Endometrial and vaginal microbiome in donkeys with and without clinical endometritis

Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies

This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.

Advances in Donkey Disease Surveillance and Microbiome Characterization in China

This review article highlights the surveillance of bacterial, viral, and parasitic diseases in donkey populations in China. Key findings highlight significant threats from Equine herpesviruses (EHV-8 and EHV-1), which cause encephalitis, abortion, and respiratory distress. Several parasitic infections including Giardia duodenalis, Cryptosporidium spp., Enterocytozoon bieneusi, and Toxoplasma gondii present important zoonotic concerns across multiple regions of China. Additionally, this review synthesizes current knowledge on donkey microbiota across various body sites and examines their functional significance in health and disease. The complex relationship between the microbiota and host health represents a critical area of research in donkeys. Recent molecular advancements have enhanced our understanding of the diverse microbial ecosystems inhabiting different body sites in donkeys and their profound impact on health outcomes. As single-stomach herbivores, donkeys possess complex microbial communities throughout their digestive tracts that are essential for intestinal homeostasis and nutritional processing. Significant variations in microbiota composition exist across different intestinal segments, with the hindgut displaying greater richness and diversity compared to the foregut. Beyond the digestive system, distinct microbial profiles have been characterized across various body sites including the skin, oral cavity, reproductive tract, and body secretions such as milk. The health implications of donkey microbiota extend to critical areas including nutrition, immune function, and disease susceptibility. Research demonstrates how dietary interventions, environmental stressors, and physiological states significantly alter microbial communities, correlating with changes in inflammatory markers, antioxidant responses, and metabolic functions. Additionally, specific microbial signatures associated with conditions like endometritis and respiratory disease suggest the potential for microbiota-based diagnostics and therapeutics. The identification of antibiotic-resistant strains of Proteus mirabilis and Klebsiella pneumoniae in donkey meat highlights food safety concerns requiring enhanced monitoring systems and standardized safety protocols. These findings provide a foundation for improved donkey healthcare management, including targeted disease surveillance, microbiota-based interventions, and protective measures for those working with donkeys or consuming donkey-derived products.

Reproductive Disorders in Donkeys: Current Evidence and Update

Reproductive disorders in donkeys present a significant challenge to their health and welfare, impacting their roles in agriculture, conservation, and companionship. With the development of large-scale donkey farming in recent years, reproductive disorders have become a limiting factor for the expansion of the donkey population. In general, donkeys suffer from a similar array of diseases like horses, but little is known about the specificities of donkey reproductive disorders. This review synthesizes current knowledge on the pathogenesis, distribution, presentation, diagnosis, treatment, and prognosis of a diverse array of reproductive disorders affecting donkeys. There are similar infectious and non-infectious causes for infertility and pregnancy loss in jennies compared with mares, but a difference in disease susceptibility does exist, which may be attributed to genetic influence, pathogen specificity, the environment, and reproductive management practices. Diagnostic and treatment plans need to be tailored towards the particularities of donkey reproductive disorders to increase donkey populations and to enhance the standard of care for this species. Enhancing reproductive health in donkeys not only ensures their sustainable use but also promotes their welfare and longevity in diverse human-animal interactions.

Reproductive Tract Microbiota of Mares

The female reproductive tract microbiota is a complex community of microorganisms that might be crucial in maintaining a healthy reproductive environment. Imbalances in the bacterial community (dysbiosis) and the reduction of beneficial organisms and pathogen proliferation are associated with disease. Endometritis is a common cause of fertility problems in mares, and it is still challenging to diagnose and treat based on routine culture results of certain microorganisms. Although high-throughput sequencing studies provide helpful information regarding the composition of the reproductive tract microbiota in mares, there are still challenges in defining a "normal" microbiota. The primary objective of this literature review is to summarize the current knowledge regarding the microbiota present in the reproductive tract of mares, including the vagina, cervix, and uterus. The second objective is to describe the relevant factors that can impact the reproductive microbiota of mares, including the estrous cycle stage, the type of species (genera) investigated, season, and geographic location. The rationality of identifying the normal microbiota in the reproductive tract of a mare will likely aid in understanding the impact of the microbiota on the host's reproductive health and contribute to the treatment and prevention of equine sub and infertility issues.

Vaginal and Uterine Microbiota of Healthy Maiden Mares during Estrus

This descriptive cross-sectional study compared the microbiota of the uterus, vagina, clitoral fossa (CF), and perineal skin in healthy maiden mares during estrus. Twelve synchronized, healthy maiden mares (3-4 years old) from one single recipient mare herd were included. Microbial communities were characterized by amplifying the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform. The uterine and vaginal microbiota had significantly lower richness (Chao-1) than the skin (p < 0.05). The uterine and vagina bacterial composition was similar in presence and abundance and could be differentiated from that of the CF and perineal skin. The microbial composition (Jaccard and Bray-Curtis distances) significantly differed across body-site locations (p < 0.05), which explained approximately 14% and 19% of the variation in microbial composition for Jaccard and Bray-Curtis distances, respectively. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant taxa in the uterus and vagina, with higher proportions of Proteobacteria in the vaginal samples compared to the uterine samples. Streptococcaceae and Staphylococcaceae were present in high abundance in the uterine and vaginal samples, while Lactobacillaceae were not (<10%). We demonstrate that the uterine and vaginal microbiota of healthy maiden mares during estrus is similar but both distinct from that of the CF and perineal skin.

Isolation of lactic acid bacteria from the reproductive tract of mares as potentially beneficial strains to prevent equine endometritis

Endometritis, the inflammation of the endometrium, is the leading cause of subfertility in mares, and therefore responsible for major economic losses in the horse industry worldwide. It is generally treated with uterine lavages combined with ecbolic agents and local or systemic antibiotics. However, since antibiotic overuse has been associated with antimicrobial resistance in mares with persistent endometritis, new prevention and treatment alternatives are needed. One such alternative could be the use of probiotic lactic acid bacteria (LAB) isolated from the host. Thanks to their species specificity, resident microbiota may restore ecological equilibrium within the host, and therefore, help prevent infections and improve physiological functions. In the present study, 257 bacterial strains were isolated from 77 healthy mares, and 88.76% (n = 228) of them were phenotypically classified as LAB. Within this group, 65.79% were able to inhibit at least one strain from each of the genera that most commonly cause equine endometritis (Streptococcus equi subsp. zooepidemicus, Escherichia coli, and Staphylococcus spp.). Five strains (RCE11, RCE20, RCE91, RCE99, and RCE167) were selected on the basis of their beneficial properties: ability to autoaggregate and adhere to equine epithelial cells, high inhibition of and co-aggregation with all the bacteria isolated from clinical cases of endometritis evaluated, and negative co-inhibition between one another. All five were finally identified as Enterococcus spp., namely E. faecium (two strains), E. hirae (two strains), and E. gallinarum (one strain). Further studies will assess their safety and biotechnological potential for the design of a multi-strain probiotic formula to prevent equine endometritis.

Clinical Aspects of Bacterial Distribution and Antibiotic Resistance in the Reproductive System of Equids

Antibiotic administration is a standard therapeutic practice for the treatment of reproductive disorders of equids. This might lead to undesirable microbial imbalance and could favour the acquisition of antibiotic resistance. Therefore, it is imperative for clinicians to understand patterns of antibiotic resistance when considering and developing treatment regimes. Continued engagement of clinicians with novel alternative approaches to treat reproductive infections would be essential in order to address this rising threat within the One Health perspective. The objectives of the present review were to present the bacterial infections in the reproductive system of equids (horses, donkeys), to upraise the literature related to the issue of antibiotic resistance of bacteria causing these infections and to discuss the topic from a clinical perspective. Initially, the review summarised the various infections of the reproductive system of equids (genital system of females, genital system of males, mammary glands) and the causal bacteria, providing relevant information about horses and donkeys. Subsequently, the clinical therapeutics of these infections were presented, taking into account the significance of antibiotic resistance of bacteria as a limiting factor in treating the infections. Finally, approaches to circumvent antibiotic resistance in clinical settings were summarized. It was concluded that awareness regarding antibiotic resistance in equine reproductive medicine would increase, as we would recognise the multifaceted problem of resistance. Actions and initiatives within the One Health approach, minimizing the potential dissemination of resistant strains to humans and to the environment, with specific applications in medicine of equids should be appropriately instituted internationally.

Reproductive Microbiomes in Domestic Livestock: Insights Utilizing 16S rRNA Gene Amplicon Community Sequencing

Advancements in 16S rRNA gene amplicon community sequencing have vastly expanded our understanding of the reproductive microbiome and its role in fertility. In humans, Lactobacillus is the overwhelmingly dominant bacteria within reproductive tissues and is known to be commensal and an indicator of fertility in women and men. It is also known that Lactobacillus is not as largely abundant in the reproductive tissues of domestic livestock species. Thus, the objective of this review is to summarize the research to date on both female and male reproductive microbiomes in domestic livestock species (i.e., dairy cattle, beef cattle, swine, small ruminants, and horses). Having a comprehensive understanding of reproductive microbiota and its role in modulating physiological functions will aid in the development of management and therapeutic strategies to improve reproductive efficiency.