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Abstract Background Although rumen development is crucial, hindgut undertakes a significant role in young ruminants’ physiological development. High-starch diet is usually used to accelerate rumen development for young ruminants, but always leading to the enteral starch overload and hindgut dysbiosis. However, the mechanism behind remains unclear. The combination of colonic transcriptome, colonic luminal metabolome, and metagenome together with histological analysis was conducted using a goat model, with the aim to identify the potential molecular mechanisms behind the disrupted hindgut homeostasis by overload starch in young ruminants. Result Compared with low enteral starch diet (LES), high enteral starch diet (HES)-fed goats had significantly higher colonic pathology scores, and serum diamine oxidase activity, and meanwhile significantly decreased colonic mucosal Mucin-2 (MUC2) protein expression and fecal scores, evidencing the HES-triggered colonic systemic inflammation. The bacterial taxa Prevotella sp. P4-67, Prevotella sp. PINT, and Bacteroides sp. CAG:927, together with fungal taxa Fusarium vanettenii, Neocallimastix californiae, Fusarium sp. AF-8, Hypoxylon sp. EC38, and Fusarium pseudograminearum, and the involved microbial immune pathways including the “T cell receptor signaling pathway” were higher in the colon of HES goats. The integrated metagenome and host transcriptome analysis revealed that these taxa were associated with enhanced pathogenic ability, antigen processing and presentation, and stimulated T helper 2 cell (TH2)-mediated cytokine secretion functions in the colon of HES goats. Further luminal metabolomics analysis showed increased relative content of chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), and decreased the relative content of hypoxanthine in colonic digesta of HES goats. These altered metabolites contributed to enhancing the expression of TH2-mediated inflammatory-related cytokine secretion including GATA Binding Protein 3 (GATA3), IL-5, and IL-13. Using the linear mixed effect model, the variation of MUC2 biosynthesis explained by the colonic bacteria, bacterial functions, fungi, fungal functions, and metabolites were 21.92, 20.76, 19.43, 12.08, and 44.22%, respectively. The variation of pathology scores explained by the colonic bacterial functions, fungal functions, and metabolites were 15.35, 17.61, and 57.06%. Conclusions Our findings revealed that enteral starch overload can trigger interrupted hindgut host-microbiome homeostasis that led to impaired mucosal, destroyed colonic water absorption, and TH2-mediated inflammatory process. Except for the colonic metabolites mostly contribute to the impaired mucosa, the nonnegligible contribution from fungi deserves more future studies focused on the fungal functions in hindgut dysbiosis of young ruminants. Video Abstract

Abstract Ruminants play a critical role in our food system by converting plant biomass that humans cannot or choose not to consume into edible high-quality food. However, ruminant excreta is a significant source of nitrous oxide (N2O), a potent greenhouse gas with a long-term global warming potential 298 times that of carbon dioxide. Natural phytochemicals or forages containing phytochemicals have shown the potential to improve the efficiency of nitrogen (N) utilization and decrease N2O emissions from the excreta of ruminants. Dietary inclusion of tannins can shift more of the excreted N to the feces, alter the urinary N composition and consequently reduce N2O emissions from excreta. Essential oils or saponins could inhibit rumen ammonia production and decrease urinary N excretion. In grazed pastures, large amounts of glucosinolates or aucubin can be introduced into pasture soils when animals consume plants rich in these compounds and then excrete them or their metabolites in the urine or feces. If inhibitory compounds are excreted in the urine, they would be directly applied to the urine patch to reduce nitrification and subsequent N2O emissions. The phytochemicals' role in sustainable ruminant production is undeniable, but much uncertainty remains. Inconsistency, transient effects, and adverse effects limit the effectiveness of these phytochemicals for reducing N losses. In this review, we will identify some current phytochemicals found in feed that have the potential to manipulate ruminant N excretion or mitigate N2O production and deliberate the challenges and opportunities associated with using phytochemicals or forages rich in phytochemicals as dietary strategies for reducing N excretion and excreta-derived N2O emissions.

Studying microRNA (miRNAs) in certain agri-food products is attractive because (1) they have potential as biomarkers that may allow traceability and authentication of such products; and (2) they may reveal insights into the products’ functional potential. The present study evaluated differences in miRNAs levels in fat and cellular fractions of tank milk collected from commercial farms which employ extensive or intensive dairy production systems. We first sequenced miRNAs in three milk samples from each production system, and then validated miRNAs whose levels in the cellular and fat fraction differed significantly between the two production systems. To accomplish this, we used quantitative PCR with both fractions of tank milk samples from another 20 commercial farms. Differences in miRNAs were identified in fat fractions: overall levels of miRNAs, and, specifically, the levels of bta-mir-215, were higher in intensive systems than in extensive systems. Bovine mRNA targets for bta-miR-215 and their pathway analysis were performed. While the causes of these miRNAs differences remain to be elucidated, our results suggest that the type of production system could affect miRNAs levels and potential functionality of agri-food products of animal origin.

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.

Abstract Background Rumen epithelial tissue plays an important role in nutrient absorption and rumen health. However, whether forage quality and particle size impact the rumen epithelial morphology is unclear. The current study was conducted to elucidate the effects of forage quality and forage particle size on rumen epithelial morphology and to identify potential underlying molecular mechanisms by analyzing the transcriptome of the rumen epithelium (RE). To achieve these objectives, 18 mid-lactation dairy cows were allocated to three groups (6 cows per group), and were fed with one of three different forage-based diets, alfalfa hay (AH), corn stover (CS), and rice straw (RS) for 14 weeks, respectively. Ruminal volatile fatty acids (VFAs) and epithelial thickness were determined, and RNA-sequencing was conducted to identify the transcriptomic changes of rumen epithelial under different forage-based diets. Results The RS diet exhibited greater particle size but low quality, the AH diet was high nutritional value but small particle size, and CS diet was low quality and small particle size. The ruminal total VFA concentration was greater in AH compared with those in CS or RS. The width of the rumen papillae was greater in RS-fed cows than in cows fed AH or CS. In total, 31, 40, and 28 differentially expressed (DE, fold change > 2, FDR

Bacillus amyloliquefaciens TL promotes broiler chicken performance by improving nutrient absorption and utilization and reducing intestinal inflammation. In this study, RNA-sequencing (RNA-seq)-based transcriptomes of ileal tissues collected from probiotic-fed and control broiler chickens were analyzed to elucidate the effects of the probiotic B. amyloliquefaciens TL, as a feed additive, on the gut immune function. In total, 475 genes were significantly differentially expressed between the ileum of probiotic-fed and control birds. The expression of genes encoding pyruvate kinase, prothymosin-α, and heat stress proteins was high in the ileum of probiotic-fed birds (FPKM > 500), but not in the control group. The gene ontology functional enrichment and pathway enrichment analyses revealed that the uniquely expressed genes in the control group were mostly involved in immune responses, whereas those in the probiotic group were involved in fibroblast growth factor receptor signaling pathways and positive regulation of cell proliferation. Bacillus amyloliquefaciens TL downregulated the expression of certain proinflammatory factors and affected the cytokine–cytokine receptor interaction pathway. Furthermore, B. amyloliquefaciens TL in broiler diets altered the expression of genes involved in immune functions in the ileum. Thus, it might contribute to improved broiler growth by regulating the immune system and reducing intestinal damage in broilers.

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

The dense and diverse community of microorganisms inhabiting the gastrointestinal tract of ruminant animals plays critical roles in the metabolism and absorption of nutrients, and gut associated immune function. Understanding microbial colonization in the small intestine of new born ruminants is a vital first step toward manipulating gut function through interventions during early life to produce long-term positive effects on host productivity and health. Yet the knowledge of microbiota colonization and its induced metabolites of small intestine during early life is still limited. In the present study, we examined the microbiota and metabolome in the jejunum and ileum of neonatal sika deer (Cervus nippon) from birth to weaning at days 1, 42, and 70. The microbial data showed that diversity and richness were increased with age, but a highly individual variation was observed at day 1. Principal coordinate analysis revealed significant differences in microbial community composition across three time points in the jejunum and ileum. The abundance of Halomonas spp., Lactobacillus spp., Escherichia–Shigella, and Bacteroides spp. tended to be decreased, while the proportion of Intestinibacter spp., Cellulosilyticum spp., Turicibacter spp., Clostridium sensu stricto 1 and Romboutsia spp. was significantly increased with age. For metabolome, metabolites separated from each other across the three time points in both jejunum and ileum. Moreover, the amounts of methionine, threonine, and putrescine were increased, while the amounts of myristic acid and pentadecanoic acid were decreased with age, respectively. The present study demonstrated that microbiota colonization and the metabolome becomes more developed in the small intestine with age. This may shed new light on the microbiota-metabolome-immune interaction during development.

It is well known that serum biochemical parameters and hormones contribute greatly to the physiological and metabolic status of dairy cows. However, few studies have focused on the variation of these serum parameters in multiparous mid-lactation cows without the interference of diet and management. A total of 287 Holstein dairy cows fed the same diet and maintained under the same management regime were selected from a commercial dairy farm to evaluate the effects of days-in-milk (DIM) and parity on serum biochemical parameters and hormone profiles. Milk yield and milk protein content were affected by DIM and parity (p < 0.05). Milk protein yield showed a numerically decreasing trend with parity, and it was relatively constant in cows with parities between 2 and 4 but lower in cows with parity 6 (p = 0.020). Ten and five serum biochemical parameters related to protein status, energy metabolism, liver and kidney function, and oxidative stress were affected by DIM and parity, respectively (p < 0.05). Glucagon, insulin-like growth factor 1 concentration, and the revised quantitative insulin sensitivity check index were significantly different (p < 0.05) among cows with different DIM. Parity had no effect on hormone concentrations. An interaction between DIM and parity effect was only detected for glucagon concentration (p = 0.015), which showed a significantly increasing trend with DIM and overall decreasing trend with parity. In summary, DIM and parity played an important role in affecting the serum biochemical parameters and/or hormones of dairy cows, with serum parameters affected more by DIM than parity.

A series of batch cultures were conducted to investigate the effects of oleic acid (OA) on in vitro ruminal dry matter degradability (IVDMD), gas production, methane (CH4) and hydrogen (H2) production, and proportion of fatty acids. Rumen fluid was collected from fistulated goats, diluted with incubation buffer, and then incubated with 500 mg Leymus chinensis meal supplemented with different amounts of OA (0, 20, 40, and 60 mg for the CON, OA20, OA40 and OA60 groups, respectively). Incubation was carried out anaerobically at 39°C for 48 h, and the samples were taken at 12, 24 and 48 h and subjected to laboratory analysis. Supplementation of OA decreased IVDMD, the cumulative gas production, theoretical maximum of gas production and CH4 production, but increased H2 production. However, no effect was observed on any parameters of rumen fermentation (pH, ammonia, production of acetate, propionate and butyrate and total volatile fatty acid production). The concentrations of some beneficial fatty acids, such as cis monounsaturated fatty acids and conjugated linoleic acid (CLA) were higher (P < 0.05) from OA groups than those from the control group at 12 h incubation. In summary, these results suggest that the OA supplementation in diet can reduce methane production and increase the amount of some beneficial fatty acids in vitro.

Meat animals are unique as experimental models for both lipid metabolism and adipocyte studies because of their direct economic value for animal production. This paper discusses the principles that regulate adipogenesis in major meat animals (beef cattle, dairy cattle, and pigs), the definition of adipose depot-specific regulation of lipid metabolism or adipogenesis, and introduces the potential value of these animals as models for metabolic research including mammary biology and the ontogeny of fatty livers.

Selection for feed efficiency is crucial for improving economic and environmental sustainability in beef cattle production. Residual feed intake (RFIfat) is a commonly used measure of feed efficiency and is determined in a drylot setting by calculating the difference between observed and expected dry matter intake (DMI), where expected feed intake is adjusted for metabolic body weight (BW), average daily gain (ADG) and body fatness. Lower RFIfatcattle are more efficient animals as they eat less than predicted for the same growth, body size and body fatness. Limited studies have been conducted evaluating the role of RFIfaton the subsequent performance of cow-calf pairs on native range. Kinsella Composite cows and calves (n = 120) grazed native pasture from July 11 to Sept 12 (summer) and from Sept 13 to Nov 2 (fall) of 2023 were included in this study. All dams had previously been evaluated for RFIfatas a heifer (8 to 12 mo of age) using the GrowSafe Feed Intake System (Vytelle, Canada). Cow and calf ADG were subjected to an analysis of covariance using lm function from stats R core package (R Core Team, 2024), with cow age (2 to 8 yr of age) as the fixed effect and RFIfatas the covariate, analyzing separately by season. An unbalanced Tukey HDS post-hoc were applied for age and p-values < 0.05 were considered significant. Weight gain was assessed on cows with an initial BW on pasture of 598.4 ± 68.4 kg, and 2 to 8 yr of age, and on calves having an initial on pasture BW of 106 ± 21.5 kg, and 65 ± 14 d of age. Cow age affected (P < 0.01) cow ADG during summer, with the youngest dams (2 yr old) gaining more weight than older animals (7 yr old; Figure 1A). No effect of RFIfatwas found on cow weight gain during summer grazing. However, during fall grazing, RFIfataffected (P < 0.01) cow ADG (Figure 1B). Low-RFIfatcows (efficient) had increased weight gain during fall grazing as compared with high-RFIfatcows (inefficient: Figure 1B). Calf ADG was not affected (P > 0.1) by cow age, cow RFIfat and cow ADG during summer and fall. We conclude that cows with low RFIfatexhibited superior body weight gain, during fall grazing on native range when forage nutrient quality and quantity become limiting. [ABSTRACT FROM AUTHOR]

Liver health is vital for growth and health of ruminants, which can directly affect their performance. High-concentrate diet (HCD) feeding, a common practice to meet the energy requirements for animal production and growth, has been known to induce liver damage, including nonalcoholic fatty liver (NAFL) and nonalcoholic steatohepatitis (NASH) in ruminants. To date, the regulatory mechanisms of liver metabolic dysfunctions in ruminants induced by HCD are not well defined. To elucidate molecular regulatory mechanisms underlying liver dysfunction in ruminants, we compared liver transcriptome and single-cell transcriptome of dairy goats that had varied responses to the HCD, aiming to underpin the key mechanisms behind resilience and susceptibility to NASH in ruminants. After feeding 30 dairy goats with low-concentrate diet (LCD, n = 15, defined as Con) or high-concentrate diet (HCD, n = 15) for 6 wk, 10 of them developed NASH (defined as NASH), while the other 5 did not showed any NASH symptom (defined as NASHtolerance, NASH-T) under HCD. Liver tissues were collected to extract RNA. The paired-end RNA-seq library was sequenced with a NovaSeq6000 sequencer (Illumina). Real-time quantitative PCR was conducted to verify the significantly different genes among groups. Liver single-cell transcriptome was performed using 10×Genomics Chromium system. Liver transcriptome analysis revealed that the expression level of genes involved in the interleukin (IL)-17 signaling pathway, including IL-17A (P = 0.035; 0.001), Act1 (P = 0.036; 0.002), FOSB (P = 0.041; 0.048) and IL-1β (P = 0.022; 0.002) in the NASH group were significantly greater than those in the Con and NASH-T groups. Hepatic single-cell RNA sequencing identified seven cell types in the liver, including hepatocytes, macrophages, T cells, endothelial cell, natural killer (NK) cell, hepatic stellate cells (HSCs), B cells. In T cell subset, significantly decreased T helper 17 (TH17) cells and increased regulatory T (Treg) cells were detected in the NASH group compared with Con and NASH-T groups. In TH17 cell, the expression levels of IL-17A (P = 0.004; 0.009) and IL-23R (P = 0.007; 0.01; the surface antibodies of TH17 cells) in NASH group were significantly greater than those in the Con and NASH-T groups. The expression levels of Foxp3 (P < 0.001; 0.013), IL-2R (P < 0.001; 0.001), CTLA-4 (P = 0.005; 0.017) and CD127 (P = 0.004; 0.009; the surface antibodies of Treg cells) in NASH group were significantly less than those in the Con and NASH-T groups. Our results revealed the role of liver immune cells in maintaining tolerance to NASH in dairy goats under HCD, which provides new understanding in pathogenesis of NASH under HCD. Further studies are needed to identify major factors that drive the changes of ratio of TH17/Treg cell. [ABSTRACT FROM AUTHOR]

The rumen harbors a complex symbiotic microbiome (bacteria, archaea, protozoa, fungi and viruses), which degrades plant cell walls and ferments sugars to the volatile fatty acids that provide energy to host. Extensive recent research has revealed that variation in rumen microbiome composition and function can directly and in directly influence many phenotypes in cattle such as feed efficiency, methane emission, metabolic health, milk and meat quality. Such findings highlight the opportunity to intervene rumen microbiome for improved productivity, health and reduced environmental footprint. More and more evidence revealed the individualized rumen microbiome and host genetics could be one of the factors in colonizing of selective rumen microbiome. This presentation will focus on to date knowledge on “heritability” of rumen microbes and explore the opportunities to breed cattle with a desired rumen microbiome for improved feed efficiency and lower emission of greenhouse gases. [ABSTRACT FROM AUTHOR]

Colonization and establishment of a balanced and healthy gut microbiome during the neonatal period can directly and indirectly influence animals by affecting the development and metabolism, nutrition absorption, barrier and immune functions, and endocrine and neuron transmitter secretions. Therefore, neonatal period represents a crucial window of time in animal’s life that induces long-term developmental and immune memory. Therefore, alterations in the early gut microbial composition and colonization trajectories lead to long-term negative effects on animals’ production and health. While the rapidly developing gut microbial community is affected by various external factors due to its instability, it provides a great opportunity for microbial intervention to alter microbial colonization trajectories and their subsequent impact on gut health. Recent advance research has been successful in restoring altered gut microbial communities by using microbial interventions such as vaginal seeding, fecal microbial transplantation, probiotics, and prebiotics. However, there is a lack of understanding on the long-term effects of these interventions on gut health in neonatal ruminants. Direct fed microbes (live naturally existing microbes that can improve health and production performance) with psychobiotic function (a type of probiotic that affect cognitive and behavioral functions of the host via the gut-brain axis) can be one of the novel microbiome solutions to target and alter the microbiome dysbiosis. The use of direct fed microbes, postbiotics and psychobiotics and their potential implications in improving calf health and productivity leads to a novel solution to the manipulation of the gut microbiome in calves. [ABSTRACT FROM AUTHOR]

The term “psychobiotics” refers to beneficial microbiota, such as Lactobacillus spp., which positively influence the hypothalamic-pituitary-adrenal axis, immune response, and inflammation via the gut-brain axis. While these bacteria are recognized for benefiting their host, research on their application in cattle is limited. Therefore, this study evaluated the impacts of administering a bovine-derived mixture of Lactobacillus spp. during early life to beef calves as a strategy to modulate long-term gut microbiota and potentially alleviate weaning stress. Crossbred beef calves [n = 32; 66 ± 11 kg of body weight (BW); 60 ± 6 d of age] were stratified by age and sex and randomly assigned to receive either two doses of an orally-administrated Lactobacillus cocktail (n = 16; 10^9 CFU; LAB) or saline solution (n = 16; CON) 3-d apart. After first inoculation (d 0), cow-calf pairs were allocated to four different paddocks (two/ treatment) for 15 d, and then, both treatments were placed in a single pen until weaning, at ~202 d of age. After weaning, calves from both treatments were housed in a single pen. Body weight was recorded, and blood samples were collected on d 0, 3, weaning, and 3- and 14-d post-weaning (PW). Data was analyzed as a completely randomized design. Plasma concentrations of phenylalanine (P = 0.04) were greater, while tyrosine (P = 0.09) and lysine (P = 0.07) tended to be greater in LAB compared with CON calves. Furthermore, LAB calves had reduced plasma concentrations of heat shock proteins 70 (P = 0.04; 0.02 vs. 0.13 ng/mL) and cortisol (P = 0.03; 108.1 vs. 121.1 ng/mL). A tendency for a treatment × day interaction was detected (P ≤ 0.07) for white blood cells (WBC), where CON calves had decreased WBC and lymphocytes (P = 0.05) on d 0 compared with LAB. Treatment did not impact average daily gain and final BW (P ≥ 0.26). Regardless of treatment, weaning stress increased plasma concentrations of haptoglobin (P < 0.01), serotonin (P = 0.06), and the counts and percentages of monocyte, eosinophils, and basophils (P < 0.01), whereas gamma-aminobutyric acid, aspartate, and insulin-like growth factor-1 concentrations decreased (P < 0.01) on d 3 PW. In conclusion, early life inoculation of suckling beef calves with a Lactobacillus spp. mixture presents promising effects on mitigating some physiological stress indicators, as indicated by decreased cortisol and heat shock protein concentrations and greater concentrations of amino acids precursor of central catecholamines. These preliminary results suggest that psychobiotics could offer a promising avenue for stress management in beef calves, potentially with long-term effects. This emphasizes the importance of future research on other physiological and behavioral indicators of weaning and other stressors to fully elucidate the potential benefits of psychobiotic inoculation in livestock management. [ABSTRACT FROM AUTHOR]

Shiga toxigenic Escherichia coli (STEC), specifically serogroups O26, O45, O111, O103, O121, O145, and O157 (Top 7), pose significant health risks. Cattle are the primary reservoir of STEC, and effective intervention remains elusive. The identification of Lactobacillus spp. with antimicrobial activity as directfed microbials (DFMs) presents a potential strategy for pathogen reduction. These strains are not only capable of favorably modulating the gut microbiota but also possess the innate ability to produce bacteriocins that can target specific pathogens including STEC. Selection of viable anti-STEC Lactobacillus strains requires assessment of the presence or absence of prophage that may revert from the lysogenic to lytic phase and affect their efficacy. This study aimed to characterize anti-STEC potential of 14 Lactobacillus strains isolated from cattle and to identify their associated bacteriocins and prophages. Antimicrobial activity of 14 Lactobacillus strains against the top 7 STEC strains was determined using live culture spot assays and cell-free supernatants (CFS) well-diffusion assays. To further assess their anti-STEC efficacy, Lactobacillus strains with the strongest activity were selected and further evaluated in MRS broth culture and rumen fluid. The ability of Lactobacillus strains to inhibit STEC attachment to Caco-2 epithelial cells was also assessed. Prokka 1.14.6, and Bagel5 were utilized to identify genes encoding bacteriocins. Additionally, PHASTEST 3.0 was utilized to identify prophages. All 14 strains demonstrated antimicrobial activity against the top 7 STEC serogroups. Notably, L. agilis strains L3 and L6, with genome sizes of 2,063,576 bp and 2,071,091 bp respectively, and L. amylovorus L7 (883,016 bp) exhibited the greatest anti-STEC activities, targeting O157, O26, O45, and O103 for L3 and L6, and O157, O45, and O103 for L7. The CFS from these strains showed antiSTEC activity at pH 4.4-4.6, but not at 7, suggesting that organic acids played a role in inhibition. In MRS, DFM reduced STEC O157:H7 by 5 to 7.4 logs after 24 h. However, in rumen fluid, no notable reduction in STEC O157:H7 was observed. Bioinformatic analysis revealed that the L7 genome encoded Helveticin-J, a Class III bacteriocin. Prophage identified included 1 intact (51,818 bp) and 1 non-intact (17,267 bp) in L3, and 2 intact (46,916 bp, 20,295 bp) and 1 non-intact (13,939 bp) in L6, while no prophage was identified in L7. This study identified novel DFMs with activity against STEC, but future studies with cattle are required to confirm their ability to inhibit STEC. [ABSTRACT FROM AUTHOR]

As the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome has an integral role in determining host feed efficiency. Counterintuitively, current evidence suggests that a less diverse rumen microbiome is associated with improved feed efficiency, possibly as a result of greater metabolic precision and avoidance of energy spilling fermentative pathways. The composition of the rumen microbiome is mainly determined by diet, but host traits such as rumen volume, rate of passage, rumination and immunity also have influence. Although less microbial diversity may improve feed efficiency in cattle fed a specific diet, reduced diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture is the energetic foundation of the rumen microbiome and considerable capital has been invested to develop additives that redirect hydrogen flow away from the reduction of CO2 to CH4 towards alternative sinks. These additives have been shown to reduce enteric CH4 emissions by 30 to 80%, but improvements in feed efficiency have been less than stoichiometric predictions. Approaches to improve the feed efficiency of cattle need to be multifaceted with consideration for host genetics, functional efficiency of the rumen microbiome, and the structure and composition of feed. Likewise, reductions in carbon emissions need to be broader than just CH4, with an appreciation of the role that cattle have within a circular bioeconomy to promote upcycling of nutrients and reductions in emissions from farming systems. Strategies to improve the efficiency of cattle production are a prerequisite for the sustainable intensification needed to ensure that the social license for milk and meat production from cattle is retained. [ABSTRACT FROM AUTHOR]

Background: A region on Sus scrofa chromosome 4 (SSC4) surrounding single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) has been reported to be strongly associated with both weight gain and serum viremia in pigs after infection with PRRS virus (PRRSV). A proposed causal mutation in the guanylate binding protein 5 gene (GBP5) is predicted to truncate the encoded protein. To investigate transcriptional differences between WUR genotypes in early host response to PRRSV infection, an RNA-seq experiment was performed on globin depleted whole blood RNA collected on 0, 4, 7, 10 and 14 days post-infection (dpi) from eight littermate pairs with one AB (favorable) and one AA (unfavorable) WUR genotype animal per litter. Results: Gene Ontology (GO) enrichment analysis of transcripts that were differentially expressed (DE) between dpi across both genotypes revealed an inflammatory response for all dpi when compared to day 0. However, at the early time points of 4 and 7dpi, several GO terms had higher enrichment scores compared to later dpi, including inflammatory response (p < 10-7), specifically regulation of NFkappaB (p < 0.01), cytokine, and chemokine activity (p < 0.01). At 10 and 14dpi, GO term enrichment indicated a switch to DNA damage response, cell cycle checkpoints, and DNA replication. Few transcripts were DE between WUR genotypes on individual dpi or averaged over all dpi, and little enrichment of any GO term was found. However, there were differences in expression patterns over time between AA and AB animals, which was confirmed by genotype-specific expression patterns of several modules that were identified in weighted gene co-expression network analyses (WGCNA). Minor differences between AA and AB animals were observed in immune response and DNA damage response (p = 0.64 and p = 0.11, respectively), but a significant effect between genotypes pointed to a difference in ion transport/homeostasis and the participation of G-coupled protein receptors (p = 8e-4), which was reinforced by results from regulatory and phenotypic impact factor analyses between genotypes. Conclusion: We propose these pathway differences between WUR genotypes are the result of the inability of the truncated GBP5 of the AA genotyped pigs to inhibit viral entry and replication as quickly as the intact GBP5 protein of the AB genotyped pigs. [ABSTRACT FROM AUTHOR]

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Background: Previously, we identified a major quantitative trait locus (QTL) for host response to Porcine Respiratory and Reproductive Syndrome virus (PRRSV) infection in high linkage disequilibrium (LD) with SNP rs80800372 on Sus scrofa chromosome 4 (SSC4). Results: Within this QTL, guanylate binding protein 5 (GBP5) was differentially expressed (DE) (p < 0.05) in blood from AA versus AB rs80800372 genotyped pigs at 7,11, and 14 days post PRRSV infection. All variants within the GBP5 transcript in LD with rs80800372 exhibited allele specific expression (ASE) in AB individuals (p < 0.0001). A transcript re-assembly revealed three alternatively spliced transcripts for GBP5. An intronic SNP in GBP5, rs340943904, introduces a splice acceptor site that inserts five nucleotides into the transcript. Individuals homozygous for the unfavorable AA genotype predominantly produced this transcript, with a shifted reading frame and early stop codon that truncates the 88 C-terminal amino acids of the protein. RNA-seq analysis confirmed this SNP was associated with differential splicing by QTL genotype (p < 0.0001) and this was validated by quantitative capillary electrophoresis (p < 0.0001). The wild-type transcript was expressed at a higher level in AB versus AA individuals, whereas the five-nucleotide insertion transcript was the dominant form in AA individuals. Splicing and ASE results are consistent with the observed dominant nature of the favorable QTL allele. The rs340943904 SNP was also 100% concordant with rs80800372 in a validation population that possessed an alternate form of the favorable B QTL haplotype. Conclusions: GBP5 is known to play a role in inflammasome assembly during immune response. However, the role of GBP5 host genetic variation in viral immunity is novel. These findings demonstrate that rs340943904 is a strong candidate causal mutation for the SSC4 QTL that controls variation in host response to PRRSV. [ABSTRACT FROM AUTHOR]

CircRNAs and lncRNAs are non-coding RNAs that regulate many biological processes at the cellular level. However, knowledge of their function and expression patterns in cattle remains scarce. We investigated circRNA and lncRNA expression profiles in four key metabolic tissues of beef cattle (rumen, liver, muscle, and subcutaneous adipose) using RNA-Seq. Bioinformatic analysis of 189 samples collected from 48 cattle identified 19,766 circRNAs and 10,615 lncRNAs across all four tissues. PCA revealed the expression profiles of both circ- and lncRNA were clearly separated by tissue, suggesting their expression patterns are tissue dependent. Moreover, both datasets contained large numbers of transcripts that were unique to each tissue, underlining the divergence in function across metabolic sites. Further functional analysis of tissue specific circRNAs using the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that lysine degradation, peroxisome, insulin resistance, and ubiquitinmediated proteolysis unique to the rumen, liver, muscle, and adipose tissues, respectively. The same analysis of the lncRNAs revealed that purine metabolism, fatty acid degradation, cAMP signaling pathway, and AGE-RAGE signaling pathway in diabetic complications were uniquely enriched in the rumen, liver, muscle, and subcutaneous adipose tissues, respectively. Together, these results revealed tissue specific metabolic pathways that may be regulated by the multiple non-coding RNAs. More specifically, circDLG1 and lncMSTRG.12092.8 were predicted to regulate the expression of Lymphocyte Antigen 6 Family Member G5B (LY6G5B) and pyruvate kinase M1/2 (PKM), Adenylate Kinase 1 (AK1), and Mitofusin 2 (MFN2), respectively, indicating regulatory roles in host immune response, glycolysis, energy balance control, and mitochondrial fusion, all of which may contribute to regulation of energy metabolism. Our findings show that expression profiles of circRNAs and lncRNAs differ among metabolic tissues, and these transcripts may play crucial roles in regulating metabolism in cattle. [ABSTRACT FROM AUTHOR]

Dendritic cells (DCs) classically promote immune responses but can be manipulated to induce antigen-specific hyporesponsiveness. It has been shown that phenotypically "immature" DCs, defined by low levels of costimulatory molecules at the cell surface, are involved in the induction of peripheral immune tolerance in autoimmunity. Paecilomyces hepiali Chen (PHC) mycelium, as a substitute for Cordyceps, has been used extensively as an immunomodulator to treat numerous diseases. In this study, the effects of an ethanol extract of PHC (EEPHC) on the phenotypic and functional maturation of bone marrow-derived DCs (BM-DCs) from NOD mice were evaluated. EEPHC significantly suppressed the expression of major histocompatibility complex (MHC) class II molecules and the costimulatory molecules CD40 and CD86 in NOD BM-DCs. These DCs also exhibited impaired production of the proinflammatory cytokine interleukin-12 (IL-12) and poor stimulatory capacity in the presence of EEPHC. Moreover, inhibition of the activation and differentiation of cultured DCs was associated with reduced DNA binding activity of nuclear factor kappa B (NF- kappaB), a transcription factor recently shown to be responsible for DC maturation. Administration of 3x10(5) EEPHC-treated DCs into NOD mice aged 3-4 weeks effectively prevented the onset of diabetes. Furthermore, splenocytes from the protected mice produced high amounts of IL-4 and IL-10 and low levels of IL-2 and interferon gamma, suggesting that these DCs deficient in NF- kappaB activity are responsible for the apparent shift in type 2 helper T cells. These novel results showed that EEPHC could specifically inhibit NF- kappaB activity and maintain DCs in a potentially tolerogenic state, permitting their use in strategies to induce immune tolerance in type 1 diabetes., (Copyright 2008 Prous Science, S.A.U. or its licensors. All rights reserved.)