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.

Reproductive microbiome and cytokine profiles associated with fertility outcomes of postpartum beef cows

Shifts from commensal bacteria (for example, Lactobacillus in the phylum Firmicutes) within the reproductive tract have been associated with changes in local reproductive immune responses and decreased fertility in humans. The objective of this study was to characterize the microbiome and cytokine concentrations before artificial insemination (AI) in vaginal and uterine flushes from postpartum beef cows. Twenty Bos indicus-influenced beef cows (approximately 60 d postpartum and free of reproductive, health, or physical issues) were enrolled. The B. indicus prostaglandin (PG) 5-d + controlled intervaginal drug-releasing estrus synchronization protocol was initiated on day -8 of the study with timed AI on d0. Blood samples were collected on days -3, -1, and 28 via coccygeal venipuncture. Vaginal and uterine flushes were collected on days -3 and -1. Based on days 28 pregnancy status determined by transrectal ultrasonography, cows were identified as either Open (n = 13) or Pregnant (n = 7). Bacterial community analyses were conducted targeting the V4 hypervariable region of the 16S rRNA gene. Cytokine analyses were performed using the RayBiotech Quantibody Bovine Cytokine Array Q1 and MyBioSource ELISA kits per the manufacturer's instructions. Statistical analyses for bacteria relative abundance were conducted using PROC NPAR1WAY and for cytokine concentrations using PROC GLM in SAS 9.4. Uterine concentrations of interferon γ, interleukin (IL)1α, and IL21 were greater in Open than in Pregnant cows (P < 0.05). Regardless of pregnancy status, uterine IL13 increased from days -3 to -1 (9.76 vs. 39.48 ± 9.28 pg/mL, respectively; P < 0.05). Uterine relative abundance of the phylum Firmicutes decreased from days -3 to -1 in Open cows (60.4% ± 0.9% vs. 48.5% ± 3.2%; P = 0.004). In Open cows, the genus Blautia decreased in relative abundance within the uterus from days -3 to -1 (2.1% ± 0.2% vs. 0.9% ± 0.1%; P = 0.002). Uterine relative abundance of the phylum Tenericutes increased from days -3 to -1 in Pregnant cows (1.0% ± 0.1% vs. 7.6% ± 4.1%; P = 0.002). In Pregnant cows, the genus Ureaplasma tended to increase within the uterus from days -3 to -1 (0.08% ± 0.06% vs. 7.3% ± 4.1%; P = 0.054). These findings suggest a distinct difference in the reproductive microbiome and cytokine profiles before AI for resulting Open vs. Pregnant cows.

Characterization of boar semen microbiome and association with sperm quality parameters

Elevated levels of bacteria within fresh extended boar semen are associated with decreased sperm longevity, therefore reducing the fertility of a semen dose. The objective of this study was to characterize the bacterial communities using 16S rRNA sequencing in freshly extended boar semen samples and relate the prevalence and diversity of the microbial population to sperm quality parameters 1) between studs, 2) between pooled and single-sire doses, and 3) over a 5-day period. Eight single-sire (n = 4 per stud) and eight pooled (n = 4 per stud) non-frozen extended semen doses were obtained from two boar studs (A and B). Pooled doses were the composite of the boar's ejaculates used in single-sire doses. Doses were subsampled for 5 d post-collection. Ten negative controls of each pooled dose (n = 2) and single-sire dose (n = 8) remained sealed until the last day. Microbiome analysis was achieved by examining the V4 hypervariable region of the 16S rRNA gene of flash-frozen samples. Two evaluators determined the average sperm motility and agglutination (0: no adhesion to 3: >50% adhesion) by averaging their estimates together at 10 random locations per slide. Stud A had greater sperm agglutination (1.6 vs. 1.0 ± 0.1; P < 0.01) than stud B. Sperm motility decreased over the 5-day period (P < 0.01) and tended (P = 0.09) to be greater in stud B than A (67.4% vs. 61.5% ± 0.02%). Compared with stud A, stud B had a greater relative abundance of Proteobacteria (60.0% vs. 47.2% ± 1.5%; P < 0.01) and a lower relative abundance of Firmicutes (22.5% vs. 31.9% ± 1.4%; P < 0.01). Moreover, stud A had a greater relative abundance of Bacteroidetes (6.3% vs. 5.3% ± 0.4%; P < 0.01) and Actinobacteria (11.5% vs. 10.1% ± 0.5%; P = 0.05) than stud B. Differences were found in alpha diversity for both Chao1 (P < 0.01) and Shannon (P < 0.01) diversity indexes among days 2, 3, 4, and 5 post-collection to day 1. For beta diversity, unweighted UniFrac metric on days 2, 3, 4, and 5 post-collection differed from those on day 1 (P < 0.01). There were significant correlations between sperm motility and relative abundance of Prevotella (r = -0.29), Ruminococcus (r = -0.24), and Bacteroides (r = -0.32). Additionally, there were significant correlations between sperm motility and Chao1 (r = -0.50) and Shannon's index (r = -0.36). These results demonstrate that differences in bacterial communities over time and between boar studs can be associated with variation in sperm quality.

PSIII-14 Reproductive Microbiome and Cytokine Profiles of Postpartum Beef Cows in Relation to Fertility

Shifts in commensal bacteria (i.e., Firmicutes) in the human microbiome are associated with compromised fertility. The objectives of this study were to characterize 1) the reproductive microbiome and 2) the cytokine concentrations prior to artificial insemination (AI) in vaginal and uterine flushes from postpartum beef cows. Twenty Bos indicus-influenced beef cows (~60 days postpartum and free of health issues) were weighed, body condition scored (BCS) then subjected to the Bee Synch II synchronization protocol on d-8 and timed AI on d0. Blood samples were collected on d-3, -1, 0, and 28. Vaginal and uterine flushes were collected on d-3 and d-1. On d28, pregnancy was determined by transrectal ultrasonography (Open, n=13 and Pregnant, n=7). Bacterial community analyses were conducted targeting the V4 hypervariable region of the 16S rRNA gene. Cytokine analyses were conducted using the RayBiotech Quantibody® Bovine Cytokine Array Q1 kit per manufacturer's instructions. Weight, BCS, and vaginal bacterial communities by phyla were not different (P &gt;0.05). In open cows, the uterine relative abundance of Firmicutes decreased between d-3 and -1 (60.4% ± 0.9% vs. 48.5% ± 3.2%, respectively; P&lt; 0.05). In pregnant cows, the uterine relative abundance of Tenericutes significantly increased between d-3 and -1 (1.0% ± 0.1% vs. 7.6% ± 4.1%, respectively; P&lt; 0.05). Additionally, the genus Ureaplasma tended to increase in relative abundance from d-3 to -1 (0.1% ± 0.1% vs. 7.3% ± 4.9%, respectively; P=0.06). Uterine concentrations of Interferon (IFN)-γ, Interleukin (IL)-1α and IL-21 were greater in open females compared to pregnant. Vaginal concentrations for IFN-α and chemokine ligand (CXCL)-10 were greater in open females compared to pregnant. Regardless of treatment, IL-13 increased from d-3 to d-1. These results suggest a distinct difference in the uterine microbiome and cytokine profiles prior to AI for resulting pregnant and open cows.

PSV-B-16 Correlation between Plasma, Uterine, and Vaginal Cytokine Concentrations in Postpartum Beef Cows Prior to Artificial Insemination

Cytokines have a vital role in reproductive immune environment during the postpartum period. Previous data evaluated uterine and vaginal cytokine concentrations prior to insemination; however, was unable to correlate these data with plasma cytokine concentrations. The objective of this study was to determine relationships between uterine, vaginal, and plasma pro- and anti-inflammatory cytokine concentrations in postpartum beef cows prior to timed artificial insemination (TAI). Bos indicus-influenced beef cows (n=20) free of any physical, health or reproductive-related issues were subjected to the Bee Synch II protocol 8 days prior (d-8) to TAI (d0). Uterine and vaginal flushes and blood were collected on d-3 and d-1. Pregnancy was determined by transrectal ultrasonography on d28 (Pregnant, n=7; Open, n=13). Using the RayBiotech Quantibody Bovine Cytokine Array 1 the following cytokines concentrations were determined: interferon (IFN)-α, IFN-γ, interleukin (IL)-13, IL-1α, IL-1-F5, IL-21, tumor necrosis factor (TNF)-α, chemokine ligand (CXCL)-9, CXCL-10, and chemokine ligand 4 (CCL4). Concentration data were analyzed using PROC GLM and correlations using Pearson correlation in SAS. For plasma samples, 8 pro-inflammatory cytokines (IFN-α, IFN-γ, IL-13, IL-1α, IL-1-F5, IL-21, CXCL-9, and TNF-α) had greater (P&lt; 0.05) concentrations in open cows compared with pregnant cows. For uterine flushes, 3 pro-inflammatory cytokines (IFN-γ, IL-1α, and IL-21) had greater (P&lt; 0.05) concentrations in open cows compared with pregnant cows. For vaginal flushes, IFN-α concentrations were greater (P&lt; 0.05) in open cows, while CXCL-10 concentrations were greater in pregnant cows. There were no significant correlations between plasma and uterine or vaginal samples (P&gt;0.05). Interestingly, for open cows there were correlations for IFN-α (r=0.46; P=0.02), IFN-γ (r=0.58; P=0.002), and IL-21 (r=0.54; P=0.004) between uterine and vaginal samples; however, no correlations were observed for pregnant cows. These results suggest a greater abundance of pro-inflammatory cytokines within the uterus, vagina, and in peripheral circulation for resulting open cows prior to TAI.

PSI-2 Analysis of Boar Semen Microbiome and Sperm Quality Parameters

Bacterial contamination of non-frozen extended boar semen has been associated with a decrease in sperm viability and longevity. The objective of this study was to analyze the microbiome of extended boar semen and sperm quality parameters 1) between studs 2) over time and 3) between pooled and single-sire doses. Sixteen pooled (n=4 per stud) and single-sire (n=4 per stud) boar semen doses (80mL) were obtained from two studs (A vs. B). Pooled doses were the composite of boars in single-sire doses. Doses were stored at 16°C and subsampled 16mL daily for five days post-collection. Each day, 5mL were flash frozen and stored at -80°C for bacterial analysis targeting the V4 hypervariable region of the 16S rRNA gene. The remaining 11mL were used to assess sperm progressive motility and agglutination (0: no adhesion to 3: &gt;50% adhesion) by two evaluators with 10 visual estimates per sample. Negative controls of each pooled (n=2 per stud) and single-sire (n=4 per stud) dose remained unopened until day 5. Statistical analyses were conducted using GLM procedure in SAS. Sperm agglutination was greater in stud A than B (1.6 vs. 1.0 ± 0.1, respectively; P&lt; 0.01). Sperm motility tended (P=0.09) to be greater in stud B than A doses (67.4% vs. 61.5% ± 0.02%, respectively), and decreased over time (P&lt; 0.01). Stud B had a greater relative abundance of Proteobacteria (60.0% vs. 47.2% ± 1.5%, respectively; P&lt; 0.01) and lower abundance of Firmicutes (22.5% vs. 31.9% ± 1.4%, respectively; P&lt; 0.01) compared to stud A. Bacterial load did not differ by stud or dose type but increased from day 1 to 3 (P&lt; 0.01). Bacterial load between days 3, 4, and 5 post-collection was not different from the negative control. Results indicate differences in the microbiome between boar studs and its influence on semen over time.