Study of vaginal microbiota of Holstein cows submitted to an estrus synchronization protocol with the use of intravaginal progesterone device

Uterine Disease in Dairy Cows: A Comprehensive Review Highlighting New Research Areas

Uterine disease is an intensely studied part of dairy cattle health management as it heavily affects many commercial dairy farms and has serious economic consequences. Forms of the disease, pathophysiology, pathogens involved and the effects of uterine disease on the health and performance of cows have already been well described by various authors. Lately, researchers' attention has shifted towards the healthy microbiome of the uterus and the vagina to put emphasis on prevention rather than treatment. This aligns with the growing demand to reduce the use of antibiotics or-whenever possible-replace them with alternative treatment options in farm animal medicine. This review provides a comprehensive summary of the last 20 years of uterine disease research and highlights promising new areas for future studies.

Description of the vaginal microbiota in nulliparous ewes during natural mating and pregnancy: preliminary signs of the male preputial microbiota modulation

The vaginal microbiota plays a key role in animals' health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams' prepuce were the same as in the ewes' vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram's preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes' vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe's reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.

Exploring the microbiome of two uterine sites in cows

Bacterial communities in the mammalian reproductive system can be rich and diverse, differing in structure and quantity depending on location. In addition, its microbiome is associated with the state of health of this tract and reproductive success. This study evaluated the microbiome composition of the uterine body (UB) and uterine horn mucosa (UH) samples using 16S rRNA sequencing of samples extracted from cows in the Amazon region. It was observed that four main phyla were shared between the uterine sites: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Linear discriminant analysis effect size and heat tree analysis showed that members of Lachnospiraceae (NK3A20 group) and Oscillospiraceae were significantly more abundant in the UB than in UH. In addition, there are more unique genera in the UB than in the UH. A higher bacterial load in UB than in UH is expected because of the exposure to external factors of UB. However, comparing the site's communities through beta diversity did not generate well-defined clustering. Thus, it can be attributed to the closeness of the sites, which would make the niches similar ecologically and microbiologically. Therefore, this research provides knowledge to understand biomarkers in the prior reproduction period.

Investigation of the vaginal microbiota of dairy cows through genetic sequencing of short (Illumina) and long (PacBio) reads and associations with gestational status

The vaginal microbiota has been shown to be important in local immune regulation and may play a role in reproduction and fertility. Next-generation sequencing (NGS) technologies have been used to characterize the bovine vaginal microbiota, mainly using short-read sequencing (Illumina). However, the main limitation of this technique is its inability to classify bacteria at the species level. The objective of this study was to characterize the bovine vaginal microbiota at the species level using long-read sequencing (PacBio) and to compare it with the results of short-read sequencing. In addition, the vaginal microbiota of cows that became pregnant after artificial insemination (AI) was compared with that of infertile animals. Thirteen Holstein cows had vaginal swabs collected prior to AI. DNA was extracted and subjected to Illumina and PacBio sequencing to characterize the V4 region and the entire 16S rRNA gene, respectively. PacBio sequencing yielded 366,509 reads that were assigned to 476 species from 27 phyla. However, none of the most abundant reads (>1%) could be classified at the species level. Illumina sequencing yielded more reads and consequently was able to detect a more observed species, but PacBio sequencing was able to detect more unique and rare species. The composition of the vaginal microbiota varies according to the sequencing method used, which might complicate the interpretation of results obtained in the majority of the current studies. The present study expands on the current knowledge of bovine microbiota, highlighting the need for further efforts to improve the current databanks.

Longitudinal Changes in Milk Microorganisms in the First Two Months of Lactation of Primiparous and Multiparous Cows

The present experiment was carried out to analyze the longitudinal changes in milk microorganisms. For this purpose, milk samples were collected from 12 healthy cows (n = 96; six primiparous cows and six multiparous cows) at eight different time points. The characteristics and variations in microbial composition were analyzed by 16S rRNA gene high-throughput sequencing. In the primiparous group, higher and more stable alpha diversity was observed in transitional and mature milk compared with the colostrum, with no significant difference in alpha diversity at each time point in the multiparous group. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota were the most dominant phyla, and Pseudomonas, UCG-005, Acinetobacter, Vibrio, Lactobacillus, Bacteroides, Serratia, Staphylococcus, and Glutamicibacter were the most dominant genera in both primiparous and multiparous cow milk. Some typically gut-associated microbes, such as Bacteroides, UCG-005, and Rikenellaceae_RC9_gut_group, etc., were enriched in the two groups. Biomarker taxa with the day in time (DIM) were identified by a random forest algorithm, with Staphylococcus showing the highest degree of interpretation, and the difference in milk microbiota between the two groups was mainly reflected in 0 d-15 d. Additionally, network analysis suggested that there were bacteria associated with the total protein content in milk. Collectively, our results disclosed the longitudinal changes in the milk microbiota of primiparous and multiparous cows, providing further evidence in dairy microbiology.

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.

Impact of oestrus synchronization devices on ewes vaginal microbiota and artificial insemination outcome

Introduction

The low pregnancy rate by artificial insemination in sheep represents a fundamental challenge for breeding programs. In this species, oestrus synchronization is carried out by manipulating hormonal regimens through the insertion of progestogen intravaginal devices. This reproductive strategy may alter the vaginal microbiota affecting the artificial insemination outcome.

Methods

In this study, we analyzed the vaginal microbiome of 94 vaginal swabs collected from 47 ewes with alternative treatments applied to the progesterone-releasing intravaginal devices (probiotic, maltodextrin, antibiotic and control), in two sample periods (before placing and after removing the devices). To our knowledge, this is the first study using nanopore-based metagenome sequencing for vaginal microbiome characterization in livestock.

Results

Our results revealed a significant lower abundance of the genera Oenococcus (Firmicutes) and Neisseria (Proteobacteria) in pregnant compared to non-pregnant ewes. We also detected a significant lower abundance of Campylobacter in the group of samples treated with the probiotic.

Discussion

Although the use of probiotics represents a promising practice to improve insemination results, the election of the suitable species and concentration requires further investigation. In addition, the use of progestogen in the synchronization devices seemed to increase the alpha-diversity and decrease the abundance of harmful microorganisms belonging to Gammaproteobacteria and Fusobacteriia classes, suggesting a beneficial effect of their use.

Reproductive Hormones Mediate Intestinal Microbiota Shifts during Estrus Synchronization in Grazing Simmental Cows

To study shifts in the intestinal microbiota during estrus synchronization in ruminants, we characterized the intestinal microbiota in grazing Simmental cows and the possible mechanism that mediates this shift. Fourteen postpartum Simmental beef cows were synchronized beginning on day 0 (D0) with a controlled internal release device (CIDR), and cloprostenol was injected on D9 when the CIDR was withdrawn. Synchronization ended with timed artificial insemination on D12. Serum and rectal samples harvested on D0, D9, and D12 were analyzed to assess the reproductive hormones and microbiota. Reproductive hormones in the serum of the host were measured using enzyme-linked immunosorbent assay. The microbiota was characterized using 16S rRNA sequencing of the V3−V4 hypervariable region, alpha diversity and beta diversity analyses (principal coordinate analysis, PCoA), cladogram of the linear discriminant analysis effect size (LEfSe) analysis, and microbiota function analysis. Levels of the reproductive hormones, except gonadotropin-releasing hormone (p > 0.05), shifted among D0, D9, and D12 (p < 0.05). Decreased community diversity (Chao1 and ACE) was observed on D12 compared with D0 (p < 0.05). The beta diversity (PCoA) of the microbiota shifted markedly among D0, D9, and D12 (p < 0.05). The LEfSe analysis revealed shifts in the intestinal microbiota communities among D0, D9, and D12 (p < 0.05 and LDA cutoff >3.0). The KEGG pathway analysis showed that carbohydrate metabolism, genetic information and processing, the excretory system, cellular processes and signaling, immune system diseases, and the metabolism were altered (p < 0.05). Reproductive hormones (especially estradiol) were correlated with the alpha diversity indices, beta diversity indices, and an abundance of biomarkers of the shifting intestinal microbiota (p < 0.05). In conclusion, the structure, composition, and function of the intestinal microbiota were shifted during estrus synchronization in a grazing Simmental cow model, and these shifts were mediated by reproductive hormones.

A Review of the Diversity of the Genital Tract Microbiome and Implications for Fertility of Cattle

Cattle have a genital microbiome that is established early in life, even before calving. Microbial influx into the reproductive system of cows, during calving or mating, is unavoidable and is likely to alter the commensal microflora composition. It is now well established that a commensal endometrial flora is largely responsible for the overall fertility of cows. These microbes are important for maintenance of structural integrity of the genital mucosal barrier, immunomodulation, and protection against pathogens. Further, the genital microbiome functions in the semiochemical communication between a male and female. An optimal balance between the abundance and diversity of the microbiome is essential to promote female genital tract health. Disruption of this balance leads to dysbiosis and genital diseases and perturbed fertility. As part of the global strategy of One World, One Health, there is a need to reduce antibiotic use in animals. This area of research has the potential to expand the knowledge about the nexus between the endometrial microbiome and fertility including being probiotic in different species.

Cows' reproductive performances and parity order influences the cervicovaginal fungal community

Fungi have already been described as etiological agents of reproductive diseases such as endometritis and infertility in cows. However, few studies have been developed to elucidate the entire cervicovaginal fungal communities in cows. Therefore, our study aimed to characterize the fungal community present in the cervix of cows with different reproductive performances. Cervicovaginal mucus was collected from 36 Angus breed cows (1.5-12 years old) on a commercial beef cattle ranch. Twenty-one cows had a history of infertility in the year prior to the collection, showing early return to estrus. Ten cows were sampled at 60-70 days postpartum being considered fertile cows. Additionally, five non-sexually active heifers were employed as control group. Ascomycota and Basidiomycota were the predominant fungal phyla in the analyzed animals. Diversity metrics of the cervicovaginal fungal community revealed statistical differences in the composition of the fungal community among infertile cows, fertile cows and non-sexually active heifers. In addition, the cervicovaginal fungal microbiota had significative increased richness and evenness in nulliparous cows and non-sexually active heifers, while in multiparous cows a decreased richness and evenness of the fungal microbiota were identified. These results provide an unprecedented understanding of the cervicovaginal fungal structure associated with infertility and parity order.

Bacterial communities from vagina of dairy healthy heifers and cows with impaired reproductive performance

Vaginal microenvironment plays a significant role in bovine fertility since its resident microorganisms interact with the host mucosa and constitutes the first barrier against ascending pathogens in the reproductive tract. In this study, the vaginal microbiome of healthy heifers (H) and cows with impaired reproductive performance, metritis complex (MT) or repeat breeders (RB), was assessed using a 16S rRNA gene sequencing approach. Analysis revealed that even though a vaginal microbiological guild (Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes, Fusobacteria and Actinobacteria) was shared among healthy heifers and cows with uterine disease; further analysis at genus level showed significant differences depending on the reproductive health status. The relative abundances of recognized uterine pathogens such as Bacteroidetes, Fusobacterium and Helcococcus were higher in MT when compared with H and RB; therefore, their presence in vagina can be considered as a risk factor for fertility. The present study describes for the first time, the composition of native bacterial communities in the vagina of cows undergoing the repeat breeding syndrome (RBS), and reports an association between this disease and the presence of Porphyromonas and unassigned genera of the Pasteurellaceae family. In addition, this work highlights the bacteria associated with a healthy vagina: genera from the families Lachnospiraceae, Rikenellaceae and the genera Acinetobacter, Bacillus, Oscillospira, CF231 and 5-7NS. Results highlighted herein, signify the potential of the evaluation of the bovine vaginal microbiome to future design therapeutic interventions to improve pregnancy rates however, further research is needed to elucidate the balance of bacterial species resulting in an optimal reproductive health.