David Anthony Kenny

The microbiome assembly of the neonatal gastrointestinal tract is critical for immune and metabolic development, and birth delivery method can influence initial microbial colonisation. Using 16S rRNA gene amplicon sequencing, we investigated the effect of transvaginal and elective caesarean section delivery on microbial composition across five gastrointestinal regions (colon, ileum, jejunum, meconium, and rumen) in Aberdeen Angus calves (transvaginal, TV; n = 12; caesarean section, CS; n = 10) across two research farms. Absolute microbial quantities were measured using 16S rRNA qPCR. Alpha diversity (Observed, Shannon, Simpson) was compared between delivery methods within each region using Wilcoxon rank-sum tests, whereas beta diversity (Bray–Curtis PERMANOVA) and differential abundance (MaAsLin2) analyses were conducted with sex and farm as fixed effects. Alpha diversity varied among gastrointestinal regions ( p < 0.05) but did not differ between delivery methods within any region (all BH-adjusted q ≥ 0.74). Gastrointestinal region was the primary determinant of microbial community composition (R ² = 0.24, p < 0.001), with delivery method explaining minimal additional variance. A statistically significant but weak Region × Delivery interaction was observed (R ² = 0.06, p = 0.02), indicating that any influence of delivery method was site-dependent rather than uniform across the gastrointestinal tract. Farm explained negligible variation (R ² = 0.01, p = 0.17) and no overall delivery method effect was detected. Per-region analyses found no statistically significant treatment effects within individual regions (all p ≥ 0.06), suggesting the interaction reflected modest region-specific trends rather than strong site-specific shifts. Microbial load and community composition were comparable between CS and TV calves at birth. Early microbial establishment was therefore primarily driven by anatomical site, with postnatal environmental exposure and host–microbe interactions likely playing a greater role than delivery method in shaping early gastrointestinal microbial assembly in neonatal beef calves.

Adipose tissue represents a major endocrine organ, playing a central role in many biochemical systems regulating metabolic status and energy homeostasis, as well as the metabolic regulation of reproductive function in cattle. The objective of this study was to evaluate the effect of differential plane of nutrition from 2 to 12 weeks of age on the molecular regulation of subcutaneous adipose in bull calves. Holstein-Friesian bull calves were offered either a high (HI; n = 15) or moderate (MOD; n = 15) plane of nutrition from 2 to 12 weeks of age. At 12 weeks of age all calves were euthanised and subcutaneous adipose samples harvested, which were then subjected to global transcriptomic and proteomic analyses. Growth rates during the differential feeding period were 0.58 and 0.88 kg/day for MOD and HI groups, respectively. A total of 1,311 mRNA, 6 miRNA and 196 proteins displayed differential abundance (adj. P-value < 0.05; fold change > 1.5) between the HI and MOD treatment groups. Pathway analysis revealed enrichment of pathways related to cholesterol biosynthesis and PPAR signalling. Results from this study identify novel genes regulating the molecular response of subcutaneous adipose tissue to an elevated plane of nutrition during the pre-weaning period in bull calves.

During the peri- and early post-partum period, the gastrointestinal tract (GIT) of the calf is colonised by a diverse microbiota. In the colon, this microbial community contributes to digestive activities, immune modulation, and overall calf health and productivity. However, the current knowledge of temporal microbial establishment in the neonatal hindgut is limited. This study focused on the ontogeny of colon microbiota establishment in Aberdeen Angus cross beef calves located across two farms, from birth through to post-weaning. Colon digesta samples were obtained from calves euthanised on days D0 (n = 7), D7 (n = 7), D14 (n = 5), D21 (n = 7), D28 (n = 5), and D96 (n = 7) of life. 16S rRNA amplicon sequencing was used to determine prokaryotic community composition. The alpha (α) and beta (β) diversity were assessed with age and farm included as fixed effects. Bacterial α-diversity increased significantly with age, showing changes in relative abundance between D7 and later stages, including D21, D28, and D96 (each p < 0.0001). PERMANOVA analysis indicated no significant difference in microbial composition between D14 and D21 (P = 0.22), suggesting a period during which compositional changes were reduced, reflecting a temporary phase of relative similarity in the colon microbiota. However, weaning altered the colon microbiota, as evidenced by the differences were observed between D28 and D96 (P < 0.001) suggested compositional shifts associated with weaning, accompanied by increased α-diversity. These observations will help to inform the design of the future, large scale studies aimed at understanding how early life microbial dynamics influence calf health, welfare, and future productive performance.

Enhanced early-life nutrition in calves holds potential for improving economically important traits, including growth rate, milk yield and reproductive development. However, the mechanisms through which these nutritional strategies affect skeletal muscle development remain to be fully elucidated. This study aimed to evaluate the impact of enhanced dietary intake during early calf-hood on the transcriptional profile of skeletal muscle tissue. Angus × Holstein-Friesian heifer dairy-calves were offered either a high (HI, n = 10) or moderate (MOD, n = 10) diet from 3 to 21 weeks of life. At 21 weeks of age, M. longissimus thoracis et lumborum tissue was harvested from all calves and subsequently subjected to mRNA sequencing. Altered early-life nutrition led to the differential expression of 482 genes in the skeletal muscle transcriptome (False discovery rate (FDR) < 0.1; fold change > 1.5) between HI and MOD calves. Differentially expressed genes were involved in processes related to metabolism, energy production and cellular growth and proliferation and included enrichment of the Sirtuin signalling pathway and skeletal muscle system development and function. The results of this study identify novel gene transcripts involved in the molecular regulation of skeletal muscle response to nutritional modulation, offering insights into muscle development and its potential impact on tissue composition.

Enhanced early-life nutrition is known to induce precocious reproductive development in the bull calf, mediated through gonadotropin releasing hormone (GnRH) stimulated gonadotropin pulsatility in the anterior pituitary gland. The objective of this study was to evaluate transcriptomic and proteomic responses within the anterior pituitary of Holstein–Friesian bull calves offered different planes of nutrition during early life. Bull calves were offered either a high (HI; n = 15) or moderate (MOD; n = 15) plane of nutrition between 2–12 weeks of age and subsequently euthanised at 12 weeks of age. The anterior pituitary tissue was harvested from all calves and miRNAseq, mRNAseq and proteomic analyses undertaken. High diet calves displayed greater growth rates compared to MOD calves (P < 0.001). Overall, 37 mRNAs and 5 miRNAs were differentially expressed between treatment groups (FDR < 0.1). Reduced expression of miR-205 together with greater expression of specific target mRNA genes (PCSK1, SERPINA1, CARTPT) in the HI calves suggested a relationship between these mRNA and miRNA. Furthermore, co-regulatory network analysis of the proteomic data revealed interactions between PCSK1, SERPINA1 and CARTPT, and proteins involved in cellular proliferation, metabolism and GnRH signalling, highlighting a role for these proteins in mediating the intersection between enhanced metabolic status with reproductive signalling in young bull calves.

Ruminants play an important role in global food security and nutrition. The rumen microbial community provides ruminants with a unique ability to convert human indigestible plant matter into high quality edible protein. However, enteric CH₄ produced in the rumen is both a potent GHG and a ME loss for ruminants. As the rumen microbiome constitutes 15% to 40% of the interanimal variation in enteric CH₄ emissions, understanding the microbiological mechanisms underpinning ruminal methanogenesis and its interaction with the host animal is crucial for developing CH₄ mitigation strategies. Variation in the relative abundance of different microbial species has been observed in cattle with contrasting residual CH₄ emission and CH₄ yield, with up to 20% of the variation in interanimal CH₄ emissions attributable to the presence of a small number of microbial species. The demonstration of ruminotypes associated with high or low CH₄ emissions suggests that interactions within complex microbial consortia and with their host are a major source of variation in CH₄ emissions. Consequently, microbiome-assisted genomic approaches are being developed to select low CH₄-emitting cattle, with breeding values for enteric CH₄ being included as part of national breeding programs. Generating rumen microbiome data for use in selection programs is expensive, therefore, identifying microbial biomarkers in milk or plasma to develop predictive models which include microbial predictors in equations based on animal-related data is required. A better understanding of the rumen microbiome has also aided the development and refinements of antimethanogenic feed additives. However, these strategies, which increase the amount of reducing equivalents in the rumen ecosystem, do not generally result in an enrichment of propionate or an improvement in animal performance. Current research aims to provide alternative sinks to reducing equivalents and to stimulate activity of commensal microbes or the supplementation of direct fed microbials to capture lost energy. Furthering our knowledge of the rumen microbiome and its interaction with the host will aid in the development of CH₄ mitigation strategies for ruminant livestock.

Background: Reproductive development may be advanced in bull calves through enhanced dietary intake during the early life period. This effect between enhanced nutrition with subsequent earlier reproductive development is orchestrated through signalling within the hypothalamic-pituitary-testicular axis. Within the hypothalamus, the arcuate nucleus (ARC) is crucial for the integration of peripheral metabolic status with subsequent gonadotropin releasing hormone (GnRH) signalling; however, the precise molecular control regulating this effect is not fully known. The aim of this study was to evaluate the global transcriptomic and proteomic responses to varied plane of nutrition during early calf-hood in young dairy bull calves. Additionally, we sought to integrate these ‘omics’ datasets to determine key genes and proteins contributing to earlier reproductive development. Between 2–12 weeks of age, 30 Holstein-Friesian bull calves (mean age: 17.5 days; mean bodyweight 48.8 kg), were offered either a high or moderate plane of nutrition with 15 calves in each group. At 12 weeks of age, all calves were euthanised and the ARC tissue isolated from each calf. The ARC tissue was then used for global transcriptomic (miRNAseq and mRNAseq) and proteomic analyses. Results: Bioinformatic analyses were undertaken to determine differentially expressed transcripts (FDR < 0.1; fold change > 1.5) between the dietary treatment groups, resulting in the identification of 1 differentially expressed miRNA (miR-2419-3p) and 83 differentially expressed mRNA in the ARC region. mRNA target gene prediction identified Complement 3 (C3) as a target of miR-2419-3p, suggesting a relationship between the two transcripts. Furthermore, through a co-regulatory network analysis conducted on the proteomics dataset, C3 was revealed as a hub protein. Additionally, through the proteomic network analysis, C3 was interacting with proteins involved in both insulin and GnRH signalling, highlighting a potential role for C3 in mediated the effect of enhanced nutritional status with earlier reproductive development within the ARC. Conclusion: This study highlights an effect of altered plane of nutrition in early life on the molecular control of the hypothalamic ARC. Additionally, results generated suggest a potential role for the C3 gene in mediating the interaction between enhanced metabolic status with reproductive development within the ARC, regulated by miR-2419-3p.

Background: Enhanced nutrition during the early calfhood period has been shown to lead to earlier pubertal development in heifer calves. This is of interest as earlier pubertal onset can subsequently facilitate earlier calving which can economically benefit production systems. Reproductive development in heifers is regulated by the hypothalamic-pituitary-ovarian signalling pathway. In particular the anterior pituitary gland is central to reproductive development, through the dynamics of gonadotropic pulsatility. However, despite clear knowledge of the influence of enhanced dietary intake on subsequent reproductive development, the molecular control governing this response in the pituitary gland within the hypothalamic-pituitary-ovarian signalling axis in heifer calves is not fully understood. The objective of this study was to examine the effect of an enhanced plane of nutrition during early life on the anterior pituitary gland of heifer calves through both transcriptomic and proteomic analyses. Between 3 and 21 weeks of age, heifer calves were offered either a high (HI, n = 14) or moderate (MOD, n = 14) plane of nutrition, designed to elicit target growth rates of 1.2 and 0.5 kg/d for HI and MOD groups, respectively. All calves were euthanised at 21 weeks of age and anterior pituitary tissue harvested for subsequent use in global transcriptomic and proteomic analyses. Results: Average daily gain was affected by diet (P < 0.001) and was 1.18 and 0.50 kg/day, for HI and MOD calves, respectively. RNAseq analysis resulted in the identification of 195 differentially expressed genes (P_adj 1.5), with 277 proteins identified as differentially abundant (P_adj 1.5) between contrasting dietary treatment groups. Biochemical pathway analysis of differentially affected genes and proteins revealed an enrichment for both growth hormone and GnRH signalling pathways (P_adj.adj.<0.05). Conclusions: Results from this study show that an enhanced dietary intake during early calfhood affected the molecular control of the anterior pituitary gland in heifer calves in early life.

Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is necessary for the accurate identification of feed efficient animals and will underpin accelerated genetic improvement of the trait. The aim of this study was to determine genes and biological processes contributing to RFI across varying breed type and dietary sources in skeletal muscle tissue. Residual feed intake was calculated in Charolais and Holstein–Friesian steers across multiple dietary phases (phase-1: high concentrate (growing-phase); phase-2: zero-grazed grass (growing-phase); phase-3: high concentrate (finishing-phase). Steers divergent for RFI within each breed and dietary phase were selected for muscle biopsy collection, and muscle samples subsequently subjected to RNAseq analysis. No gene was consistently differentially expressed across the breed and diet types examined. However, pathway analysis revealed commonality across breeds and diets for biological processes including fatty acid metabolism, immune function, energy production and muscle growth. Overall, the lack of commonality of individual genes towards variation in RFI both within the current study and compared to the published literature, suggests other genomic features warrant further evaluation in relation to RFI.