An artificial intelligence approach of feature engineering and ensemble methods depicts the rumen microbiome contribution to feed efficiency in dairy cows.

Genetic selection has remarkably helped U.S. dairy farms to decrease their carbon footprint by more than doubling milk production per cow over time. Despite the environmental and economic benefits of improved feed and milk production efficiency, there is a critical need to explore phenotypical variance for feed utilization to advance the long-term sustainability of dairy farms. Feed is a major expense in dairy operations, and their enteric fermentation is a major source of greenhouse gases in agriculture. The challenges to expanding the phenotypic database, especially for feed efficiency predictions, and the lack of understanding of its drivers limit its utilization. Herein, we leveraged an artificial intelligence approach with feature engineering and ensemble methods to explore the predictive power of the rumen microbiome for feed and milk production efficiency traits, as rumen microbes play a central role in physiological responses in dairy cows. The novel ensemble method allowed to further identify key microbes linked to the efficiency measures. We used a population of 454 genotyped Holstein cows in the U.S. and Canada with individually measured feed and milk production efficiency phenotypes. The study underscored that the rumen microbiome is a major driver of residual feed intake (RFI), the most robust feed efficiency measure evaluated in the study, accounting for 36% of its variation. Further analyses showed that several alpha-diversity metrics were lower in more feed-efficient cows. For RFI, [Ruminococcus] gauvreauii group was the only genus positively associated with an improved feed efficiency status while seven other taxa were associated with inefficiency. The study also highlights that the rumen microbiome is pivotal for the unexplained variance in milk fat and protein production efficiency. Estimation of the carbon footprint of these cows shows that selection for better RFI could reduce up to 5 kg of diet consumed per cow daily, potentially reducing up to 37.5% of CH4. These findings shed light that the integration of artificial intelligence approaches, microbiology, and ruminant nutrition can be a path to further advance our understanding of the rumen microbiome on nutrient requirements and lactation performance of dairy cows to support the long-term sustainability of the dairy community.

Host and rumen microbiome contributions to feed efficiency traits in Holstein cows.

It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.

Reproduction in the era of genomics and automation.

Much progress has been made in the reproductive efficiency of lactating dairy cows across the USA in the past 20years. The standardisation of evaluation of reproductive efficiency, particularly with greater focus on metrics with lesser momentum and less lag-time such as 21-day pregnancy rates (21-day PR), and the recognition that subpar reproductive efficiency negatively impacted profitability were major drivers for the changes that resulted in such progress. Once it became evident that the genetic selection of cattle for milk yield regardless of fertility traits was associated with reduced fertility, geneticists raced to identify fertility traits that could be incorporated in genetic selection programs with the hopes of improving fertility of lactating cows. Concurrently, reproductive physiologists developed ovulation synchronisation protocols such that after sequential treatment with exogenous hormones, cows could be inseminated at fixed time and without detection of oestrus and still achieve acceptable pregnancy per service. These genetic and reproductive management innovations, concurrently with improved husbandry and nutrition of periparturient cows, quickly started to move reproductive efficiency of lactating dairy cows to an upward trend that continues today. Automation has been adopted in Israel and European countries for decades, but only recently have these automated systems been more widely adopted in the USA. The selection of dairy cattle based on genetic indexes that result in positive fertility traits (e.g. daughter pregnancy rate) is positively associated with follicular growth, resumption of ovarian cycles postpartum, body condition score and insulin-like growth factor 1 concentration postpartum, and intensity of oestrus. Collectively, these positive physiological characteristics result in improved reproductive performance. Through the use of automated monitoring devices (AMD), it is possible to identify cows that resume cyclicity sooner after calving and have more intense oestrus postpartum, which are generally cows that have a more successful periparturient period. Recent experiments have demonstrated that it may be possible to adopt targeted reproductive management, utilising ovulation synchronisation protocols for cows that do not have intense oestrus postpartum and relying more heavily on insemination at AMD-detected oestrus for cows that display an intense oestrus postpartum. This strategy is likely to result in tailored hormonal therapy that will be better accepted by the public, will increase the reliance on oestrus for insemination, will improve comfort and reduce labour by reducing the number of injections cows receive in a lactation, and will allow for faster decisions about cows that should not be eligible for insemination.

Sequencing and characterization of Helcococcus ovis: a comprehensive comparative genomic analysis of virulence.

BACKGROUND: Helcococcus ovis (H. ovis) is an emerging bacterial pathogen that commonly causes opportunistic respiratory, mammary, and uterine infections across mammalian hosts. This study applied long- and short-read whole genome sequencing technologies to identify virulence factors in five H. ovis isolates with low, medium, and high virulence phenotypes. RESULTS: The resulting assemblies contained one circular chromosome ranging from 1,744,566 to 1,850,083 bp in length and had a mean GC content of 27.6%. Phylogenetic and nucleotide identity analyses found low virulence strain KG38 to be part of a clade that forms an outgroup apart from the rest of the H. ovis taxon. Assembling the first complete genomes of the species revealed major genomic rearrangements in KG38. One to six prophage regions were identified in each genome. A novel pathogenicity island was found exclusively in the two high virulence strains (KG37 and KG104), along with two hypothetical transmembrane proteins designated as putative VFs. Finally, three zinc ABC transporters and three Type-II/IV secretion systems were identified as possible virulence determinants in this species. The low virulence strain KG38 has fewer intact paralogs of these operons in its genome compared to the higher virulence isolates, which strongly suggests a role in virulence. This strain is also missing four putative virulence factors (VFs) found in other isolates associated with adherence (collagen adhesin precursor), immune evasion (choline-binding protein A and a PspA-like hypothetical protein) and cell wall synthesis (glycerol-3-phosphate cytidylyltransferase). CONCLUSIONS: In this study, we assembled reference-quality complete genomes for five H. ovis strains to identify putative virulence factors. Phylogenetic analyses of H. ovis isolates revealed the presence of a clade representing a potentially novel species within the genus Helcococcus. A novel pathogenicity island and two hypothetical transmembrane proteins were found exclusively in high-virulence strains. The identification of Zinc ABC transporters and Type-II/IV secretion systems as possible virulence determinants, along with the differences in operon content between the low and high virulence isolates, strongly suggests they also play a role in the bacterium's pathogenicity. Taken together, these findings are a valuable first step toward deciphering the pathogenesis of H. ovis infections.

Targeted reproductive management for lactating Holstein cows: Reducing the reliance on exogenous reproductive hormones.

Adoption of automated monitoring devices (AMD) affords the opportunity to tailor reproductive management according to the cow's needs. We hypothesized that a targeted reproductive management (TRM) would reduce the use of reproductive hormones while increasing the percentage of cows pregnant 305 d in milk (DIM). Holstein cows from 2 herds (n = 1,930) were fitted with an AMD at 251.0 ± 0.4 d of gestation. Early-postpartum estrus characteristics (EPEC; intense estrus = heat index ≥70; 0 = minimum, 100 = maximum) of multiparous cows were evaluated at 40 (herd 1) or 41 (herd 2) DIM and EPEC of primiparous cows were evaluated at 54 (herd 1) or 55 (herd 2) DIM. Control cows received the first artificial insemination at fixed time (TAI; primiparous, herd 1 = 82 and herd 2 = 83 DIM; multiparous, herd 1 = 68 and herd 2 = 69 DIM) following the Double-Ovsynch (DOV) protocol. Cows enrolled in the TRM treatment were managed as follows: (1) cows with at least one intense estrus were inseminated upon AMD detected estrus for 42 d and, if not inseminated, were enrolled in the DOV protocol; and (2) cows without an intense estrus were enrolled in the DOV protocol at the same time as cows in the control treatment. Control cows were re-inseminated based on visual or patch aided detection of estrus, whereas TRM cows were re-inseminated as described for control cows with the aid of the AMD. Cows received a GnRH injection 27 ± 3 d after insemination and, if diagnosed as nonpregnant, completed the 5-d Cosynch protocol and received TAI 35 ± 3 d after insemination. Among cows in the TRM treatment, 55.8 and 42.9% of primiparous and multiparous cows, respectively, received the first insemination in spontaneous estrus. The interaction between treatment and parity affected pregnancy 67 d after the first AI (primiparous: control = 37.6%, TRM = 27.4%; multiparous: control = 41.0%, TRM = 44.7%). The TRM treatment increased re-insemination in estrus (control = 48.3%, TRM = 70.5%). Pregnancy 67 d after re-inseminations tended to be affected by the interaction between treatment and EPEC (no intense estrus: control = 25.3%, TRM = 32.0%; intense estrus: control = 32.9%, TRM = 32.2%). The interaction between treatment and EPEC affected pregnancy by 305 DIM (no intense estrus: control = 80.8%, TRM = 88.2%; intense estrus: control = 87.1%, TRM = 86.1%). Treatment did not affect the number of reproductive hormone treatments among cows that had not had an intense estrus (control = 10.5 ± 0.3, TRM = 9.1 ± 0.2 treatments/cow), but cows in the TRM treatment that had an intense estrus received fewer reproductive hormone treatments than cows in the control treatment (2.0 ± 0.1 vs. 9.6 ± 0.2 treatments/cow). Selecting multiparous cows for first AI in estrus based on EPEC reduced the use of reproductive hormones without impairing the likelihood of pregnancy to first AI. The use of AMD for re-insemination expedited the establishment of pregnancy among cows that did not display an intense estrus early postpartum.

Establishing Galleria mellonella as an invertebrate model for the emerging multi-host pathogen Helcococcus ovis.

Helcococcus ovis (H. ovis) can cause disease in a broad range of animal hosts, including humans, and has been described as an emerging bacterial pathogen in bovine metritis, mastitis, and endocarditis. In this study, we developed an infection model that showed H. ovis can proliferate in the hemolymph and induce dose-dependent mortality in the invertebrate model organism Galleria mellonella (G. mellonella). We applied the model and identified H. ovis isolates with attenuated virulence originating from the uterus of a healthy post-partum dairy cow (KG38) and hypervirulent isolates (KG37, KG106) originating from the uterus of cows with metritis. Medium virulence isolates were also isolated (KG36, KG104) from the uterus of cows with metritis. A major advantage of this model is that a clear differentiation in induced mortality between H. ovis isolates was detected in just 48 h, resulting in an effective infection model able to identify virulence differences between H. ovis isolates with a short turnaround time. Histopathology showed G. mellonella employs hemocyte-mediated immune responses to H. ovis infection, which are analogous to the innate immune response in cows. In summary, G. mellonella can be used as an invertebrate infection model for the emerging multi-host pathogen Helcococcus ovis.

Genetic analysis of fetal loss in Holstein cattle.

Pregnancy loss is recognized as one of the major factors contributing to poor reproductive performance in dairy cattle. Here, we performed a comprehensive genetic analysis of fetal loss, defined as a pregnancy loss that occurs after detection of a viable embryo around 42 d of gestation. The objectives of this study were to reveal (1) whether fetal loss is heritable and, hence, whether it will respond to selection, and (2) to what extent current fertility traits, such as daughter pregnancy rate, are associated with fetal loss. Data consisted of 59,308 confirmed pregnancy or fetal loss records distributed across nulliparous heifers and primiparous and multiparous cows. We defined fetal loss as a binary trait (yes vs. no) or as an ordinal trait (pregnancy maintenance, early fetal loss ≤150 d of gestation, and late fetal loss >150 d of gestation), and we assessed both linear and threshold models. Heritability estimates for fetal loss ranged from 1 to 18%, depending upon parity, trait definition, and statistical model used. Heritability estimates were greater for lactating cows than for nonlactating nulliparous heifers. Threshold models were able to capture more additive genetic variance and, thus, yielded higher heritability estimates than linear models. Notably, fetal loss traits were highly genetically correlated with each other but only weakly correlated with current fertility traits included in the national genetic evaluation. Overall, our study provides evidence that fetal loss is heritable enough to make genetic selection for reducing fetal loss and improving pregnancy maintenance feasible. In addition, our results suggest that fetal loss is largely independent from current traits used to select for cow fertility, and thus current breeding efforts have unfortunately little effect on reducing the incidence of fetal loss.

Validation of a fully automated chemiluminescent immunoassay for cattle serum and plasma progesterone measurement.

Introduction: Monitoring circulating progesterone concentration ([P4]) is an important component of basic and applied reproduction research and clinical settings. IMMULITE® 2000 XPi (Siemens Healthineers, Cary, NC) is a newly upgraded fully automated immunoassay system marketed for human use to measure concentrations of different measurands including P4. Objectives: Our objective was therefore to characterize the analytical performance of the IMMULITE® 2000 XPi P4 immunoassay (IPI) across the reportable range in serum and plasma of cattle. Methods: The IPI validation protocols included characterization of the method linearity, within-run, and between-run precision through calculation of the coefficient of variation (CV). The method accuracy was assessed through the calculation of the spiking-recovery (SR) bias across the reportable range (0.2-40.0 ng/mL). Passing-Bablok regression and Bland-Altman plots were used to determine the interlaboratory bias for two laboratories. Three types of observed total error (TEo) were calculated based on the considered type of bias, TEoSR (spiking-recovery), TEoRB (range-based bias), and TEoAB (average-based bias). Results: The IPI was linearly related to the true value (R 2 = 0.997) across the reportable range. The within-run and between-run precision (CV%) of the IPI for both serum and plasma [P4] of clinical relevance (1, 2, 5, and 10 ng/mL) were <5 and <10%, respectively. The TEo reported here for serum and plasma at [P4] of 1 and 5 ng/mL was ~20 and 25%, respectively. Of interest, the three types of TEo were relatively similar regardless of the considered bias. Conclusions: We concluded that the automated IPI provides a precise, accurate, reliable, and safe method for measuring [P4] in both serum and plasma of cattle. Consistent with the manufacturer's recommendations, the serum matrix is more accurate than plasma.

Genes and pathways associated with pregnancy loss in dairy cattle.

Pregnancy loss directly impairs reproductive performance in dairy cattle. Here, we investigated genetic factors associated with pregnancy loss following detection of a viable embryo around 42 days of gestation. The objectives of this study were to perform whole-genome scans and subsequent gene-set analyses for identifying candidate genes, functional gene-sets and gene signaling pathways implicated in pregnancy loss in US Holstein cows. Data consisted of about 58,000 pregnancy/abortion records distributed over nulliparous, primiparous, and multiparous cows. Threshold models were used to assess the binary response of pregnancy loss. Whole-genome scans identified at least seven genomic regions on BTA2, BTA10, BTA14, BTA16, BTA21, BTA24 and BTA29 associated with pregnancy loss in heifers and lactating cows. These regions harbor several candidate genes that are directly implicated in pregnancy maintenance and fetal growth, such as CHST14, IGF1R, IGF2, PSEN2, SLC2A5 and WNT4. Moreover, the enrichment analysis revealed at least seven significantly enriched processes, containing genes associated with pregnancy loss, including calcium signaling, cell-cell attachment, cellular proliferation, fetal development, immunity, membrane permeability, and steroid metabolism. Additionally, the pathway analysis revealed a number of significant gene signaling pathways that regulate placental development and fetal growth, including Wnt, Hedgehog, Notch, MAPK, Hippo, mTOR and TGFß pathways. Overall, our findings contribute to a better understanding of the genetic and biological basis of pregnancy loss in dairy cattle and points out novel strategies for improving pregnancy maintenance via marker-assisted breeding.

Effect of estrous detection strategy on pregnancy outcomes of lactating Holstein cows receiving artificial insemination and embryo transfer.

Objectives of the current experiment were to evaluate the effects on reproductive performance of adding an automated estrous detection (AED) device to the reproductive management of Holstein cows. In addition, we aimed to determine whether the AED device would equally influence the reproductive performance of cows receiving artificial insemination and those receiving embryo transfer. Cows (n = 1,244) were observed daily for estrous detection by trained farm personnel with the aid of a tail head mounting device. Cows (n = 641) enrolled in the AED treatment were fitted with a neck-mounted automated estrus detection device, and cows enrolled in the control (CTRL, n = 603) treatment were not fitted with the AED device. Cows not detected in estrus by 54 ± 3 DIM received 1 injection of PGF2α, and those not detected in estrus by 68 ± 3 DIM were enrolled in an ovulation synchronization protocol. The hazard of first service tended to be affected by treatment [CTRL: referent, AED: adjusted hazard ratio (AHR) = 1.11, 95% confidence interval (CI) = 0.98, 1.25], and we determined a tendency for the AED treatment to reduce the proportion of cows receiving the first service at fixed time (39.7 ± 5.7 vs. 45.5 ± 5.8%). After the first service, high-producing cows enrolled in the AED treatment were more likely to be pregnant (19.1 ± 2.4 vs. 31.8 ± 3.0%), but no differences between the AED and CTRL treatments were observed among low-producing cows (24.9 ± 2.9 vs. 24.7 ± 2.9%). The hazard of second service was affected by treatment (CTRL: referent, AED: AHR = 1.22, 95% CI = 1.01, 1.47), and the AED treatment reduced the proportion of cows receiving the second service at fixed time compared with the CTRL treatment (15.7 ± 2.2 vs. 21.9 ± 2.5%). After the second service, the AED treatment tended to increase the proportion of cows pregnant (31.0 ± 3.0 vs. 24.9 ± 2.6%) and tended to reduce the proportion of cows that lost pregnancy between the first and second pregnancy exams (9.7 ± 3.3 vs. 16.7 ± 4.6%). The interaction between treatment and type of service did not affect percentage of cows pregnant and pregnancy loss to the first and second services. The hazard of pregnancy was affected by the interaction between treatment and milk yield, in that cows with above the median milk yield in the AED treatment became pregnant at a faster rate than CTRL cows, but no difference between treatments was observed among cows with milk yield below the median. Cows with above the median milk yield had shorter duration of estrus and were less likely to have activity peak at estrus ≥89 (0 = minimum, 100 = maximum). The current experiment suggests that AED devices may improve reproductive performance not only by increasing service rates but also by improving accuracy of estrous detection. According to the current experiment, high-producing cows may benefit most from the addition of AED devices to reproductive management.

Haematological and biochemical profiles during the puerperium in dairy cows - Short communication.

The main aim of the current study was to assess the prevalence of anaemia in Holstein dairy cows during the puerperium, and the haematological and biochemical profile of dairy cows with and without anaemia. The study was conducted in seven dairy herds in São Paulo State, Brazil. The evaluated sample comprised a total of 336 Holstein cows. Blood samples were collected at postpartum day 25 ± 3. Haematological analysis included white blood cell, red blood cell and platelet count, haematocrit value, haemoglobin concentration, mean corpuscular volume, mean corpuscular haemoglobin and mean corpuscular haemoglobin concentration. The biochemical profile encompassed cholesterol, non-esterified fatty acids, ß-hydroxybutyrate, albumin, globulin, fibrinogen, calcium and total bilirubin concentrations. The prevalence of anaemia was 16.3% in all herds, and this was not affected by clinical diseases, milk production, parity and body score condition. Moreover, anaemic cows had lower red blood cell count, haematocrit, haemoglobin, serum cholesterol and calcium concentrations and higher white blood cell and platelet counts, mean corpuscular haemoglobin, red cell distribution width, non-esterified fatty acids, ß-hydroxybutyrate, fibrinogen and globulin concentrations when compared with non-anaemic cows. The results indicate changes in energy balance and an inflammatory process in anaemic cows.

Effect of presynchronization with prostaglandin F2α before the 5-d timed AI protocol on ovarian responses and pregnancy in dairy heifers.

The objectives were the determine the effects of presynchronization with PGF2α 2 days before the 5-d timed artificial insemination (AI) protocol on ovarian responses and pregnancy per AI (P/AI) in dairy heifers. The hypothesis was that PGF2α would induce responsive heifers to be in proestrus at the initiation of the timed AI protocol, which was expected to improve ovulatory responses and P/AI. Weekly cohorts of Holstein heifers were blocked by age and, within block, randomly assigned to remain as control (CON; n = 255) or receive PGF2α on experiment Day -10 (PG; n = 255). All heifers were subjected to the 5-d timed AI protocol (Day -8, GnRH + intravaginal progesterone controlled internal drug release insert; Day -3, PGF2α and insert removal; Day -2, PGF2α; and Day 0, GnRH and AI). A subset of 22 blocks of heifers (n = 43) had their ovaries scanned by ultrasonography on experiment Days -8, -3, 0, and 2 and blood was sampled and analyzed for concentrations of progesterone on experiment Days -8, -7, -5, and -3. Pregnancy was diagnosed on experiment Days 32 and 60. On the day of the first GnRH of the timed AI protocol, PG heifers had smaller concentration of progesterone in plasma (CON = 4.5 ±â€¯0.5 vs. PG = 0.5 ±â€¯0.5 ng/mL), but larger follicular diameter (CON = 9.1 ±â€¯0.5 vs. PG = 11.0 ±â€¯0.5 mm), and a greater proportion of them had a follicle with at least 8.0 mm in diameter (CON = 61.9 vs. PG = 90.9%) than CON heifers, which resulted in increased ovulation to GnRH (CON = 19.0 vs. PG = 86.3%). Ovulation to the initial GnRH of the protocol increased as the concentration of progesterone in plasma decreased, from less than 20% when progesterone was greater than 5.0 ng/mL to more than 65% when progesterone was less than 1.0 ng/mL. More CON than PG heifers spontaenously ovulated before the day of timed AI. Detection of estrus on the day of timed AI did not differ between treatments (CON = 50.9 vs. PG = 46.6%), but P/AI on Days 32 (CON = 52.9 vs. PG = 61.1%) and 60 (CON = 49.0 vs. PG = 57.1%) after insemination tended to be greater for PG than CON; however, the benefit to presynchronization was observed in heifers inseminated with conventional (CON = 54.7 vs. PG = 67.4%), but not in heifers inseminated with sex-sorted semen (CON = 50.9 vs. PG = 52.8%). Administration of PGF2α 2 days before initiating the timed AI protocol induced heifers to be in proestrus, which enhanced ovulation to the initial GnRH and favored pregnancy per AI, particularly in heifers inseminated with conventional semen.

Genomic merit for reproductive traits. I: Estrous characteristics and fertility in Holstein heifers.

Genetic selection of dairy cattle in the United States has included reproductive traits (daughter pregnancy rate, DPR; heifer conception rate, HCR), which is believed to have partly contributed to halting the decline in reproductive performance. The objectives of the current study were to evaluate the association among genomic merit for DPR (GDPR) and HCR (GHCR) with estrous characteristics measured by an automated device. Holstein heifers (n = 1,005) were genotyped at 2 mo of age and were classified into quartiles (Q1 = lowest, Q4 = highest) according to the GDPR and GHCR values of the study population. At 10 to 11 mo of age, heifers were fitted with a collar that recorded activity and rumination and determined the occurrence of estrus according to changes in activity and rumination compared with the individual's baseline values. Estrous characteristics of spontaneous estruses (SPE) and PGF2α-synchronized estruses (PGSE) were recorded. Heifers had their estrous cycle synchronized with PGF2α and following detection of estrus received either artificial insemination or embryo transfer according to the herd's genetic selection program. Heifers in Q2 (17.7 ± 0.3 h) of GHCR tended to have longer SPE than heifers in Q4 (16.7 ± 0.3 h). The interaction between GDPR and GHCR was associated with the likelihood of activity peak (0 = no estrus, 100 = maximum activity) ≥80 at SPE because, among heifers in Q3 and Q4 of GHCR, those in Q1 of GDPR were less likely to have an activity peak ≥80. Heifers in Q1 and Q2 of GDPR had reduced hazard of estrus within 7 d of the first PGF2α treatment compared with heifers in Q4 of GDPR. Heifers in Q1 (16.1 ± 0.4 h) of GDPR had shorter PGSE than heifers in Q2 (17.6 ± 0.4 h) and Q4 (17.4 ± 0.4 h) and tended to have shorter PGSE than heifers in Q3 (17.4 ± 0.4 h). Rumination nadir on the day of PGSE was greater for heifers in Q1 (-30.1 ± 0.9 min/d) of GDPR compared with heifers in Q4 (-33.7 ± 0.9 min/d). Among heifers receiving only artificial insemination, those in Q1 of GHCR (adjusted hazard ratio = 0.65; 95% confidence interval = 0.48-0.88) became pregnant at a slower rate than heifers in Q4. Genomic merit for HCR was negatively associated with SPE but tended to be positively associated with hazard of pregnancy, whereas GDPR was positively associated with PGSE and hazard of estrus. Selection of dairy cattle for DPR and HCR may improve reproductive performance through different pathways, namely estrous characteristics and pregnancy establishment.

Genomic merit for reproductive traits. II: Physiological responses of Holstein heifers.

Fertility traits were recently added to the evaluation of genetic merit, allowing for the selection of Holstein cattle with improved reproductive performance. In the current study, we investigated the associations among genomic merit for daughter pregnancy rate (GDPR) and heifer conception rate (GHCR) and physiological responses during proestrus and diestrus. Holstein heifers (n = 99) were classified based on GDPR [high = 3.26 ± 0.76 (1.6 to 5.3), n = 48; low = -0.17 ± 0.75 (-1.8 to 1.0), n = 51] and GHCR [high = 2.75 ± 0.77 (1.5 to 5.5), n = 49; low = 0.06 ± 0.67 (-2.1 to 1.2), n = 50]. Heifers were fitted with an automated estrous detection device, were treated with PGF2α for synchronization of estrus, and received either artificial insemination or embryo transfer at detected estrus. Blood was sampled at the time of PGF2α treatment, within 24 h of the onset of estrus (d 0), and on d 7, 14, 19 ± 2, 28, and 35. Blood samples from all heifers were analyzed for concentrations of estradiol (d 0) and progesterone (on the day of PGF2α treatment and d 0, 7, and 14). Blood samples from heifers pregnant on d 38 ± 3 were analyzed for concentrations of progesterone (d 0, 7, 14, 19 ± 2, 28, and 35), pregnancy-specific protein B (d 19 ± 2, 28, and 35), and insulin-like growth factor 1 (d 0, 7, 14, 19 ± 2, 28, and 35). Expression of mRNA for interferon-stimulated gene 15 in peripheral leukocytes isolated from blood collected on d 19 ± 2 was determined. Ovaries were scanned by ultrasound daily from d 0 to 4 or until ovulation was detected. Heifers with low GHCR tended to be less likely to be detected in estrus (78.0 vs. 91.8%). Estradiol concentration on d 0 was greater for heifers with high GDPR (4.53 ± 0.23 vs. 3.79 ± 0.23 pg/mL). The ovulatory follicle was larger for heifers with high GDPR (16.28 ± 0.33 vs. 14.55 ± 0.35 mm), whereas heifers with high GHCR tended to have smaller ovulatory follicles (15.00 ± 0.31 vs. 15.83 ± 0.37 mm). Heifers with high GDPR tended to be more likely to ovulate within 96 h of the onset of estrus (90.7 vs. 75.0%). Among heifers pregnant on d 38 ± 3, GDPR and GHCR were not associated with mRNA expression for interferon-stimulated gene 15. Heifers with high GDPR had greater concentration of pregnancy-specific protein B from d 28 to 35 (3.03 ± 0.15 vs. 2.48 ± 0.1 ng/mL). Heifers with high GHCR tended to have greater insulin-like growth factor 1 concentration from d 7 to 35 (108.0 ± 3.2 vs. 97.7 ± 4.2 ng/mL). Our results suggest that selection for Holstein cattle for GDPR may have positive effects on reproductive performance through changes in ovarian follicle development and steroidogenesis. Although selection of Holstein cattle for GHCR may negatively affect estrous expression by affecting ovarian follicle growth, selection for GHCR may improve reproductive performance by altering the somatotropic axis.

Longitudinal metagenomic profiling of bovine milk to assess the impact of intramammary treatment using a third-generation cephalosporin.

Antimicrobial usage in food animals has a direct impact on human health, and approximately 80% of the antibiotics prescribed in the dairy industry are used to treat bovine mastitis. Here we provide a longitudinal description of the changes in the microbiome of milk that are associated with mastitis and antimicrobial therapy. Next-generation sequencing, 16 S rRNA gene quantitative real-time PCR, and aerobic culturing were applied to assess the effect of disease and antibiotic therapy on the milk microbiome. Cows diagnosed with clinical mastitis associated with Gram-negative pathogens or negative aerobic culture were randomly allocated into 5 days of Ceftiofur intramammary treatment or remained as untreated controls. Serial milk samples were collected from the affected quarter and the ipsilateral healthy quarter of the same animal. Milk from the mastitic quarter had a higher bacterial load and reduced microbial diversity compared to healthy milk. Resolution of the disease was accompanied by increases in diversity indexes and a decrease in pathogen relative abundance. Escherichia coli-associated mastitic milk samples had a remarkably distinct bacterial profile, dominated by Enterobacteriaceae, when compared to healthy milk. However, no differences were observed in culture-negative mastitis samples when compared to healthy milk. Antimicrobial treatment had no significant effect on clinical cure, bacteriological cure, pathogen clearance rate or bacterial load.

Biology of Preimplantation Conceptus at the Onset of Elongation in Dairy Cows.

The objectives of this study were to characterize changes in transcriptome of preimplantation conceptuses at the onset of elongation and associated changes in uterine histotroph composition and endometrial physiology. Lactating dairy cows (n = 160) had their ovulation synchronized by artificial insemination (study Day 0). On Day 15, uteri were flushed and endometrium tissue collected. Recovered conceptuses were classified based on morphology/length as ovoid (1-4 mm), tubular (5-19 mm), and filamentous (20-60 mm). Total RNA (n = 48) was subjected to transcriptome analysis. The uterine fluid (n = 30) was evaluated by mass spectrophotometry. Transcriptome analyses revealed drastic changes in the transition from ovoid to tubular and from tubular to filamentous. Differentially expressed genes were associated with cellular movement, cell-to-cell signaling, cellular assembly and organization, lipid metabolism, small molecule biochemistry, and molecular transport. Specific changes included reorganization of cytoskeleton and cell migration, arginine metabolism, growth factors signaling, and lipid metabolism. Functional analysis revealed fatty acids and peroxisome proliferator activated receptor gamma as upstream regulators of transcriptome changes. Expression of PPARG increased 17-fold during the onset of elongation and was highly correlated with genes involved in lipid metabolism. The histotroph was rich in amino acids, lipids, saccharides, and other intermediate metabolites, and important changes in composition occurred in the presence of a conceptus. Pregnancy had a major impact on the concentrations of important lipids in the uterine fluid and expression of genes in the endometrium. Collectively, conceptus elongation involves remarkable changes in transcriptome, composition of the histotroph, and endometrial physiology, which help elucidate important events in uterine and conceptus biology at the onset of elongation.