Investigating relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using mediation analysis with structural equation modeling.

The rumen microbiome is crucial for converting feed into absorbable nutrients used for milk synthesis, and the efficiency of this process directly impacts the profitability and sustainability of the dairy industry. Recent studies have found that the rumen microbial composition explains part of the variation in feed efficiency traits, including dry matter intake, milk energy, and residual feed intake. The main goal of this study was to reveal relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using structural equation models. Our specific objectives were to (i) infer the mediation effects of the rumen microbiome on feed efficiency traits, (ii) estimate the direct and total heritability of feed efficiency traits, and (iii) calculate the direct and total breeding values of feed efficiency traits. Data consisted of dry matter intake, milk energy, and residual feed intake records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. We implemented structural equation models such that the host genome directly affects the phenotype (GP → P) and the rumen microbiome (GM → P), while the microbiome affects the phenotype (M → P), partially mediating the effect of the host genome on the phenotype (G → M → P). We found that 7 to 30% of microbes within the rumen microbial community had structural coefficients different from zero. We classified these microbes into 3 groups that could have different uses in dairy farming. Microbes with heritability <0.10 but significant causal effects on feed efficiency are attractive for external interventions. On the other hand, 2 groups of microbes with heritability ≥0.10, significant causal effects, and genetic covariances and causal effects with the same or opposite sign to feed efficiency are attractive for selective breeding, improving or decreasing the trait heritability and response to selection, respectively. In general, the inclusion of the different microbes in genomic models tends to decrease the trait heritability rather than increase it, ranging from -15% to +5%, depending on the microbial group and phenotypic trait. Our findings provide more understanding to target rumen microbes that can be manipulated, either through selection or management interventions, to improve feed efficiency traits.

Progesterone profiles in postpartum dairy cows with inflammatory disorders.

The objective of this prospective cohort study was to determine if progesterone (P4) profiles differed between dairy cows with or without inflammatory disorders early postpartum. A total of 708 cows from 2 commercial herds were enrolled 3 wk before parturition and examined for clinical health disorders (retained placenta, metritis, displaced abomasum, mastitis, or lameness) until 5 wk postpartum. Serum haptoglobin (Hp) was measured in blood at 2 and 6 (±2) DIM, metritis was assessed at 4, 8, 11, and 15 DIM, and purulent vaginal discharge and endometritis (≥6% polymorphonuclear cells in endometrial cytology sampled by cytobrush) were assessed at 35 ± 3 DIM. As Hp ≥0.8 g/L or endometritis were associated with ovarian dysfunction in previous studies, cows with serum Hp ≥0.8 g/L at either time point and endometritis, regardless of clinical disease, were classified as the cohort with inflammatory disorders (INFLAM; n = 139). Clinically healthy cows without difficult calving or twin birth, with Hp <0.8 g/L at both sampling times, without endometritis, and BCS ≥3.00 (1 to 5 scale) were classified as healthy (n = 133). Cows with only one of the 2 conditions (high Hp or endometritis) were excluded. Cohorts had serum P4 measured twice weekly from 35 to 70 (±3) DIM, and the first detected luteal phase (LP) during the sampling period was defined as the interval from onset of luteal activity (P4 increase to ≥1 ng/mL) until decline of P4 to <1 ng/mL. The odds of prolonged LP (≥21 d), average LP length, peak P4, and time to P4 decline (hazard rate) were analyzed using multivariable mixed logistic, linear, or Cox proportional hazard regression models including INFLAM status, parity, sampling day (when applicable), and herd as a random effect considering the covariates of season, milk yield at first DHIA test, and DIM at onset of cyclicity or LP length (when applicable). Cows with INFLAM had greater odds of prolonged LP (LSM ± SEM; 67% vs. 37% ± 7), greater average LP length (17 vs. 15 ± 2 d), lesser P4 at d 4 (4.6 vs. 5.5 ± 0.3 ng/mL) and d 7 (6.0 vs. 7.7 ± 0.3 ng/mL) of the LP, and lesser peak P4 (6.9 vs. 8.2 ± 0.3 ng/mL) during the LP than healthy cows. Status of INFLAM was associated with time to P4 decline in multiparous but not primiparous cows; the LP of INFLAM multiparous cows was less likely to have luteolysis (P4 decline) by d 14 [adjusted hazard ratio (AHR) and 95% CI: 0.54; 0.31 to 0.94] or by d 21 (AHR: 0.32; 0.12 to 0.84) than in healthy multiparous cows. In conclusion, postpartum cows with markers of systemic inflammation at wk 1 and uterine inflammation at wk 5 had altered luteal function (prolonged LP and lower P4 concentrations) before first breeding, which is a possible pathway linking postpartum health disorders and infertility.

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.

Sow hematological parameters in late pregnancy and an investigation as to whether these parameters are predictors of stillbirths in a Canadian sow herd.

Animal and objective: The objectives of this study were to produce hematological reference intervals for late-pregnancy sows and to assess whether there were associations between sow hematological end points and the number of stillborn pigs. Procedure: Whole blood was collected from 272 healthy pregnant sows ~1 wk before farrowing, and complete blood (cell) counts and hemoglobin determinations were obtained. Sows were monitored during farrowing, and litter characteristics, including number of stillborn piglets, were recorded. Results and conclusion: Values for red blood cells, hemoglobin, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular concentration, platelets, and white blood cells were significantly higher in Parity 1 sows compared to older sows. The mean (± SD) litter size was 14.5 ± 3.4 pigs, with 1.5 ± 2.0 stillborn pigs per litter. There was no significant association between any hematological end point (except white blood cell counts) and the likelihood of a stillborn piglet in a litter. There was a relationship between parity and stillbirth (P < 0.05), with higher-parity sows being more likely than younger sows to produce a stillborn piglet. Although it had been reported that anemic sows were more likely to have stillbirths, perhaps the relatively high mean hemoglobin concentration of sows in this study resulted in the lack of a relationship.

Paramètres hématologiques des truies en fin de gestation et enquête visant à déterminer si ces paramètres sont des prédicteurs de mortinatalités dans un troupeau de truies canadien. Animal et objectif: Les objectifs de cette étude étaient de produire des intervalles de référence hématologiques pour les truies en fin de gestation et d'évaluer s'il existait des associations entre les paramètres hématologiques des truies et le nombre de porcelets mort-nés. Procédure: Du sang total a été collecté auprès de 272 truies gravides en bonne santé environ 1 semaine avant la mise bas, et une numération cellulaire complète et des déterminations d'hémoglobine ont été obtenues. Les truies ont été surveillées pendant la mise bas et les caractéristiques de la portée, y compris le nombre de porcelets mort-nés, ont été enregistrées. Résultats et conclusion: Les valeurs des globules rouges, de l'hémoglobine, du volume corpusculaire moyen, de l'hémoglobine corpusculaire moyenne, de la concentration corpusculaire moyenne, des plaquettes et des globules blancs étaient significativement plus élevées chez les truies de parité 1 que chez les truies plus âgées. La taille moyenne (± ET) des portées était de 14,5 ± 3,4 porcs, avec 1,5 ± 2,0 porcs mort-nés par portée. Il n'y avait aucune association significative entre un quelconque paramètre hématologique (à l'exception du nombre de globules blancs) et la probabilité d'avoir un porcelet mort-né dans une portée. Il y avait une relation entre la parité et la mortinatalité (P < 0,05), les truies ayant une parité plus élevée étant plus susceptibles que les truies plus jeunes de produire un porcelet mort-né. Bien qu'il ait été rapporté que les truies anémiques étaient plus susceptibles d'avoir des mortinatalités, la concentration moyenne d'hémoglobine relativement élevée des truies dans cette étude a peut-être entraîné l'absence de relation.(Traduit par Dr Serge Messier).

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.

Defining the Effect of Oxytocin Use in Farrowing Sows on Stillbirth Rate: A Systematic Review with a Meta-Analysis.

The objective of this systematic review and meta-analysis was to identify the benefits and possible adverse side effects of oxytocin use during farrowing. Randomized controlled trials that were published in English within the last 50 years were eligible for inclusion. Eligible research needed to contain the PICO elements: population (P)-sows at farrowing; intervention (I):-oxytocin given to sows-comparator (C): sows at farrowing not given oxytocin, as well as sows given different dosages and/or different timing of administration; and outcomes (O):-stillbirths, sow mortality, and piglet viability. Four bibliographic databases were used: PubMed, CAB Direct, Web of Science Core Collection, and ProQuest Dissertations, and Theses Global. In addition, we performed a manual search of the table of contents in the American Association of Swine Veterinarians database for relevant conference proceedings and reports. To assess the risk of bias at the study level, a modified version of the Cochrane 2.0 ROB was used. Meta-analyses were performed to examine the average stillbirth rate, farrowing duration, and birth interval between piglets using random-effect standardized mean difference (SMD) models. To explore heterogeneity, a sub-group analysis was performed on the objectives of the study, dose, time, and route of administration. Of the 46 studies eligible for meta-analyses, only 25 had sufficient information. The pooled analyses of the random effect model demonstrated that the average number of stillborn pigs was lower in the comparator group (SMD = 0.23; CI95% = 0.1, 0.36), and both the farrowing duration (SMD = -8.4; CI95% = -1.1, -0.60) and the birth interval between piglets (SMD = -1.41; CI95% = -1.86, -0.97) were shorter in the oxytocin group. The majority of the studies had an overall risk of bias of 'some concerns'. It was concluded that the use of oxytocin increases the overall number of stillborn piglets, but decreases the farrowing duration and time interval between piglets. However, future studies should focus on the effect of oxytocin on the experience of dystocia among sows.

Association of lipid-related genes implicated in conceptus elongation with female fertility traits in dairy cattle.

Elongation of the preimplantation conceptus is a requirement for pregnancy success in ruminants, and failures in this process are highly associated with subfertility in dairy cattle. Identifying genetic markers that are related to early conceptus development and survival and utilizing these markers in selective breeding can improve the reproductive efficiency of dairy herds. Here, we evaluated the association of 1,679 SNP markers within or close to 183 candidate genes involved in lipid metabolism of the elongating conceptus with different fertility traits in US Holstein cattle. A total of 27,371 bulls with predicted transmitting ability records for daughter pregnancy rate, cow conception rate, and heifer conception rate were used as the discovery population. The associations found in the discovery population were validated using 2 female populations (1,122 heifers and 2,138 lactating cows) each with 4 fertility traits, including success to first insemination, number of services per conception, age at first conception for heifers, or days open for cows. Marker effects were estimated using a linear mixed model with SNP genotype as a linear covariate and a random polygenic effect. After multiple testing correction, 39 SNP flagging 27 candidate genes were associated with at least one fertility trait in the discovery population. Of these 39 markers, 3 SNP were validated in the heifer population and 4 SNP were validated in the cow population. The 3 SNP validated in heifers are located within or near genes CAT, MYOF, and RBP4, and the 4 SNP validated in lactating cows are located within or close to genes CHKA, GNAI1, and HMOX2. These validated genes seem to be relevant for reducing pregnancy losses, and the SNP within these genes are excellent candidates for inclusion in genomic tests to improve reproductive performance in dairy cattle.

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.

Symposium review: Lipids as regulators of conceptus development: Implications for metabolic regulation of reproduction in dairy cattle.

Pregnancy losses are substantial in dairy cattle and threaten reproductive efficiency. A substantial proportion of these losses occur during early stages of conceptus development, including the elongation phase. Elongation of the preimplantation conceptus is a prerequisite for maternal recognition, implantation, and survival of pregnancy. The onset of elongation occurs when concentrations of lipids in endometrial epithelial cells are increased, and it requires substantial coordination of lipid metabolism by conceptus cells. The nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) seems to have a central role in coordinating gene expression in trophectoderm cells at the onset of elongation, particularly of genes involved in lipid metabolism. Numerous fatty acids are natural ligands of PPARγ and their concentrations in the histotroph are likely important to PPARγ activity and its downstream effects on conceptus biology. Changes in concentration or composition of fatty acids in the histotroph could alter conceptus development. Inflammatory diseases and excessive loss of body reserves are prevalent problems in postpartum dairy cows and represent important risk factors for early pregnancy loss in the subsequent breeding period. Although cows affected by these conditions likely have reduced developmental capacity of oocytes, embryo transfer studies indicate that impaired uterine environment also contributes to their subfertility. Long-lasting effects of these conditions on energy and lipid homeostasis might alter composition of the histotroph and could help explain developmental failures occurring during conceptus formation attributable to impaired uterine environment. Targeting of uterine lipid metabolism and PPARγ activity during preimplantation conceptus development through prevention of disease and optimized feed intake postpartum and through nutraceutical diets at the time of breeding are potential strategies to improve pregnancy survival and consequently reproductive efficiency in dairy cows.

Reproductive Systems for North American Dairy Cattle Herds.

Reproductive inefficiency compromises the profitability of dairy herds and the health and longevity of individual cows. In the average dairy herd, the combination of estrus detection and ovulation synchronization protocols yields the best economic return. Genomic selection of animals is particularly profitable in situations in which little is known about their genetic potential. Biosensor systems in milking parlors may allow for the design of reproductive strategies tailored for cows according to their physiologic needs while optimizing economic return.

Role of lipids on elongation of the preimplantation conceptus in ruminants.

Elongation of the preimplantation conceptus is a prerequisite for successful pregnancy in ruminants and depends on histotroph secretion by the endometrium. Lipids are an essential component of the histotroph, and recent studies indicate that lipids have important roles in the elongation phase of conceptus development. The onset of elongation is marked by dynamic changes in the transcriptome of trophectoderm cells, which are associated with lipid metabolism. During elongation, the trophectoderm increases transcript expression of genes related to uptake, metabolism and de novo biosynthesis of fatty acids and prostaglandins. Expression of the gene PPARG increases substantially, and activation of the transcription factor PPARG by binding of lipid ligands appears to be crucial for the coordination of cell biology during elongation. Lipids accumulated in the epithelial cells of the endometrium during diestrus are likely the most important source of fatty acids for utilization by the conceptus and become available in the uterine lumen through exporting of exosomes, microvesicles, carrier proteins and lipoproteins. Targeting of uterine lipid metabolism and PPARG activity during preimplantation conceptus development through nutraceutical diets may be a good strategy to improve pregnancy survival and reproductive efficiency in ruminants.

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.

Low doses of bovine somatotropin enhance conceptus development and fertility in lactating dairy cows.

Objectives were to evaluate the effects of administering either one or two low doses of slow-release recombinant bovine somatotropin (bST) on hormone concentrations, conceptus development, and fertility in dairy cows. Cows from two farms were detected in estrus on or after 50 days postpartum (n = 1483), inseminated, and enrolled in the study (Day 0). Within farm, cows were blocked by parity and assigned randomly to receive a single placebo injection at insemination (control), a single injection with 325 mg of bST at insemination (S-bST), or two injections with 325 mg of bST administered on Days 0 and 14 (T-bST). From a subset of cows, blood was collected twice weekly from Day 0 to 42 for determination of hormone concentrations and on Day 19 for isolation of leucocytes and analysis of transcript abundance of selected interferon-stimulated genes. Pregnancy was diagnosed on Days 31 and 66, and ultrasonographic morphometry of the conceptus was performed on Days 34 and 48 in a subset of cows. Cows that received T-bST had increased plasma concentrations of GH and IGF1 for 4 wk, increased mRNA expression of ISG15 and RTP4 in leukocytes, earlier rise in the pregnancy-specific protein B in plasma of pregnant cows, increased conceptus size, and enhanced fertility. Cows that received S-bST had increased concentrations of GH and IGF1 for only 2 wk and it was insufficient to alter conceptus development and fertility. In conclusion, supplementation with low doses of bST during the pre- and peri-implantation periods enhanced conceptus development, reduced embryonic losses, and improved fertility in dairy cows.