Investigating relationships between the host genome, rumen microbiome, and dairy cow feed efficiency using mediation analysis with structural equation modeling
Guillermo Martinez-Boggio, Hugo F Monteiro, Fabio S Lima, Caio C Figueiredo, Rafael S Bisinotto, José E P Santos, Bruna Mion, Flavio S Schenkel, Eduardo S Ribeiro, Kent A Weigel, Guilherme J M Rosa, Francisco Peñagaricano
DOI: 10.3168/jds.2024-24675
Abstract
The rumen microbiome is crucial for converting feed into absorbable nutrients used for milk synthesis, and the efficiency of this process directly affects 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, the rumen microbiome, and dairy cow feed efficiency using structural equation models. Our specific objectives were to (1) infer the mediation effects of the rumen microbiome on feed efficiency traits, (2) estimate the direct and total heritability of feed efficiency traits, and (3) 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), and 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, in order to improve feed efficiency traits.
Revealing host genome-microbiome networks underlying feed efficiency in dairy cows
Guillermo Martinez-Boggio, Hugo F Monteiro, Fabio S Lima, Caio C Figueiredo, Rafael S Bisinotto, José E P Santos, Bruna Mion, Flavio S Schenkel, Eduardo S Ribeiro, Kent A Weigel, Guilherme J M Rosa, Francisco Peñagaricano
DOI: 10.1038/s41598-024-77782-z
Abstract
Ruminants have the ability to digest human-inedible plant materials, due to the symbiotic relationship with the rumen microbiota. Rumen microbes supply short chain fatty acids, amino acids, and vitamins to dairy cows that are used for maintenance, growth, and lactation functions. The main goal of this study was to investigate gene-microbiome networks underlying feed efficiency traits by integrating genotypic, microbial, and phenotypic data from lactating dairy cows. Data consisted of dry matter intake (DMI), net energy secreted in milk, and residual feed intake (RFI) records, SNP genotype, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows. We first assessed marginal associations between genotypes and phenotypic and microbial traits through genomic scans, and then, in regions with multiple significant hits, we assessed gene-microbiome-phenotype networks using causal structural learning algorithms. We found significant regions co-localizing the rumen microbiome and feed efficiency traits. Interestingly, we found three types of network relationships: (1) the cow genome directly affects both rumen microbial abundances and feed efficiency traits; (2) the cow genome (Chr3: 116.5 Mb) indirectly affects RFI, mediated by the abundance of Syntrophococcus, Prevotella, and an unknown genus of Class Bacilli; and (3) the cow genome (Chr7: 52.8 Mb and Chr11: 6.1-6.2 Mb) affects the abundance of Rikenellaceae RC9 gut group mediated by DMI. Our findings shed light on how the host genome acts directly and indirectly on the rumen microbiome and feed efficiency traits and the potential benefits of the inclusion of specific microbes in selection indexes or as correlated traits in breeding programs. Overall, the multistep approach described here, combining whole-genome scans and causal network reconstruction, allows us to reveal the relationship between genome and microbiome underlying dairy cow feed efficiency.
Procurement and preservation of neonatal porcine cardiac tissue
Lauren M Gilbertsen, Tara L Goertzen, Mallery L Larson, Lucelia M Pereira, Aidan S Bradshaw, Raney L Hazan, Georgia F Patyna, Abigail H Thomas, Emma S Scudder, Jennifer A Sexton, Jeff Olivarez, Alyssa M Marre, Lais Malavasi, Daniel P Fitzsimons
DOI: 10.1152/ajpheart.00362.2024
Abstract
The porcine and human heart are remarkably similar in cardiac physiology and biochemistry. Translational research involving the porcine biomedical model is becoming increasingly applicable for the study of human cardiac function in health and disease. Presently, few protocols exist for collecting experimentally viable cardiac tissue from large animal models, particularly during neonatal maturation. To address this deficiency, we have developed a technique to procure and preserve ventricular tissue from neonatal piglets at day 3 (n = 4) and day 30 (n = 6) postpartum. Piglets were subjected to a strict sedation, anesthesia, and analgesia regimen. During surgery, cardiopulmonary indices of electrocardiogram, heart rate, systolic and diastolic blood pressure, respiration rate, peripheral O2 saturation, and end-tidal CO2 were monitored continuously to ensure normal cardiac function. Before cardiectomy, each heart was perfused with an intravenous administration of heparin (10 mL/kg) and ice-cold Custodiol HTK cardioplegia solution (10 mL/kg). After cardiac explantation, myocardial samples (dimensions: 1 × 1 × 1 cm) were dissected from the left and right ventricles and snap-frozen in liquid nitrogen. Analysis via SDS-PAGE densitometry demonstrated that myofibrillar proteins are stable and undegraded. Western Blots showed full expression of protein. These results suggest that the detailed cardiac tissue procurement technique preserves the experimental viability of the cardiac tissue and prevents the degradation of myofibrillar proteins.NEW & NOTEWORTHY This project’s objective was to develop a technique for procuring and preserving cardiac tissue from a porcine model. Porcine is a rapidly emerging animal model to study cardiovascular disease and has recently been popularized due to advancements in CRISPR-cas9 technology. The technique, originally derived from human heart transplant protocols, involves full anesthetic and analgesic regimens and the use of saline heparin and cardioplegia solution to preserve tissue integrity.
Transcriptomics of bovine sperm and oocytes
Vanmathy Kasimanickam, John Kastelic, Ramanathan Kasimanickam
DOI: 10.1016/j.anireprosci.2024.107630
Abstract
Traditionally, sperm and embryos were studied using microscopy to assess morphology and motility. However, OMICS technologies, especially transcriptomic analysis, are now being used to screen the molecular dynamics of fertility markers at cellular and molecular levels, with high sensitivity. Transcriptomics is the study of the transcriptome – RNA transcripts produced by the genome – using high-throughput methods to understand how the RNAs are expressed. In this review, we have discussed gene contributions to sperm structure and function and their role in fertilization and early embryo development. Further, we identified miRNAs shared by sperm, oocytes, and early embryos and their roles in fertilization and early embryo development.