animals. Developing an efficient diet supplement with immediate effects on sperm quality is a promising tool for human reproduction and for domesticated animal species. This study aims at elucidating the effect of a short-time probiotic supplementation consisting of a mixture of two probiotic bacteria with proven antioxidant and anti-inflammatory activities on zebrafish sperm quality and male behavior. For this purpose, three homogeneous groups of males in terms of motility (<60%) were established. The control group was fed with a normal standard diet. The other received supplements: One group (vehicle control) was fed with maltodextrin and the other received a probiotic preparation based on a mixture (1:1) of Lactobacillus rhamnosus CECT8361 and Bifidobacterium longum CECT7347. The feeding regime was 21 days corresponding with a single spermatogenesis in zebrafish. The preparation did not modify animal weight, positively affected the number of fluent males, increased sperm concentration, total motility, progressive motility, and fast spermatozoa subpopulations. Moreover, the animals fed with the supplement showed different behavior patterns compared to control groups. Our results suggest a diet-related modulation on the exploration activity indicating a lower stress-like conduct. The studied formulation described here should be considered as advantageous in male reproductive biotechnology.

Testicular microbiome in azoospermic men-first evidence of the impact of an altered microenvironment

STUDY QUESTION

Given the relevant role of the extracellular microenvironment in regulating tissue homeostasis, is testicular bacterial microbiome (BM) associated with germ cell aplasia in idiopathic non-obstructive azoospermia (iNOA)?

SUMMARY ANSWER

A steady increase of dysbiosis was observed among testis with normal spermatogenesis vs. iNOA with positive sperm retrieval and iNOA with complete germ cell aplasia.

WHAT IS KNOWN ALREADY

Tissue-associated BM has been reported to be a biologically important extracellular microenvironment component for numerous body habitats, but not yet for the human testis.

STUDY DESIGN, SIZE, DURATION

Cross-sectional study, investigating tissue-associated BM in the testis of (i) five men with iNOA and negative sperm retrieval at microdissection testicular sperm extraction (microTESE); (ii) five men with iNOA and positive sperm retrieval at microTESE; and (iii) five normozoospermic men upon orchiectomy. Every testicular specimen was histologically classified and analyzed in terms of bacterial community.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Massive ultra-deep pyrosequencing was applied to investigate testis microbiome. Metagenome was analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Tissue-associated bacterial load was quantified by digital droplet PCR.

MAIN RESULTS AND THE ROLE OF CHANCE

Normozoospermic men showed small amounts of bacteria in the testis, with Actinobacteria, Bacteroidetes, Firmicutes Proteobacteria as the dominating phyla; iNOA individuals had increased amounts of bacterial DNA (P = 0.02), associated with decreased taxa richness due to the lack of Bacteroidetes and Proteobacteria (P = 2 × 10⁻⁵). Specimens with negative sperm retrieval at microTESE depicted complete germ cell aplasia and a further decrease in terms of Firmicutes and Clostridia (P < 0.05), a complete lack of Peptoniphilus asaccharolyticus, but increased amount of Actinobacteria.

LIMITATIONS, REASONS FOR CAUTION

The limited number of specimens analyzed in this preliminary study deserves external validation. The paraneoplastic microenvironment could have an impact on the residential bacterial flora.

WIDER IMPLICATION OF THE FINDINGS

Human testicular microenvironment is not microbiologically sterile, containing low amounts of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. A dysbiotic bacterial community was associated with iNOA and complete germ cell aplasia. Novel findings on testicular BM could support future translational therapies of male-factor infertility.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by URI-Urological Research Institute free funds. Authors declared no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.

Evaluation of the ejaculate microbiota by real-time PCR and culture-based technique

Among other things male sterility can be caused by inflammatory diseases of the urogenital tract, often associated with opportunistic microorganisms. Thus, it is necessary to implement modern methods for the detection and identification of opportunistic microorganisms in the urogenital tract. The aim of the work was to conduct comparative analysis of the ejaculate microbiota from men of the reproductive age and studied using quantitative polymerase chain reaction (PCR) and culture method. 86 samples of ejaculate collected from men aged 18–57 years after observing sexual abstinence for 3–5 days were examined. With culture study in 50% of samples we observed growth of gram positive facultative anaerobic bacteria in the amount less than 103 CFU/ml; in 16.3% of samples — the growth of bacteria was not observed. With real-time PCR in each sample 8–15 groups of microorganisms were detected (including the prevailing groups) in the amount of 102–106 GE/ml. In all 86 samples obligate anaerobes that cannot not be cultured in vitro were detected. The predominant groups of microorganisms, as determined by real-time PCR, were detected by the culture method only in 24.4% of cases.

Reappraising the exteriorization of the mammalian testes through evolutionary physiology

A number of theories have been proposed to explain the exteriorization of the testicles in most mammalian species. None of these provide a consistent account for the wide variety of testicular locations found across the animal kingdom. It is proposed that testicular location is the result of coordinate action of testicular tissue ecologies to sustain preferential states of homeostatic equipoise throughout evolutionary development in response to the advent of endothermy.

Sperm Microbiota and Its Impact on Semen Parameters

Compared to its female counterpart, the microbiota of the male genital tract has not been studied extensively. With this study, we aimed to evaluate the bacterial composition of seminal fluid and its impact on sperm parameters. We hypothesized that a dysbiotic microbiota composition may have an influence on sperm quality. Semen samples of 26 men with normal spermiogram and 68 men with at least one abnormal spermiogram parameter were included in the study. Samples were stratified based on total sperm count, spermatozoa concentration, progressive motility, total motility and spermatozoa morphology. Microbiota profiling was performed using 16S rRNA gene amplicons sequencing and total bacterial load was determined using a panbacterial quantitative PCR. Semen samples broadly clustered into three microbiota profiles: Prevotella-enriched, Lactobacillus-enriched, and polymicrobial. Prevotella-enriched samples had the highest bacterial load (p < 0.05). Network analysis identified three main co-occurrence modules, among which two contained bacteria commonly found in the vaginal flora. Genera from the same module displayed similar oxygen requirements, arguing for the presence of different ecological niches for bacteria that colonize semen through the passage. Contrary to our hypothesis, shifts in overall microbiota composition (beta-diversity) did not correlate with spermiogram parameters. Similarly, we did not find any difference in microbial richness or diversity (alpha-diversity). Differential abundance testing, however, revealed three specific genera that were significantly enriched or depleted in some of the sperm quality groups (p < 0.05). Prevotella relative abundance was increased in samples with defective sperm motility while Staphylococcus was increased in the corresponding control group. In addition, we observed an increased relative abundance of Lactobacillus in samples with normal sperm morphology. Our study indicates that overall bacterial content of sperm might not play a major role in male infertility. Although no major shifts in microbiota composition or diversity were found, the differential abundance of specific bacterial genera in the sperm suggests that a small subset of microbes might impact the spermatozoal physiology during sperm transition, more specifically motility and morphology. Further studies are required to challenge this finding and develop potential strategies to induce the formation of a healthy seminal microbiota.

Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study

Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of “area” is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.

β-Defensins: Farming the Microbiome for Homeostasis and Health

Diverse commensal populations are now regarded as key to physiological homeostasis and protection against disease. Although bacteria are the most abundant component of microbiomes, and the most intensively studied, the microbiome also consists of viral, fungal, archael, and protozoan communities, about which comparatively little is known. Host-defense peptides (HDPs), originally described as antimicrobial, now have renewed significance as curators of the pervasive microbial loads required to maintain homeostasis and manage microbiome diversity. Harnessing HDP biology to transition away from non-selective, antibiotic-mediated treatments for clearance of microbes is a new paradigm, particularly in veterinary medicine. One family of evolutionarily conserved HDPs, β-defensins which are produced in diverse combinations by epithelial and immune cell populations, are multifunctional cationic peptides which manage the cross-talk between host and microbes and maintain a healthy yet dynamic equilibrium across mucosal systems. They are therefore key gatekeepers to the oral, respiratory, reproductive and enteric tissues, preventing pathogen-associated inflammation and disease and maintaining physiological normality. Expansions in the number of genes encoding these natural antibiotics have been described in the genomes of some species, the functional significance of which has only recently being appreciated. β-defensin expression has been documented pre-birth and disruptions in their regulation may play a role in maladaptive neonatal immune programming, thereby contributing to subsequent disease susceptibility. Here we review recent evidence supporting a critical role for β-defensins as farmers of the pervasive and complex prokaryotic ecosystems that occupy all body surfaces and cavities. We also share some new perspectives on the role of β-defensins as sensors of homeostasis and the immune vanguard particularly at sites of immunological privilege where inflammation is attenuated.

Deciphering the effect of reproductive tract microbiota on human reproduction

BACKGROUND

The female reproductive tract contains an active microbiome comprising mainly bacteria from the Lactobacillus genus, which is associated with a healthy microbiome state. However, spatio-temporal fluctuations of this microbiome that occur in response to internal and external factors may impact the physiology of the reproductive tract organs and even lead to pathological states.

METHODS

Current literature covering the reproductive tract microbiome is summarized and contextualized in this review.

MAIN FINDINGS

This review presents the current knowledge about the bacterial composition of the lower and upper reproductive tract as well as the impact of the microbiota on women's health and reproduction. We place special focus on the impact of the endometrial microbiome in infertility and assisted reproductive technologies.

CONCLUSION

The assessment of the reproductive tract microbiome adds a new microbiological perspective to human reproduction, pregnancy, and onset of new life, highlighting the importance of considering the evaluation of microbial communities to improve personalized care in reproductive medicine and women's health.

Shaping Microbiota During the First 1000 Days of Life

The data obtained in prior studies suggest that early microbial exposition begins prior to conception and gestation. Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning early microbiota exposure within the male and the female reproductive tracts at the point of conception and during gestation, focusing on the potential impact on infant development during the first 1000 days of life. Furthermore, we conclude that some dietary strategies including specific probiotics could become potentially valuable tools to modulate the gut microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.

Gut microbiome changes in overweight male adults following bowel preparation

Background

Human gut microbiome has an essential role in human health and disease. Although the major dominant microbiota within individuals have been reported, the change of gut microbiome caused by external factors, such as antibiotic use and bowel cleansing, remains unclear. We conducted this study to investigate the change of gut microbiome in overweight male adults after bowel preparation, where none of the participants had been diagnosed with any systemic diseases.

Methods

A total of 20 overweight, male Taiwanese adults were recruited, and all participants were omnivorous. The participants provided fecal samples and blood samples at three time points: prior to bowel preparation, 7 days after colonoscopy, and 28 days after colonoscopy. The microbiota composition in fecal samples was analyzed using 16S ribosome RNA gene amplicon sequencing.

Results

Our results demonstrated that the relative abundance of the most dominant bacteria hardly changed from prior to bowel preparation to 28 days after colonoscopy. Using the ratio of Prevotella to the sum of Prevotella and Bacteroides in the fecal samples at baseline, the participants were separated into two groups. The fecal samples of the Type 1 group was Bacteroides-dominant, and that of the Type 2 group was Prevotella-dominant with a noticeable presence Bacteroides. Bulleidia appears more in the Type 1 fecal samples, while Akkermensia appears more in the Type 2 fecal samples. Of each type, the gut microbial diversity differed slightly among the three collection times. Additionally, the Type 2 fecal microbiota was temporarily susceptible to bowel cleansing. Predictive functional analysis of microbial community reveals that their activities for the mineral absorption metabolism and arachidonic acid metabolism differed significantly between the two types. Depending on their fecal type, the variance of triglycerides and C-reactive protein also differed between the two types of participants.

Conclusions

Depending upon the fecal type, the microbial diversity and the predictive functional modules of microbial community differed significantly after bowel preparation. In addition, blood biochemical markers presented somewhat associated with fecal type. Therefore, our results might provide some insights as to how knowledge of the microbial community could be used to promote health through personalized clinical treatment.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5285-6) contains supplementary material, which is available to authorized users.

Male Partners of Infertile Couples With Seminal Positivity for Markers of Bacterial Vaginosis Have Impaired Fertility

To access the possibility that key markers of bacterial vaginosis (KM-BV) could affect seminal parameters and thus fertility a prospective cohort study was designed (a) to develop rapid and sensitive multiplex polymerase chain reaction (M-PCR) assays to screen 13 key markers of bacterial vaginosis (KM-BV) in semen specimens, (b) to determine the prevalence of KM-BV in semen from randomized male partners of couples seeking fertility evaluation. A total of 229 semen samples were included in the study from males who visited the Sperm Analysis Section of Brazil between October 2015 and March 2016. Eligible men were 18 years or older and had a semen analysis due fertility evaluation (after failing to conceive with their partner after 1 year of unprotected intercourse). Basic seminal parameters were analyzed, and KM-BV was detected by M-PCR assays. M-PCR assays clearly distinguished 13 KM-BV in 146 semen samples (63.8%), mainly Gardnerella vaginalis (50.7%). Some important associations occurred between the presence of KM-BV in semen and changes in seminal parameters. KM-BV is commonly present in the semen of males seeking fertility evaluation and could potentially play significant roles in male subfertility and/or infertility.

[Impact of air quality on practices and results in the IVF laboratory]

The concept of Air Quality often refers to particulate and microbiological contamination of ambiant air. European Directive 2006/86/CE encompass the IVF process and specify a class A air quality for manipulation of tissue and cells, in a class D environment (A over D rule). Recognizing the paramount importance of ensuring the highest microbiological and particulate safety in the IVF laboratory, it is equally important to take into account practicability issues and the financial burden of these recommendations, as well as the utter need to protect gametes and embryo viability during their IVF journey. The usefulness of such stringent recommendations may also be questionned given the absence of published cases of airborne contaminations and related patients infections after embryo transfer. The European directive stems from pharmaceutical standards and were not specifically designed for human IVF. Gametes and embryos are indeed extremely sensitive to physical and chemical stress and require strict temperature, osmolarity and pH control, as well as an absence of chemical contamination during manipulation and culture. These conditions are hardly obtained when using laminar flow hoods. Following concerns raised by many experts in the field, exceptions to the A over D rule were added in the 2006/86/CE Directives. This narrative review discusses all these aspects in a critical way and compare scientific and legal requirements applying to IVF practices in different regions of the world.

Postnovo: Postprocessing Enables Accurate and FDR-Controlled de Novo Peptide Sequencing

De novo sequencing offers an alternative to database search methods for peptide identification from mass spectra. Since it does not rely on a predetermined database of expected or potential sequences in the sample, de novo sequencing is particularly appropriate for samples lacking a well-defined or comprehensive reference database. However, the low accuracy of many de novo sequence predictions has prevented the widespread use of the variety of sequencing tools currently available. Here, we present a new open-source tool, Postnovo, that postprocesses de novo sequence predictions to find high-accuracy results. Postnovo uses a predictive model to rescore and rerank candidate sequences in a manner akin to database search postprocessing tools such as Percolator. Postnovo leverages the output from multiple de novo sequencing tools in its own analyses, producing many times the length of amino acid sequence information (including both full- and partial-length peptide sequences) at an equivalent false discovery rate (FDR) compared to any individual tool. We present a methodology to reliably screen the sequence predictions to a desired FDR given the Postnovo sequence score. We validate Postnovo with multiple data sets and demonstrate its ability to identify proteins that are missed by database search even in samples with paired reference databases.

Pseudomonas aeruginosa: A risk factor for fertility in male mice

The present study was designed to evaluate the effect of P. aeruginosa on reproductive potential of male mice via a series of in vitro and in vivo experiments. In vitro studies involved sperm parameters, Mg²⁺ATPase activity and acrosome status. In vivo study employed male mice which in the right vas deferens received 20 μl of either PBS (Group I) or 10⁴ cfu of P. aeruginosa (Group II). The animals were sacrificed on day 3, 7 and 14 and various parameters viz. body weight, TSI (%), bacterial load, spermiogram {i.e. sperm count, motility (%), viability (%) and morphology}, lipid peroxidation and tissue histopathology were evaluated. The results revealed that cell free supernatant of P. aeruginosa resulted in reduced motility, viability, Mg²⁺dependent ATPase activity and premature acrosomal loss of mouse spermatozoa in vitro. In vivo study showed that in comparison to group I, group II revealed significant alterations in all the parameters on all the days of sacrifice. Further, when reproductive organs of right and left side of mice in group II were compared, the right side demonstrated more devastating effects in terms of altered TSI (%) of testis and cauda epididymis, higher bacterial counts, azoospermia, increased malondialdehyde levels and severe inflammation in tissue histopathology in comparison to left side where bacteria disseminated in reduced numbers, thereby, resulting in insignificant changes in TSI (%), spermiogram, malondialdehyde levels and tissue histology. This study demonstrates that the colonization of P. aeruginosa in male genital tract could be a risk factor for fertility.

No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases

Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.

The matter of the reproductive microbiome

The preconceptional presence of microbiota in the female and male reproductive organs suggests that fertilization is taking place in a nonsterile environment and contributes to reproductive success. The concept of embryonic development in a sterile uterus has also been challenged with recent reports of the existence of a microbiome of the placenta, amniotic fluid and the fetal gut in normal, uncomplicated pregnancies. The maternal origins of the microbiota colonising the fetus and its surroundings are unknown as are the mechanisms of maternal-to-fetal transfer. In this review, we aim to highlight the preconception male and female microbiome, the maternal vaginal and gut microbiome during pregnancy and the fetal microbiome, including their possible roles in reproduction, and maternal and neonatal pregnancy outcome.

Impact of sexual debut on culturable human seminal microbiota

Micro-organisms are tightly integrated into host-microbiota ecosystem. Microbiota of human semen has been studied so far mostly in case of infertility or prostatitis. We aimed to reveal possible impact of sexual debut on seminal microbiota in healthy young men. The study group included 68 young healthy men, of them 12 men without sexual experience, 11 men with single lifetime sexual partner and 45 men with multiple lifetime sexual partners. Basic semen parameters were similar for all subgroups, and no correlation between sexual experience and WBC counts in semen was found. A man could harbour one to nine different bacteria in his semen; the total concentration of bacteria ranged from 2.3 to 7.3 log₁₀ CFU/mL of semen. Lower total bacterial concentration and lower bacterial diversity was observed in men without sexual experience than in sexually experienced men (p < 0.05), with significant positive correlation between these two parameters (r = 0.54; p < 0.0001). In conclusion, the sexual debut is associated with the enrichment of seminal microbiota but not with the influx of WBC or changes in basic seminal parameters.