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The Role of Reproductive Microbiota in Animal Fertility and Reproductive...
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The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Reproduction".

Deadline for manuscript submissions: 1 October 2026 | Viewed by 5522

Editors

Dr. Aleksandar Cojkic

E-Mail Website
Guest Editor
Department of Clinical Sciences, Swedish University of Agricultural Science, Uppsala, Sweden
Interests: veterinary medicine; reproduction; reproductive biotechnology; bacteriology; antimicrobial resistance
Dr. Michal Ďuračka

E-Mail Website
Guest Editor
AgroBioTech Research Centre, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
Interests: male reproduction; sperm; andrology; antibiotics; bioactive compounds

Special Issue Information

Dear Colleagues,

Recent advances in microbiome research have highlighted the critical role of reproductive microbiota in animal fertility, reproductive health, and breeding programs. The reproductive microbiota, comprising the diverse microbial communities inhabiting the reproductive system, can significantly influence the quality of sperm, the development of embryos, and the overall success of reproduction. Understanding the interactions between host organisms and their microbiota provides insights that could enhance the success of reproduction, the prevention of diseases, and animal conservation efforts.

In both male and female reproductive systems, the balance of microbial populations plays an important role in maintaining reproductive health. Moreover, the microbiota of other organ systems, such as the gastrointestinal tract and mammary glands, may indirectly influence reproductive health via complex microbiome–host interactions. The incorporation of microbiota-based strategies into assisted reproductive technologies and conservation programs offers opportunities regarding the enhancement of reproductive outcomes in both domestic and wild animal populations.

By addressing these key issues, this Special Issue aims to provide a clearer understanding of how the reproductive microbiota influence fertility, reproductive health, and breeding practices. It is our hope that this Special Issue will stimulate further research and contribute to the development of innovative microbiota-based interventions that improve reproductive outcomes in both domestic and wild animals.

Dr. Aleksandar Cojkic
Dr. Michal Ďuračka
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • reproductive microbiota
  • animal fertility
  • male reproductive health
  • female reproductive tract
  • mammary gland microbiota
  • microbiome-host interactions
  • assisted reproductive technologies
  • animal conservation

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Published Papers (5 papers)

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Research

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16 pages, 12026 KB  
Article
Epimedii Folium Supplementation Improves Semen Quality, Hormonal Profile, and Immune Function by Modulating Gut Microbiota and Seminal Metabolites in Aged Boars
by Bin Ran, Shengxin Luo, Chenxi Zhou, Long Wen, Junjie Wu, Yunxiang Zhao, Xiaoping Zhu, Zhili Li and Mengjie Liu
Animals 2026, 16(12), 1833; https://doi.org/10.3390/ani16121833 - 14 Jun 2026
Viewed by 381
Abstract
This study aimed to investigate the effects of dietary Herba Epimedii Folium (HEF) supplementation on semen quality, reproductive hormones, immune parameters, gut microbiota, and seminal plasma metabolites in aged boars, and to evaluate its potential for extending their reproductive lifespan. A total of [...] Read more.
This study aimed to investigate the effects of dietary Herba Epimedii Folium (HEF) supplementation on semen quality, reproductive hormones, immune parameters, gut microbiota, and seminal plasma metabolites in aged boars, and to evaluate its potential for extending their reproductive lifespan. A total of 18 Bama boars (approximately 3 years of age) were randomly assigned to three groups (n = 6 per group). The control group received a basal diet, while the treatment groups were fed the basal diet supplemented with 3 g/kg or 5 g/kg of HEF for 8 weeks. The results showed that adding HEF to the diet of aged boars increased the motility and concentration of their sperm and reduced the proportion of abnormal sperm. Treatment with 3 g/kg HEF increased serum LH and IgG levels, whereas the 5 g/kg dose elevated IgA levels in both serum and seminal plasma, as well as IgG levels in seminal plasma. Furthermore, 16S rRNA sequencing revealed that dietary HEF supplementation reduced the relative abundance of Streptococcus and Oscillospiraceae UCG-002 in the gut of aged boars. PICRUSt2 analysis predicted that pathways involved in lysine biosynthesis, arginine and proline metabolism, glycine, serine and threonine metabolism, and amino acid-related enzymes were enriched in the HEF treatment group. Semen metabolite profiling showed that the HEF treatment enriched several key metabolites, including 5-hydroxytryptophan, acetylcarnitine, tretinoin, methyltestosterone, prostaglandin A3, and prostaglandin B2. Spearman correlation analysis revealed a negative association between Streptococcus abundance and sperm motility, whereas acetylcarnitine, 5-hydroxytryptophan, and prostaglandin A3 were positively associated with motility. Furthermore, 5-hydroxytryptophan levels were positively linked to both sperm concentration and serum LH. In summary, our study demonstrates that Epimedii Folium may enhance the semen quality of aged Bama boars by improving the intestinal microbiota and the metabolic profile of seminal plasma. These findings may offer a theoretical basis for optimizing reproduction and conserving germplasm resources in aged Bama miniature pigs. Full article
(This article belongs to the Special Issue The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health)
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21 pages, 4138 KB  
Article
Fecal Microbial Community Characteristics of Oula and Hu Sheep and Their Correlation with Semen Quality
by Lu Shao, Peidi Zhao, Jiaxun Dong, Xiuxiu Weng and Wanhong Li
Animals 2026, 16(6), 953; https://doi.org/10.3390/ani16060953 - 18 Mar 2026
Viewed by 513
Abstract
Semen quality and fecal microbial composition were compared between native Oula rams reared on the Qinghai–Tibet Plateau and Hu sheep rams introduced from lowland regions. Semen quality was analyzed in eight adult Oula rams and eight Hu rams, and fecal microbial composition was [...] Read more.
Semen quality and fecal microbial composition were compared between native Oula rams reared on the Qinghai–Tibet Plateau and Hu sheep rams introduced from lowland regions. Semen quality was analyzed in eight adult Oula rams and eight Hu rams, and fecal microbial composition was assessed via 16S rRNA sequencing. Results indicated that sperm acrosome integrity was significantly higher in Hu sheep than in Oula sheep (p < 0.001); other semen parameters showed no significant differences. Significant differences were also observed in fecal microbial communities between the two breeds. Compared with Hu sheep, Oula sheep exhibited higher microbial abundance and diversity at the phylum level, particularly Campylobacterota, Euryarchaeota, Planctomycetota, Verrucomicrobiota, Myxococcota, and Deferibacterota (p < 0.05). At the genus level, Oula sheep had significantly higher abundances of Treponema, Campylobacter, Methanobrevibacter, UCG-009, Family_XIII_AD3011_group, [Eubacterium]nodatum group, Candidatus Soleaferrea, Akkermansia, and unidentified_Ruminococcaceae (p < 0.05). Correlation analysis indicated associations between sheep semen quality and the top 30 abundant fecal microbial genera. Six genera showed significant positive correlations with acrosome integrity rate, and eight genera exhibited significant negative correlations (p < 0.05). Two genera were correlated positively with plasma membrane integrity rate (p < 0.05). Prevotellaceae_UCG-004 was positively correlated with sperm motility and Progressive Motility spermatozoa proportion (p < 0.05); Ruminococcus showed a significant positive correlation with sperm linear motility and a significant negative correlation with acrosome integrity rate (p < 0.05). These findings indicate that the microbial groups enriched in Oula sheep fecal samples and exhibiting negative correlations with acrosome integrity—including Ruminococcus, Treponema, Akkermansia, and Euryarchaeota—are associated with sperm quality through physiological adaptation mechanisms specific to high-altitude environments. Full article
(This article belongs to the Special Issue The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health)
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21 pages, 2852 KB  
Article
Bacterial and Fungal Dynamics of the Uterine Microbiota in Postpartum Beef Cows Supplemented with Grape Pomace
by Inga Merkelytė, Šarūnė Marašinskienė, Rasa Nainienė, Urtė Pelenė, Laura Šakarnytė and Artūras Šiukščius
Animals 2026, 16(5), 810; https://doi.org/10.3390/ani16050810 - 5 Mar 2026
Viewed by 892
Abstract
The bovine uterus, once considered sterile, is now recognized as a dynamic microbial ecosystem that undergoes substantial changes during the postpartum period and plays a critical role in reproductive health. This study investigated the composition and temporal dynamics of the uterine bacterial and [...] Read more.
The bovine uterus, once considered sterile, is now recognized as a dynamic microbial ecosystem that undergoes substantial changes during the postpartum period and plays a critical role in reproductive health. This study investigated the composition and temporal dynamics of the uterine bacterial and fungal microbiota in postpartum Angus cows and showed that dietary grape pomace bolus supplementation was associated with temporal shifts in microbial community composition, including changes in selected bacterial taxa and increased fungal community stability. A total of 19 cows were allocated to control (n = 10) or treatment groups (n = 9), with treated animals receiving slow-release grape pomace boluses administered every three weeks from 21 days prepartum until 60–70 days postpartum. Uterine lavage samples were collected during the first (days 4–12) and ninth (days 63–70) postpartum weeks and analyzed using amplicon-based sequencing targeting the bacterial 16S rRNA (V3–V4) region and the fungal ITS2 region. The uterine microbiota exhibited pronounced temporal changes, with Firmicutes predominating in the early postpartum period and an increased abundance of potentially pathogenic Fusobacteria and Bacteroidetes observed by week nine postpartum, particularly in control cows. Grape pomace supplementation was associated with a more favorable bacterial profile, including a reduced relative abundance of key uterine pathogens such as Fusobacterium necrophorum and Trueperella pyogenes. The uterine mycobiome was dominated by Ascomycota across all groups; however, supplemented cows showed greater fungal community stability and a lower prevalence of opportunistic genera, including Candida spp. In conclusion, dietary grape pomace supplementation may beneficially modulate both bacterial and fungal uterine microbiota during the postpartum period, suggesting its potential as a natural strategy to support uterine microbial homeostasis and reproductive health in beef cows. Full article
(This article belongs to the Special Issue The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health)
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22 pages, 1855 KB  
Article
Taxonomic Profile of Cultivable Microbiota from Adult Sheep Follicular Fluid and Its Effects on In Vitro Development of Prepubertal Lamb Oocytes
by Slavcho Mrenoshki, Letizia Temerario, Antonella Mastrorocco, Grazia Visci, Elisabetta Notario, Marinella Marzano, Nicola Antonio Martino, Daniela Mrenoshki, Giovanni Michele Lacalandra, Graziano Pesole and Maria Elena Dell’Aquila
Animals 2025, 15(13), 1951; https://doi.org/10.3390/ani15131951 - 2 Jul 2025
Viewed by 1388
Abstract
The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing [...] Read more.
The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing follicles and used for microbiota propagation. Bacterial pellets underwent 16S rRNA gene sequencing and targeted culturomics, whereas cell-free supernatants were used as supplements for the in vitro maturation (IVM) of slaughtered PLOs. For the first time, bacteria presence in adult sheep FF was detected, with the first report of Streptococcus infantarius subsp. infantarius (as a species) and Burkholderia cepacia (as a genus and species) in either animal or human FF. The short- and long-term effects of bacterial metabolites on PLO maturation and embryonic development were demonstrated. As short-term effects, the addition of FF microbiota metabolites did not affect the oocyte nuclear maturation and mitochondria distribution pattern, except in one of the examined supernatants, which reduced all quantitative bioenergetic/oxidative parameters. As long-term effects, one of them reduced the total cleavage rate after in vitro embryo culture (IVC). In conclusion, microbiota/bacteria are present in adult sheep FF and may influence reproductive outcomes in vitro. Future studies may reveal the beneficial in vitro effects using the microbiome from preovulatory follicles. Full article
(This article belongs to the Special Issue The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health)
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Review

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26 pages, 514 KB  
Review
The Equine Reproductive Microbiota: Composition, Dynamics, Dysbiosis, and Implications for Fertility in Mares and Stallions
by Urtė Pelenė, Artūras Šiukščius, Rasa Nainienė, Inga Merkelytė and Rūta Šveistienė
Animals 2026, 16(9), 1414; https://doi.org/10.3390/ani16091414 - 5 May 2026
Viewed by 1333
Abstract
The equine reproductive microbiota has emerged as an important factor influencing reproductive health and fertility in both mares and stallions. Traditionally, the equine uterus was considered sterile, and microbial presence was interpreted primarily in the context of infection. However, sequencing-based studies have demonstrated [...] Read more.
The equine reproductive microbiota has emerged as an important factor influencing reproductive health and fertility in both mares and stallions. Traditionally, the equine uterus was considered sterile, and microbial presence was interpreted primarily in the context of infection. However, sequencing-based studies have demonstrated that the reproductive tract, including the uterus and semen, contains detectable microbial communities or microbial DNA signatures, challenging this traditional paradigm. In mares, the vaginal microbiota is consistently dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, whereas the uterine environment represents a low-biomass niche in which interpretation is complicated by contamination risk and the inability of sequencing-based methods to distinguish viable from nonviable microorganisms. Culture-based studies consistently identify opportunistic pathogens such as Streptococcus equi subsp. zooepidemicus, Escherichia coli, and Pseudomonas aeruginosa in association with endometritis and persistent breeding-induced endometritis, while sequencing-based studies suggest broader community-level dysbiosis rather than simple pathogen presence. In stallions, semen is not sterile and commonly contains taxa such as Porphyromonas, Corynebacterium, Peptoniphilus, and other opportunistic bacteria that may influence sperm quality and microbial transmission to mares during breeding. However, most reported associations remain correlative, and direct longitudinal evidence for persistent stallion-to-mare microbial transmission is limited. This review synthesizes current evidence on microbial composition, hormonal influences, dysbiosis, and reproductive implications of the equine reproductive microbiota, integrating culture-based and sequencing-based findings while emphasizing methodological limitations associated with low-biomass samples. Improved understanding of these microbial ecosystems may support more evidence-based reproductive diagnostics and microbiome-informed fertility management in horses. Full article
(This article belongs to the Special Issue The Role of Reproductive Microbiota in Animal Fertility and Reproductive Health)
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