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.

Seminal cell-free DNA as a potential marker for in vitro fertility of Nellore bulls.

PURPOSE: This study aimed to identify a marker for freezability and in vitro fertility of sperm samples before freezing. METHODS: Semen was collected from nine Nelore bulls; half of the ejaculate was used for seminal plasma cell-free DNA (cfDNA) quantification, and the other half was cryopreserved. Evaluation of sperm movement using computer-assisted semen analysis and plasma membrane integrity and stability, acrosomal integrity, apoptosis, and mitochondrial potential using flow cytometry were performed on fresh and frozen/thawed semen at 0, 3, 6, and 12 h after thawing. Frozen/thawed sperm was also used for in vitro embryo production. cfDNA was extracted from each bull, and the total DNA and number of cell-free mitochondrial DNA (cfmtDNA) copies were quantified. Semen from each animal was used for IVF, and cleavage, blastocyst formation, and cell counts were evaluated. RESULTS: Two groups were formed and compared based on the concentrations of cfDNA and cfmDNA present: low-cfDNA and high-cfDNA and low-cfmtDNA and high-cfmtDNA. Up to 12 h post-thawing, there were no differences between the groups in the majority of the sperm parameters evaluated. Cleavage, day 6 and 7 blastocyst rates, and the number of cells were higher in the high cfDNA group than in the low cfDNA group. Similar results were observed for cfmtDNA, except for the number of cells, which was similar between the groups. CONCLUSION: The concentration of cfDNA and the relative number of copies of cfmtDNA in seminal plasma cannot predict the freezability of semen but can be used to predict in vitro embryo production.

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.

Effects of replacing inorganic salts of trace minerals with organic trace minerals in the pre- and postpartum diets on mineral status, antioxidant biomarkers, and health of dairy cows.

Our objectives were to evaluate the effects of complete replacement of supplementary inorganic salts of trace minerals (ITM; cobalt (Co), copper (Cu), manganese (Mn), zinc (Zn) sulfates and sodium (Na) selenite) by organic trace minerals (OTM; Co, Cu, Mn, Zn proteinates, and selenized yeast) in both pre- and postpartum diets on trace minerals (TM) concentrations in body fluids and liver, antioxidant and inflammation biomarkers in blood, and postpartum health of dairy cows. Pregnant cows were blocked by parity and body condition score and randomly assigned to ITM (n = 136) or OTM (n = 137) 45 d before expected calving. Both groups received the same pre- and postpartum diets except for the source of supplementary TM. The day of calving was considered study d 0 and blood was collected on d -45, -21, -14, -10, -7, -3, 0, 3, 7, 10, 14, 23, 65, and 105 for analyses of TM and biomarkers. Concentrations of TM were also investigated in the liver (d 105), milk (d 7, 23, 65, 105), urine (d -21, 21, 65, 105), ruminal fluid and feces (d -21, 21, 65). Incidence of clinical and subclinical health conditions were evaluated. Complete replacement of ITM by OTM resulted in greater concentration of selenium (Se) in serum (0.084 vs. 0.086 µg/mL; P < 0.01), milk (0.24 vs. 0.31 µg/g; P < 0.01), and ruminal fluid (0.54 vs. 0.58 µg/g; P = 0.06), and reduced concentration of Se in urine (1.54 vs. 1.23 µg/g; P<0.01). For concentration of Co in serum, an interaction between treatment and time was detected (P < 0.01). Cows supplemented with OTM had greater concentrations of Co on d -7 and 0 (0.30 vs. 0.33 ng/mL; P < 0.01) but lower concentrations of Co on d 23, 65, and 105 (0.34 vs. 0.31 ng/mL; P < 0.05), in addition to reduced concentration of Co in feces (1.08 vs. 0.99 µg/g; P = 0.04) and, for multiparous only, in urine (0.019 vs. 0.014 µg/g; P < 0.01). Cows supplemented with OTM had lower postpartum concentrations of glutamate dehydrogenase (20.8 vs. 17.8 U/L; P < 0.05) and higher albumin on d -10 (36.0 vs. 36.7 g/L; P = 0.04) and 23 (36.9 vs. 37.6 g/L; P = 0.03) relative to calving. Primiparous cows fed OTM had lower concentration of ceruloplasmin in plasma (55 vs. 51 mg/L; P ≤ 0.05). Cows supplemented with OTM had less incidence of lameness (14% vs. 7%; P = 0.05), elevated nonesterified fatty acids (NEFA) (61% vs. 44%; P < 0.01), and multiple metabolic problems (35% vs. 20%; P < 0.01). Despite the lack of differences in Cu, Mn, and Zn concentrations and antioxidant capacity, complete replacement of ITM by OTM altered concentrations of Se and Co, supported liver and hoof health, and reduced the risk of postpartum elevated NEFA.

Trace minerals (TM) are important for oxidative balance and immunity of cows. Different forms of TM are available for dietary supplementation of dairy cows. We tested whether replacing inorganic salts of TM by organic sources of TM in both pre- and postpartum diets improve TM concentration in body fluids and liver, antioxidant capacity in blood, and postpartum health of dairy cows. Despite the lack of difference in antioxidant capacity and in concentrations of Cu, Mn, and Zn, the complete replacement of inorganic salts by organic sources altered concentrations of Se and Co in circulation, and reduced the concentration of biomarkers associated with inflammation and liver damage, and the risk of lameness and postpartum metabolic problems.

Intrafollicular lipopolysaccharide injection delays ovulation in cows.

The aim of this study was to evaluate effects of intra-follicular (i.f.) treatment with lipopolysaccharide (LPS) on follicular and luteal development in cows. There were 18 non-lactating cows assigned to two groups to address this aim: control group (n = 9), which received an i.f. injection of saline; and LPS group (n = 9), which received an i.f. injection of 1 µg of LPS per mL of follicular fluid. Cows were treated with an intravaginal P4 releasing device (IVD) and estradiol benzoate on D0. On D4 and D5 cows were treated with cloprostenol sodium and on D7 the IVD was removed. At 12 h after IVD removal, cows were administered the i.f. injection of LPS or saline. After administration of these treatments, follicular development was evaluated every 12 h until ovulation. The LPS treatment increased blood flow in pre-ovulatory follicles (P = 0.05). Follicle growth was reduced by LPS injection (P < 0.02) resulting a longer period to the time of ovulation for cows in the LPS than control group (P = 0.03). The percentage of cows having ovulations was less for the LPS than control group (P = 0.03). The diameter of the CL, CL blood flow and P4 concentrations 5 and 12 days after ovulation did not differ between groups (P> 0.05). In conclusion, intra-follicular treatment with LPS resulted in a decreased rate of follicle growth, delayed timing of ovulations and a lesser number of cows having ovulations.

Early embryonic development of bovine oocytes challenged with LPS in vitro or in vivo.

The aim of this study was to evaluate the effect of exposing bovine oocytes to lipopolysaccharides (LPS) in vivo and in vitro on early embryo development. In experiment 1, cumulus oocyte complexes (COCs, n = 700/group) were challenged with 0, 0.1, 1.0 or 5.0 µg/mL of LPS during in vitro maturation (IVM). Later, in vitro fertilization (IVF) and in vitro culture (IVC) were performed. In experiment 2, COCs (n = 200/group) matured and in vitro fertilized without LPS were subjected to IVC with the same doses of LPS from experiment 1. In experiment 3, heifers received two injections of saline solution (n = 8) or 0.5 µg/kg of LPS (n = 8) 24 h apart, and 3 days later, COCs were recovered and submitted to IVM, IVF, and IVC. In experiments 1 and 3, the expression of TLR4, TNF, AREG and EREG genes in cumulus cells was evaluated. Exposure to 1 and 5 µg/mL of LPS during IVM decreased nuclear maturation (39.4 and 39.6%, respectively) compared with control (63.6%, P < 0.05). Despite that, no effect on cleavage and blastocyst rates were observed. Exposure to LPS during IVC did not affect embryonic development. In vivo exposure to LPS decreased the in vitro cleavage rate (54.3 vs 70.2%, P = 0.032), but cleaved embryos developed normally. Number of cells per embryo and gene expression were not affected by the LPS challenge in any experiment. In conclusion, although in vitro exposure to LPS did not affect early embryo development, in vivo LPS exposure reduced cleavage rate.

Effect of recombinant bovine somatotropin (rbST) treatment on follicular population and development in non-lactating dairy cows.

The aim of this study was to evaluate the long-term effects of recombinant bovine somatotropin (rbST) on follicle population and ovulatory follicle development in non-lactating dairy cows. Twenty-one Jersey cows were allocated in rbST (n=11) or control (n=10) groups. On day -60, cows in rbST group received 500 mg of somatotropin (s.c. Lactotropin®, Elanco). On day 0, control and rbST cows received an intravaginal progesterone-releasing device (1.9 g, CIDR®, Zoetis) and GnRH (100 mg, IM, Factrel®, Zoetis). On day 8, cows received PGF2α (25 mg, IM, Lutalyse®, Zoetis) and the CIDR® was removed. Twelve hours after device removal (D8), serum, follicular fluid and granulosa cells samples were collected. Serum and follicular concentration of estradiol (E2) and progesterone (P4) were analyzed. Total RNA was extracted from granulosa cells to measure gene expression of LHCGR, STAR, HSD-3B1, CYP11A1, CYP19A1, CYP17A1, IGFR and PAPPA by real-time PCR. Ultrasonography was performed on days -60, -53, -46, -14, -7, 0 and 8 for antral follicle count. Results were analyzed by repeated measures ANOVA and t-test. There was no effect of rbST treatment on the number of follicles during the 60 days period, as well as no effect on serum and follicular fluid E2 and follicular fluid P4 at the moment of follicle aspiration. There was a reduction in PAPPA (P = 0.006), CYP11A1 (P = 0.04) and CYP19A1 (P = 0.002) mRNA levels in granulosa cells of the pre-ovulatory follicle of rbST treated cows. In conclusion, a single dose of rbST did not have long-term effects on antral follicle population, serum and follicular E2/P4 concentrations in non-lactating dairy cows. Despite that, rbST injection decreased granulosa cell expression of genes related to steroidogenesis in the pre-ovulatory follicle.

Effect of high-density lipoprotein on oocyte maturation and bovine embryo development in vitro.

High-density lipoprotein (HDL) is the main lipoprotein in the follicular fluid, and it has anti-inflammatory, antioxidant and cryoprotectant properties. The anti-inflammatory potential and antioxidant potential are derived from its lipid composition, especially the apolipoprotein AI (ApoAI) and paraoxonase 1 (PON1). The aim of this study was to evaluate the effect of HDL during in vitro maturation (IVM) on oocyte maturation and early bovine embryo development. For this, cumulus-oocyte complexes (COCs) were obtained from bovine ovaries collected at a local slaughterhouse. COCs (n = 2,250) were allocated into three groups (n = 50 COCs/group) according to the addition of HDL protein (HDL-P) during IVM for 22 hr: 0 (control), 50 and 150 mg/dl. After IVM, COCs were inseminated (in vitro fertilization) and cultivated for 7 days. Total cholesterol concentration, total protein, triglycerides and ApoAI concentrations on IVM medium increased proportionally to HDL-P addition. However, PON1 activity was not detected in any treatment. The addition of HDL-P did not affect nuclear maturation rate, endogenous reactive oxygen species and glutathione levels in COCs (p > 0.05). The highest HDL-P concentration (150 mg/dl) decreased cleavage and blastocyst rate (p < 0.05). Moreover, the HDL-P 150 mg/dl group had lower cellular count/blastocyst than the 50 mg/dl group (p < 0.05). However, the addition of HDL-P did not affect relative gene expression of evaluated genes. In conclusion, the complex HDL/ApoAI obtained from human plasma, in the absence of PON1 activity during in vitro oocyte maturation, decreased initial embryo development.

Seroprevalence estimate and associated risk factors for neosporosis in dairy cattle in the northwest region of Rio Grande do Sul State, Brazil / Estimativa da soroprevalência e fatores de risco para neosporose em rebanhos leiteiros na região Noroeste do estado do Rio Grande do Sul, Brasil

ABSTRACT: The aim of this study was to estimate neosporosis seroprevalence and its associated risk factors in milk herds (Bos taurus taurus) located in the northwestern region of Rio Grande do Sul State, Brazil. Three hundred twenty-two blood samples were collected from dairy cows on 18 farms in 17 cities of this region. An epidemiologic questionnaire was completed for each farm. It consisted of questions about the general characteristics of the herd, reproduction, and animal management. Serum samples were tested for Neospora caninum using a commercial enzyme-linked immunosorbent assay (ELISA) kit. Results indicated a seroprevalence of Neospora in 88.9% (16/18) of herds and 31.1% (100/322) of individuals. Risk factor analyses demonstrated that culling by reproductive disorder (OR = 0.6), flooding (OR = 0.5), and commercial sale (OR = 0.4) were associated with seroprevalence. Nevertheless, the purchase of replacement animals in the herd played an important role in disease occurrence (OR = 2.2). Results of this study suggested that Neospora caninum was present in the studied herds under investigation and that there are risk factors associated with its seroprevalence on the farms of the northwestern of Rio Grande do Sul.

RESUMO: O objetivo desse estudo foi estimar a soroprevalência da neosporose e os possíveis fatores de risco em rebanhos (Bos taurus taurus) localizados na mesorregião Noroeste do Rio Grande do Sul, Brasil. Foram coletadas 322 amostras de sangue de bovinos leiteiros, em 18 propriedades localizadas em 17 munícipios desta mesorregião. Um questionário epidemiológico foi aplicado em cada propriedade, contendo questões relacionadas às características gerais dos rebanhos, dados reprodutivos e manejo animal. As amostras de soro foram testadas através do teste de imunoensaio enzimático (ELISA) para Neospora caninum. Os resultados demonstraram uma soroprevalência de Neospora de 88,9% (16/18) entre os rebanhos e 31,1% (100/322) entre os indivíduos. Entre os fatores de risco analisados foi observado que descarte por problemas reprodutivos (OR=0,6), presença de áreas alagadiças (OR=0,5) e venda comercial (OR=0,4) estavam associados a soroprevalência. No entanto, a compra de animais substituídos no rebanho desempenhou um papel significativo na ocorrência da doença (OR=2,2). Os resultados desse estudo sugerem que o Neospora caninum esteve presente nos rebanhos estudados, bem como, existem fatores associados com a soroprevalência nas propriedades da mesorregião do Noroeste do Rio Grande do Sul.

Selection of porcine oocytes in vitro through brilliant cresyl blue staining in distinct incubation media.

Staining with brilliant cresyl blue (BCB) may be used for oocyte selection, but BCB staining itself and the most commonly used selection medium (DMPBS) may compromise the development of porcine oocytes in vitro. This study evaluated DNA fragmentation, nuclear maturation, the area of migration of cortical granules (CG) and embryo development for stained (BCB+) and unstained (BCB-) oocytes incubated in DMPBS and in a modified medium (ReproPel) tested for the first time. Unexposed (UN), BCB+ and BCB- oocytes were incubated composing six groups: DMPBS/UN; DMPBS/BCB+; DMPBS/BCB-; ReproPel/UN; ReproPel/BCB+; and ReproPel/BCB-. There were more BCB+ oocytes in ReproPel than in DMPBS (P < 0.05). The DNA fragmentation was evaluated for oocytes in DMPBS/BCB+, DMPBS/BCB-, ReproPel/BCB+, ReproPel/BCB- and in porcine follicular fluid (control). The frequency of oocytes with no DNA fragmentation was greatest (64.6%) in DMPBS/BCB+ and lowest in ReproPel/BCB+ and ReproPel/BCB- (26.8 and 34.1%, respectively) (P < 0.05). Nuclear maturation rates were greater (P < 0.05) for DMPBS/BCB+ (63.1%), ReproPel/UN (55.1%) and ReproPel/BCB+ (50.2%) than for DMPBS/UN (40.8%) and ReproPel/BCB- (35.5%). The area of CG was greater (P < 0.05) for ReproPel/BCB- (80.7%) and DMPBS/UN (77.6%) than for ReproPel/UN (34.7%). Cleavage rates for DMPBS/BCB+ and ReproPel/BCB+ were greater than for DMPBS/UN (P < 0.05). Blastocyst development rates were greatest (P < 0.05) for ReproPel/UN and ReproPel/BCB+. In both media, BCB staining was apparently unable to select competent oocytes, which likely occurred due to toxicity. Despite the similar nuclear maturation and area of CG compared with DMPBS, oocytes selected in ReproPel presented impaired DNA integrity.