The origins of the Guinness stout yeast.

Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.

Immunoproteomic analysis of the serum IgG response to cell wall-associated proteins of Staphylococcus aureus strains belonging to CC97 and CC151.

CC97 and CC151 are two of the most common Staphylococcus aureus lineages associated with bovine intramammary infection. The genotype of the infecting S. aureus strain influences virulence and the progression of intramammary disease. Strains from CC97 and CC151 encode a distinct array of virulence factors. Identification of proteins elaborated in vivo will provide insights into the molecular mechanism of pathogenesis of these lineages, as well as facilitating the development of tailored treatments and pan-lineage vaccines and diagnostics. The repertoire of genes encoding cell wall-anchored (CWA) proteins was identified for S. aureus strains MOK023 (CC97) and MOK124 (CC151); MOK023 encoded more CWA proteins than MOK124. Serum collected during an in vivo challenge trial was used to investigate whether the humoral response to cell wall proteins was strain-specific. Immunoproteomic analysis demonstrated that the humoral response in MOK023-infected cows predominantly targeted high molecular weight proteins while the response in MOK124-infected cows targeted medium or low molecular weight proteins. Antigenic proteins were identified by two-dimensional serum blotting followed by mass spectometry-based identification of immunoreactive spots, with putative antigens subsequently validated. The CWA proteins ClfB, SdrE/Bbp and IsdA were identified as immunogenic regardless of the infecting strain. In addition, a number of putative strain-specific imunogens were identified. The variation in antigens produced by different strains may indicate that these strains have different strategies for exploiting the intramammary niche. Such variation should be considered when developing novel control strategies including vaccines, therapeutics and diagnostics.

Maternal and/or post-weaning supplementation with Bacillus altitudinis spores modulates the microbial composition of colostrum, digesta and faeces in pigs.

This study examined the effects of maternal and/or post-weaning Bacillus altitudinis supplementation on the microbiota in sow colostrum and faeces, and offspring digesta and faeces. Sows (n = 12/group) were assigned to: (1) standard diet (CON), or (2) CON supplemented with probiotic B. altitudinis spores (PRO) from day (d)100 of gestation to weaning (d26 of lactation). At weaning, offspring were assigned to CON or PRO for 28d, resulting in: (1) CON/CON, (2) CON/PRO, (3) PRO/CON, and (4) PRO/PRO, after which all received CON. Samples were collected from sows and selected offspring (n = 10/group) for 16S rRNA gene sequencing. Rothia was more abundant in PRO sow colostrum. Sow faeces were not impacted but differences were identified in offspring faeces and digesta. Most were in the ileal digesta between PRO/CON and CON/CON on d8 post-weaning; i.e. Bacteroidota, Alloprevotella, Prevotella, Prevotellaceae, Turicibacter, Catenibacterium and Blautia were more abundant in PRO/CON, with Firmicutes and Blautia more abundant in PRO/PRO compared with CON/CON. Lactobacillus was more abundant in PRO/CON faeces on d118 post-weaning. This increased abundance of polysaccharide-fermenters (Prevotella, Alloprevotella, Prevotellaceae), butyrate-producers (Blautia) and Lactobacillus likely contributed to previously reported improvements in growth performance. Overall, maternal, rather than post-weaning, probiotic supplementation had the greatest impact on intestinal microbiota.

Antibacterial plant combinations prevent postweaning diarrhea in organically raised piglets challenged with enterotoxigenic Escherichia coli F18.

Antibiotics and zinc oxide restrictions encourage the search for alternatives to combat intestinal pathogens, including enterotoxigenic Escherichia coli (ETEC), a major cause of postweaning diarrhea (PWD) in pigs. PWD causes important economic losses for conventional and organic farming. This study investigated the effect of dietary supplementation with garlic and apple pomace or blackcurrant on infection indicators and the fecal microbiota of organic-raised piglets challenged with ETEC-F18. For 21 days, 32 piglets (7-weeks-old) were randomly assigned to one of four groups: non-challenge (NC); ETEC-challenged (PC); ETEC-challenged receiving garlic and apple pomace (3 + 3%; GA); ETEC-challenged receiving garlic and blackcurrant (3 + 3%; GB). ETEC-F18 was administered (8 mL; 109 CFU/ml) on days 1 and 2 postweaning. The 1st week, PC had lower average daily gain than those in the NC, GA, and GB groups (P < 0.05). NC pigs showed neither ETEC-F18 shedding nor signs of diarrhea. The PC group had higher diarrhea incidence and lower fecal dry matter than NC (≈5-10 days; 95% sEBCI). The GA and GB groups showed reduced ETEC-F18 and fedA gene shedding, higher fecal dry matter, and lower diarrhea incidence than the PC (≈5-9 days; 95% sEBCI). The NC, GA, and GB had normal hematology values during most of the study, whereas the PC had increased (P < 0.05) red blood cells, hemoglobin, and hematocrit on day 7. Haptoglobin and pig-MAP increased in all groups, peaking on day 7, but PC showed the greatest increase (P < 0.05). The fecal microbiota of PC pigs had reduced α-diversity (day 7; P < 0.05) and higher volatility (days 3-14; P < 0.05). Escherichia, Campylobacter, and Erysipelothrix were more abundant in the PC than in the NC, GB, and GA groups (log2FC > 2; P < 0.05), whereas Catenibacterium, Dialister, and Mitsoukella were more abundant in the NC, GB, and GA than in the PC group (log2FC > 2; P < 0.05). Prevotella and Lactobacillus were more abundant in the GB group (log2FC > 2, P < 0.05). In conclusion, dietary supplementation of GA and GB limited ETEC proliferation, reduced PWD, and beneficially impacted the fecal microbiota's diversity, composition, and stability.

The transcriptomic response of bovine uterine tissue is altered in response to sperm from high- and low-fertility bulls†.

Despite stringent quality control checks, some bulls with apparently normal semen quality yield lower than expected pregnancy rates. This study profiled the transcriptome and performed histological analysis of the bovine uterus in response to sperm from high-fertility (HF) and low-fertility (LF) bulls. Postmortem uterine biopsies and uterine explants were collected from heifers 12 h after a fixed time artificial insemination (AI) to a synchronized estrus with frozen-thawed semen from five HF (fertility rate 4.01% ± 0.25) and five LF (fertility rate - 11.29% ± 1.11; mean ± SEM) bulls. Uterine biopsies were also collected from control (CTRL) heifers, which were not inseminated. RNA-sequencing and histological analysis were performed for differential gene expression and neutrophil quantification. In the HF treatment relative to CTRL heifers, there were 376 genes significantly differentially expressed in the endometrium with just one gene differentially expressed in the LF treatment relative to CTRL heifers. Comparing the HF and LF treatments directly, there were 40 significantly differentially expressed genes (P < 0.05). Transcriptomic analysis shows a predominant role for the inflammatory marker Interleukin-1 alpha, which was further confirmed by immunohistochemistry. Quantification of neutrophils in the endometrium showed a significant effect of sperm; however, there was no difference in neutrophil numbers between HF and LF groups. In conclusion, this novel study clearly shows a distinct inflammatory response to sperm in the endometrium and a divergent transcriptomic response to semen from HF and LF bulls.

Genome Sequence of an Ungulate Tetraparvovirus 1 from a Nasal Swab of an Irish Beef-Suckler Calf.

Here, we report the genome sequence of strain UTPV1/AB belonging to the species Ungulate tetraparvovirus 1 (UTPV1). UTPV1/AB was isolated in the east of Ireland, directly from a nasal swab of a beef-suckler calf diagnosed with bovine respiratory disease on a farm in County Meath (longitude, 6°65'W; latitude, 53°52'N).

Genome Sequence of Bovine Coronavirus Variants from the Nasal Virome of Irish Beef Suckler and Pre-weaned Dairy Calves Clinically Diagnosed with Bovine Respiratory Disease.

We report 24 bovine coronavirus (BCoV) genome sequences from Ireland. BCoV was sequenced directly from nasal swabs that had been collected during a bovine respiratory disease (BRD) outbreak among recently purchased beef suckler and pre-weaned dairy calves.

Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.

Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.

Cervical immune activation during the luteal phase may compromise subsequent trans-cervical ram sperm transport†.

Worldwide, cervical artificial insemination using frozen-thawed semen yields low pregnancy rates. The only exception to this is in Norway, where vaginal insemination with frozen-thawed semen yields pregnancy rates in excess of 60% and which has been attributed to the specific ewe breed used. Our previous work demonstrated differences in cervical gene expression at the follicular phase of the estrous cycle in ewe breeds with known differences in pregnancy rates. In this study, we characterized the cervical transcriptome of the same ewe breeds [Suffolk, Belclare, Fur, and Norwegian White Sheep (NWS)] during the luteal phase, as an optimal environment at the luteal phase could better prepare the cervix for sperm migration through the cervix at the subsequent follicular phase. High-quality RNA extracted from postmortem cervical tissue was analyzed by RNA sequencing. After stringent filtering, 1051, 1924, and 611 differentially expressed genes (DEGs) were detected in the low-fertility Suffolk breed compared with Belclare, Fur, and NWS, respectively. Gene ontology analysis identified increased humoral adaptive immune response pathways in Suffolk. Increased expression of multiple immune genes supports the presence of an active immune response in the cervix of Suffolk ewes, which differentiates them significantly from the other three ewe breeds. Inflammatory pathways were upregulated in the Suffolk, resulting in higher expression of the potent pro-inflammatory cytokines. Therefore, higher levels of pro-inflammatory cytokines indicate unresolved inflammation in the cervix of the low-fertility Suffolk breed that could contribute to reduced cervical sperm transport in the next follicular phase.

Ewe breed differences in the cervical transcriptome at the follicular phase of a synchronised oestrous cycle.

BACKGROUND: Cervical artificial insemination (AI) with frozen-thawed semen results in unacceptably low pregnancy rates internationally. The exception is in Norway, where vaginal deposition of frozen-thawed semen to a natural oestrous routinely yields pregnancy rates in excess of 70%. Previous studies by our group has demonstrated that this is due to differences in cervical sperm transport. However, a potentially important contributory factor is that ewes are inseminated to a natural oestrous in Norway but to a synchronised oestrous across most of the rest of the world. In this study, we interrogated the gene expression of the sheep cervix of four ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen under the effect of exogenous hormones to synchronise the oestrous cycle. These four ewe breeds (n = 8 to 11 ewes per breed) are from two countries: Ireland (Belclare and Suffolk; medium and low fertility, respectively) and Norway (Norwegian White Sheep (NWS) and Fur; both with high fertility compared to the Irish ewe breeds). RESULTS: RNA extracted from cervical biopsies collected from these breeds was analysed by RNA-sequencing and differential gene expression analysis. Using the low-fertility Suffolk breed as a reference level; 27, 1827 and 2641 genes were differentially expressed in Belclare, Fur and NWS ewes, respectively (P <  0.05 and FC > 1.5). Gene ontology (GO) analysis revealed that Fur and NWS had an up-regulation of enriched pathways involved in muscle contraction and development compared to Suffolk. However, there was a down-regulation of the immune response pathway in NWS compared to Suffolk. In addition, GO analysis showed similar expression patterns involved in muscle contraction, extracellular matrix (ECM) development and cell-cell junction in both Norwegian ewe breeds, which differed to the Irish ewe breeds. CONCLUSIONS: This novel study has identified a number of conserved and breed-specific biological processes under the effect of oestrous synchronisation that may impact cervical sperm transport during the follicular phase of the reproductive cycle.

Immunoproteomic analysis of the secretome of bovine-adapted strains of Staphylococcus aureus demonstrates a strain-specific humoral response.

Staphylococcus aureus is a common pathogen associated with bovine intramammary infection. A number of distinct S. aureus lineages are associated with such infections although there is a dearth of knowledge regarding the major immunogenic antigens associated with each lineage and whether these antigens provide protection against heterologous strains. Identification of the major immunogenic antigens of the predominant bovine-adapted S. aureus lineages would assist in the design of effective vaccines and diagnostic tests to control intramammary infections caused by S. aureus. The aim of this study was to characterise the serum IgG response to S. aureus extracellular proteins in cows infected with strains from different lineages, as well as to identify antigenic proteins produced by these strains. Genotypic characterisation found that strain MOK124 (CC151) encoded more toxins, including the ruminant-specific leukocidin LukMF, compared to strain MOK023 (CC97). In addition, MOK124 secreted more toxins in vitro, compared to MOK023. Immunoproteomic analysis was performed using sera from cows infected with either MOK023 or MOK124. One-dimensional serum blotting revealed that cows infected with MOK023 predominantly generated a humoral response against high molecular weight proteins while cows infected with MOK124 primarily generated a humoral response against low molecular weight proteins. Two-dimensional serum blotting demonstrated that antibodies produced by an MOK023 infected cow could cross react with some of the extracellular proteins produced by MOK124 and vice versa. Mass spectrometry analysis of immunoreactive proteins identified common candidate immunogens produced by both strains, including α-hemolysin and ß-hemolysin. In addition, strain-specific candidate immunogens were also identified. This study demonstrates that genes encoding important S. aureus secreted virulence factors, the production of cognate gene products, and the humoral immune response to infection is, to an extent, strain-dependent. However, the identification of some common candidate immunogens suggests that there are proteins that can be exploited for further vaccine or diagnostic research that targets S. aureus strains from a variety of lineages.

Biochemical and molecular characterization of sialylated cervical mucins in sheep†.

Sialic acid occupies terminal positions on O-glycans of cervical mucins, where they contribute to the increased viscosity of mucin thereby regulating sperm transport. This study characterized the sialylated cervical mucins from follicular phase mucus of six European ewe breeds with known differences in pregnancy rates following cervical artificial insemination (AI) using frozen-thawed semen at both synchronized and natural estrus cycles. These were Suffolk (low fertility) and Belclare (medium fertility) in Ireland, Ile de France and Romanov (both with medium fertility) in France, and Norwegian White Sheep (NWS) and Fur (both with high fertility) in Norway. Expression of mucin and sialic acid related genes was quantified using RNA-sequencing in cervical tissue from Suffolk, Belclare, Fur, and NWS only. Cervical tissue was also assessed for the percentage of cervical epithelial populated by mucin secreting goblet cells in the same four ewe breeds. Biochemical analysis showed that there was an effect of ewe breed on sialic acid species, which was represented by Suffolk having higher levels of Neu5,9Ac2 compared with NWS (P < 0.05). Suffolk ewes had a lower percentage of goblet cells than Fur and NWS (P < 0.05). Gene expression analysis identified higher expression of MUC5AC, MUC5B, ST6GAL1, and ST6GAL2 and lower expression of ST3GAL3, ST3GAL4, and SIGLEC10 in Suffolk compared with high fertility ewe breeds (P < 0.05). Our results indicate that specific alterations in sialylated mucin composition may be related to impaired cervical sperm transport.

Intestinal microbiota modulation and improved growth in pigs with post-weaning antibiotic and ZnO supplementation but only subtle microbiota effects with Bacillus altitudinis.

The objective was to evaluate the effect of dietary Bacillus altitudinis spore supplementation during day (D)0-28 post-weaning (PW) and/or D29-56 PW compared with antibiotic and zinc oxide (AB + ZnO) supplementation on pig growth and gut microbiota. Eighty piglets were selected at weaning and randomly assigned to one of five dietary treatments: (1) negative control (Con/Con); (2) probiotic spores from D29-56 PW (Con/Pro); (3) probiotic spores from D0-28 PW (Pro/Con); (4) probiotic spores from D0-56 PW (Pro/Pro) and (5) AB + ZnO from D0-28 PW. Overall, compared with the AB + ZnO group, the Pro/Con group had lower body weight, average daily gain and feed intake and the Pro/Pro group tended to have lower daily gain and feed intake. However, none of these parameters differed between any of the probiotic-treated groups and the Con/Con group. Overall, AB + ZnO-supplemented pigs had higher Bacteroidaceae and Prevotellaceae and lower Lactobacillaceae and Spirochaetaceae abundance compared to the Con/Con group, which may help to explain improvements in growth between D15-28 PW. The butyrate-producing genera Agathobacter, Faecalibacterium and Roseburia were more abundant in the Pro/Con group compared with the Con/Con group on D35 PW. Thus, whilst supplementation with B. altitudinis did not enhance pig growth performance, it did have a subtle, albeit potentially beneficial, impact on the intestinal microbiota.

Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype.

BACKGROUND: Mastitis is an economically important disease of dairy cows with Staphylococcus aureus a major cause worldwide. Challenge of Holstein-Friesian cows demonstrated that S. aureus strain MOK124, which belongs to Clonal Complex (CC)151, caused clinical mastitis, while strain MOK023, belonging to CC97, caused mild or subclinical mastitis. The aim of this study was to elucidate the molecular mechanisms of the host immune response utilising a transcriptomic approach. Milk somatic cells were collected from cows infected with either S. aureus MOK023 or MOK124 at 0, 24, 48, 72 and 168 h post-infection (hpi) and analysed for differentially expressed (DE) genes in response to each strain. RESULTS: In response to MOK023, 1278, 2278, 1986 and 1750 DE genes were found at 24, 48, 72 and 168 hpi, respectively, while 2293, 1979, 1428 and 1544 DE genes were found in response to MOK124 at those time points. Genes involved in milk production (CSN1, CSN10, CSN1S2, CSN2, a-LACTA and PRLR) were downregulated in response to both strains, with a more pronounced decrease in the MOK124 group. Immune response pathways such as NF-κB and TNF signalling were overrepresented in response to both strains at 24 hpi. These immune pathways continued to be overrepresented in the MOK023 group at 48 and 72 hpi, while the Hippo signalling, extracellular matrix interaction (ECM) and tight junction pathways were overrepresented in the MOK124 group between 48 and 168 hpi. Cellular composition analysis demonstrated that a neutrophil response was predominant in response to MOK124, while M1 macrophages were the main milk cell type post-infection in the MOK023 group. CONCLUSIONS: A switch from immune response pathways to pathways involved in maintaining the integrity of the epithelial cell layer was observed in the MOK124 group from 48 hpi, which coincided with the occurrence of clinical signs in the infected animals. The higher proportion of M1 macrophages in the MOK023 group and lack of substantial neutrophil recruitment in response to MOK023 may indicate immune evasion by this strain. The results of this study highlight that the somatic cell transcriptomic response to S. aureus is dependent on the genotype of the infecting strain.

Microbial Quality of Liquid Feed for Pigs and Its Impact on the Porcine Gut Microbiome.

There is evidence that spontaneous fermentation frequently occurs in liquid pig feed that is intended to be delivered as fresh liquid feed, often with a resultant deterioration in the microbial and nutritional quality of the feed, which can negatively affect pig health and growth. Strategies including controlled fermentation with microbial inoculants, pre-fermentation or soaking of the cereal fraction of the diet, enzyme supplementation and dietary acidification have been employed to inhibit pathogens and prevent deterioration of feed nutritional quality, with promising results obtained in many cases. This review evaluates the impact of these strategies on the microbial quality of liquid feed and discusses how they can be further improved. It also investigates if/how these strategies impact the pig gut microbiota and growth performance of liquid-fed pigs. Finally, we review liquid feed system sanitisation practices, which are highly variable from farm to farm and discuss the impact of these practices and whether they are beneficial or detrimental to liquid feed microbial quality. Overall, we provide a comprehensive review of the current state of knowledge on liquid feed for pigs, focusing on factors affecting microbial quality and strategies for its optimisation, as well as its impact on the pig gut microbiome.

Conserved and breed-specific differences in the cervical transcriptome of sheep with divergent fertility at the follicular phase of a natural oestrus cycle.

BACKGROUND: The outcome of cervical artificial insemination (AI) with frozen-thawed semen in sheep is limited by the inability of sperm to traverse the cervix of some ewe breeds. Previous research has demonstrated that cervical sperm transport is dependent on ewe breed, as sperm can traverse the cervix in greater numbers in some higher fertility ewe breeds. However, the molecular mechanisms underlying ewe breed differences in sperm transport through the cervix remain unknown. In this study, we aimed to characterise the cervical transcriptome of four European ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen at the follicular phase of a natural oestrous cycle. Cervical post mortem tissue samples were collected from two Irish ewe breeds (Belclare and Suffolk; medium and low fertility, respectively) and from two Norwegian ewe breeds (Norwegian White Sheep (NWS) and Fur; high fertility compared to both Irish breeds) at the follicular phase of a natural oestrous cycle (n = 8 to 10 ewes per breed). RESULTS: High-quality RNA extracted from biopsies of the mid-region of the cervix was analysed by RNA-sequencing and Gene Ontology (GO). After stringent filtering (P <  0.05 and FC > 1.5), a total of 11, 1539 and 748 differentially expressed genes (DEGs) were identified in Belclare, Fur and NWS compared to the low fertility Suffolk breed, respectively. Gene ontology analysis identified significantly enriched biological processes involved in muscle contraction, extracellular matrix (ECM) development and the immune response. Gene co-expression analysis revealed similar patterns in muscle contraction and ECM development modules in both Norwegian ewe breeds, which differed to the Irish ewe breeds. CONCLUSIONS: These breed-specific biological processes may account for impaired cervical sperm transport through the cervix in sheep during the follicular phase of the reproductive cycle. This novel and comprehensive dataset provides a rich foundation for future targeted initiatives to improve cervical AI in sheep.

Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes.

We investigated how protein quantity (10%-30%) and quality (casein and whey) interact with dietary fat (20%-55%) to affect metabolic health in adult mice. Although dietary fat was the main driver of body weight gain and individual tissue weight, high (30%) casein intake accentuated and high whey intake reduced the negative metabolic aspects of high fat. Jejunum and liver transcriptomics revealed increased intestinal permeability, low-grade inflammation, altered lipid metabolism, and liver dysfunction in casein-fed but not whey-fed animals. These differential effects were accompanied by altered gut size and microbial functions related to amino acid degradation and lipid metabolism. Fecal microbiota transfer confirmed that the casein microbiota increases and the whey microbiota impedes weight gain. These data show that the effects of dietary fat on weight gain and tissue partitioning are further influenced by the quantity and quality of the associated protein, primarily via effects on the microbiota.

An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake.

The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.

Effects of dietary n-3-PUFA supplementation, post-insemination plane of nutrition and pregnancy status on the endometrial transcriptome of beef heifers.

Supplementation of cattle diets with n-3-polyunsaturated fatty acids (PUFA) can improve reproductive efficiency. Conversely, short-term fluctuations in feed supply can impact pregnancy establishment. The objectives of this study were to examine the effects of (1) dietary supplementation with n-3-PUFA and (2) post-insemination plane of nutrition on the endometrial transcriptome. Beef crossbred heifers were offered concentrate based diets fortified with n-3-PUFA (PUFA; n = 32) or not (CONT; n = 28) for 30 days prior to breeding at a synchronised oestrous. Following artificial insemination, heifers were allocated within treatment to either a high or low plane of nutrition. Heifers were maintained on these diets for 16 days following which endometrial tissue was harvested at slaughter for subsequent RNAseq analysis. The influence of pregnancy status on the endomentrial transcriptome, within each dietary treatment group, was also examined. Post-insemination diet affected (P < 0.05) the endometrial transcriptome. Specifically, within n-3-PUFA-supplemented heifers, genes involved in embryonic development and mTOR signalling pathways, important in pregnancy establishment, were identified as differentially expressed. Results indicate that dietary supplementation of cattle diets with n-3-PUFA may have a positive effect on the expression of key fertility-related genes and pathways, during the critical window of maternal recognition of pregnancy, particularly where animals are underfed.

Growth performance and hematological changes of weaned beef calves diagnosed with respiratory disease using respiratory scoring and thoracic ultrasonography.

This study investigated 1) the effect of clinical bovine respiratory disease (BRD) and associated lung consolidations on growth performance and hematological profiles of recently weaned beef calves and 2) the relationship between clinical respiratory signs and lung consolidation detected by thoracic ultrasonography (TUS). One hundred and fifty-three weaned beef calves (209 days old [SD: 35.8] and 306 kg [SD: 26.3], at arrival) purchased and transported from auction markets were accommodated indoors in concrete slatted floor pens. Calves were weighed weekly from arrival until day 28 and on day 65 post-arrival. Assessment of BRD and blood sample collection for hematological profiles were performed on scheduled days (at arrival, on days 7, 14, and 28) and on other days upon BRD diagnosis. Animals were assessed for BRD using a total clinical respiratory score (CRS) of five clinical signs (rectal temperature, ear position, cough, nasal secretion, and eye secretion with each ranging from normal [0] to abnormal [3]) and TUS scores (normal [0] to lung consolidation ≥ 1 cm2 [2]). Based on CRS, 35% of calves were CRS+ (CRS ≥ 5) and 65% were CRS- (CRS < 5). Although no lung consolidations (TUS-) were detected at arrival, 34% of calves developed lung consolidation (≥1 cm2) (TUS+) during the first 28 d post-arrival. Only fever (>39.6 °C) and nasal discharge were weakly associated (r = 0.19, P <0.05) with lung consolidation. On the day of BRD detection, neutrophil number and neutrophil:lymphocyte ratio were 58% and 73% greater, respectively, in BRD calves with lung consolidation compared with healthy calves. From day 0 to 65, calf average daily gain (ADG) did not differ (P >0.05) between CRS+ and CRS- calves but was 0.09 kg/d lower (P < 0.05) for TUS+ compared with TUS- calves. Calves classified as BRD (CRS + TUS ≥ 5) with lung consolidation had lower (P < 0.05) ADG from arrival until day 28 than healthy calves and BRD calves without lung consolidation (0.11 ± 0.10 vs. 0.53 ± 0.07 vs. 0.57 ± 0.10 kg/d, respectively); however, no differences in ADG were observed from day 0 to 65. Conventional methods to diagnose BRD failed to detect calves with lung lesions. TUS is a useful tool to detect lung lesions and its implementation in combination with CRS should provide a more accurate and early diagnosis of BRD, which is fundamental to successful treatment, animal welfare, and growth performance.