A metabolomics approach to uncover the effects of grain diets on rumen health in dairy cows

Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions

Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.

Changes in Rumen Epithelial Morphology and Transcriptome, Rumen Metabolome, and Blood Biochemical Parameters in Lactating Dairy Cows with Subacute Rumen Acidosis Following Rumen Content Transplantation

Interventions targeting the gut microbiota, such as fecal microbiota transplantation, prove effective in repairing the intestinal barrier and facilitating the recovery of its function and metabolism. However, the regulatory mechanisms governing the remodeling of rumen epithelial morphology and function, rumen metabolism, and host metabolism in cows of subacute ruminal acidosis (SARA) remain poorly understood. Here, we explored the changes in rumen epithelial morphology and transcriptome, rumen metabolome, and blood biochemical parameters in SARA cows following rumen content transplantation (RCT). The entire experiment consisted of 2 periods: the SARA induction period and the RCT period. During the SARA induction period, 12 ruminally cannulated lactating Holstein cows were randomly allocated into 2 groups, fed either a conventional diet [CON; n = 4; 40% concentrate, dry matter (DM) basis] or a high-grain diet (HG; n = 8; 60% concentrate, DM basis). Following the SARA induction period, the RCT period started. The HG cows were randomly assigned to 2 groups: the donor-recipient (DR) group and the self-recipient (SR) group. Rumen contents were entirely removed from both groups before RCT. For the DR group, cows were administered 70% rumen content from the CON cows, paired based on comparable body weight; for the SR group, each cow received 70% self-derived rumen content. The results revealed no significant differences in the thicknesses of the stratum corneum, granulosum, and spinosum/basale layers, as well as the total depth of the epithelium between the SR and DR groups. All these measurements exhibited a decreasing trend and fluctuations over time after the transfer. Notably, these fluctuations tended to stabilize at 13 or 16 d after RCT in the SR group, whereas they tended to stabilize after 8 or 13 d of transfer for the DR group. Transcriptome sequencing revealed that a total of 277 differentially expressed genes (DEGs) were identified between the 2 groups. Enrichment analysis showed that the DEGs were significantly enriched in 11 Gene Ontology biological processes and 14 KEGG pathways. The DEGs corresponding to almost any of these 11 biological process terms and 14 pathways showed mixed up- or downregulation following RCT. Metabolomics analysis indicated that a total of 33 differential metabolites were detected between the SR and DR groups, mainly enriched in 5 key metabolic pathways, including plant polysaccharides and starch degradation, lipid metabolism, amino sugar and nucleotide metabolism, purine metabolism, and Krebs cycle. Among them, the levels of differential metabolites associated with the degradation of plant polysaccharides and starches, metabolism of amino sugars and nucleotides, and purine metabolism pathways were significantly elevated in the DR cows. The results of blood biochemical parameters showed that the triglyceride concentration of the DR cows was increased than that of the SR cows, comparable to the level observed in the CON cows during the SARA induction period. Generally, our findings indicated that RCT facilitated the recovery of rumen epithelial morphological structure but did not promote its function recovery. Moreover, RCT enhanced rumen plant polysaccharide and starch degradation, amino sugar and nucleotide sugar metabolism, as well as purine metabolism. Additionally, it further promoted the recovery of plasma metabolites related to lipid metabolism.

Untargeted metabolomics and metagenomics reveal signatures for intramammary ceftiofur treatment and lactation stage in the cattle hindgut

The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.

Variations in colostrum metabolite profiles in association with sow parity

Information about the full spectrum of metabolites present in porcine colostrum and factors that influence metabolite abundances is still incomplete. Parity number appears to modulate the concentration of single metabolites in colostrum. This study aimed to 1) characterize the metabolome composition and 2) assess the effect of parity on metabolite profiles in porcine colostrum. Sows (n = 20) were divided into three parity groups: A) sows in parity 1 and 2 (n = 8), B) sows in parity 3 and 4 (n = 6), and C) sows in parity 5 and 6 (n = 6). Colostrum was collected within 12 h after parturition. A total of 125 metabolites were identified using targeted reversed-phase high-performance liquid chromatography-tandem mass spectrometry and anion-exchange chromatography-high resolution mass spectrometry. Gas chromatography additionally identified 19 fatty acids (FAs). Across parities, colostrum was rich in creatine and creatinine, 1,3-dioleyl-2-palmitatoylglycerol, 1,3-dipalmitoyl-2-oleoylglycerol, and sialyllactose. Alterations in colostrum concentrations were found for eight metabolites among parity groups (P < 0.05) but the effects were not linear. For instance, colostrum from parity group C comprised 75.4% more valine but 15.7%, 34.1%, and 47.9% less citric, pyruvic, and pyroglutamic acid, respectively, compared to group A (P < 0.05). By contrast, colostrum from parity group B contained 39.5% more spermidine than from group A (P < 0.05). Of the FAs, C18:1, C16:0, and C18:2 n6 were the main FAs across parities. Parity affected four FAs (C18:3n3, C14:1, C17:0ai, and C17:1), including 43.1% less α-linolenic acid (C18:3n3) in colostrum from parity group C compared to groups A and B (P < 0.05). Signature feature ranking identified 1-stearoyl-2-hydroxy-sn-glycero-3-phosphatidylcholine and the secondary bile acid hyodeoxycholic acid as the most discriminative metabolites, showing a higher variable importance in the projection score in colostrum from parity group A than from groups B and C. Overall, results provided a comprehensive overview about the metabolome composition of sow colostrum. The consequences of the changes in colostrum metabolites with increasing parity for the nutrient supply of the piglets should be investigated in the future. The knowledge gained in this study could be used to optimize feeding strategies for sows.

New biochemical pathways for forming short-chain fatty acids during fermentation in rumen bacteria

Short-chain fatty acids (SCFA) are essential to cattle as a source of energy and for other roles in metabolism. These molecules are formed during fermentation by microbes in the rumen, but even after decades of study, the biochemical pathways responsible for forming them are not always clear. Here we review recent advances in this area and their importance for improving animal productivity. Studies of bacterial genomes have pointed to unusual biochemical pathways in rumen organisms. One study found that 8% of rumen organisms forming acetate, a major SCFA, had genes for a pathway previously unknown in bacteria. The existence of this pathway was subsequently confirmed biochemically in propionibacteria. The pathway was shown to involve 2 enzymes that convert acetyl-coenzyme A to acetate. Similar studies have revealed new enzymatic steps for forming propionate and butyrate, other major SCFA. These new steps and pathways are significant for controlling fermentation. With more precise control over SCFA, cows can be fed more precisely and potentially reach higher productivity.

Effects of dietary energy levels on microorganisms and short-chain fatty acids of rumen and tight junction proteins in Honghe Yellow cattle

This study was conducted to investigate the effects of dietary energy levels on microorganisms and short-chain fatty acids (SCFAs) of rumen and the expression of tight junction proteins in Honghe Yellow cattle. A total of fifteen male Honghe Yellow cattle were randomly divided into three treatments (five replicates per treatment), consisting of formulated energy concentrations of 5.90 MJ/kg (high-energy diet, group H), 5.60 MJ/kg (medium-energy diet, group M) and 5.30 MJ/kg (low-energy diet, group L). The results showed that compared with group H, the expression of Claudin-1 in rumen epithelium of groups M and L was increased, but the expression of ZO-1 was decreased (p < 0.05). Moreover, compared with group H, group M down-regulated the expression of Occludin and Claudin-1 in the brain (p < 0.05). For rumen bacteria, the dominant phyla included Bacteroidetes and Firmicutes, the abundance of Actinobacteriota in groups M and L was significantly increased compared with group H (p < 0.05). At the genus level, the relative abundance of Corynebacterium, Eubacterium_nodatum_group and Neisseraceae in groups M and L was significantly decreased compared with group H (p < 0.05). For rumen fungi, the dominant phyla included Basidiomycota, Ascomycota and Neocariastigomycota, the relative abundance of Ascomycetes was significantly higher than that of groups M and L compared with group H (p < 0.05). At the genus level, the relative abundance of Neocelimastigaceae and Myceliophthora in groups M and L was significantly reduced compared with group H (p < 0.05). Furthermore, the expression of Claudin-1 in rumen epithelium was significantly positively correlated with Actinobacteriota, Corynebacterium and Neisseriaceae. The expression of ZO-1 in the spinal cord was significantly positively correlated with Myceliophthora. The expression of Occludin in brain was positively correlated with valerate content (p < 0.05). In summary, dietary energy levels affected the rumen microbiota of Honghe Yellow cattle. The expression of Claudin-1 in rumen epithelium and the total SCFAs concentration were increased with decreasing dietary energy levels, but the expression of Claudin-1 in brain and ZO-1 in the spinal cord were reduced with decreasing dietary energy levels. Meanwhile, the rumen microbiota and SCFAs were significantly correlated with the expression of TJP.

Exhalomics as a noninvasive method for assessing rumen fermentation in dairy cows: Can exhaled-breath metabolomics replace rumen sampling?

Previously, we used secondary electrospray ionization-mass spectrometry (SESI-MS) to investigate the diurnal patterns and signal intensities of exhaled (EX) volatile fatty acids (VFA) of dairy cows. The current study aimed to validate the potential of an exhalomics approach for evaluating rumen fermentation. The experiment was conducted in a switchback design, with 3 periods of 9 d each, including 7 d for adaptation and 2 d for sampling. Four rumen-cannulated original Swiss Brown (Braunvieh) cows were randomly assigned to 1 of 2 diet sequences (ABA or BAB): (A) low starch (LS; 6.31% starch on a dry matter basis) and (B) high starch (HS; 16.2% starch on a dry matter basis). Feeding was once per day at 0830 h. Exhalome (with the GreenFeed System), and rumen samples were collected 8 times to represent every 3 h of a day, and EX-VFA and ruminal (RM)-VFA were analyzed using SESI-MS and HPLC, respectively. Furthermore, the VFA concentration in the gas phase (HR-VFA) was predicted based on RM-VFA and Henry's Law (HR) constants. No interactions were identified between the types of diets (HS vs. LS) and the measurement methods on daily average VFA profiles (RM vs. EX or HR vs. EX), suggesting a consistent performance among the methods. Additionally, when the 3-h interval VFA data from HS and LS diets were analyzed separately, no interactions were observed between methods and time of day, indicating that the relative daily pattern of VFA molar proportions was similar regardless of the VFA measurement method used. The results revealed that the levels of acetate sharply increased immediately after feeding, trailed by an increase in the acetate:propionate ratio and a steady increase for propionate (2 h after feeding the HS diet, 4 h for LS), and butyrate. This change was more pronounced for the HS diet than the LS diet. However, there was no overall diet effect on the VFA molar proportions, although the measurement methods affected the molar proportions. Furthermore, we observed a strong positive correlation between the levels of RM and EX acetate for both diets (HS: r = 0.84; LS: r = 0.85), RM and EX propionate (r = 0.74), and RM and EX acetate:propionate ratio (r = 0.80). Both EX-VFA and RM-VFA exhibited similar responses to feeding and dietary treatments, suggesting that EX-VFA could serve as a useful proxy for characterizing RM-VFA molar proportions to evaluate rumen fermentation. Similar relationships were observed between RM-VFA and HR-VFA. In conclusion, this study underscores the potential of exhalomics as a reliable approach for assessing rumen fermentation. Moving forward, research should further explore the depth of exhalomics in ruminant studies to provide a comprehensive insight into rumen fermentation metabolites, especially across diverse dietary conditions.

Comparison of LC-MS-based methods for the determination of carboxylic acids in animal matrices

Carboxylic acids (CAs) are key players in human and animal metabolism. As they are hardly retained under reversed-phase liquid chromatography (RP-LC) conditions in their native form, derivatization is an option to make them accessible to RP-LC and simultaneously increase their response for mass spectrometric detection. In this work, two RP-LC tandem mass spectrometry-based methods using aniline or 3-nitrophenylhydrazine (3-NPH) as derivatization agents were compared with respect to several factors including completeness of derivatization, apparent recoveries (RAs) in both cow feces and ruminal fluid, and concentrations obtained in feces and ruminal fluid of cows. Anion exchange chromatography coupled to high-resolution mass spectrometry (AIC-HR-MS) served as reference method. Derivatization efficiencies were close to 100% for 3-NPH derivatization but variable (20-100%) and different in solvent solutions and matrix extracts for aniline derivatization. Likewise, average RAs of 13C-labeled short-chain fatty acids as internal standards were around 100% for 3-NPH derivatization but only 45% for aniline derivatization. Quantification of CAs in feces and ruminal fluid of cows initially fed a forage-only diet and then transitioned to a 65% high-grain diet which yielded similar concentrations for 3-NPH derivatization and AIC-HR-MS, but concentrations determined by aniline derivatization were on average five times lower. For these reasons, derivatization with aniline is not recommended for the quantitative analysis of CAs in animal samples.

- Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation

Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.

Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies

BACKGROUND

Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.

RESULTS

The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.

CONCLUSIONS

This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.

Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls

The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Ruminant production holds a pivotal position within the global animal production and agricultural sectors. As population growth escalates, posing environmental challenges, a heightened emphasis is directed toward refining ruminant production systems. Recent investigations underscore the connection between the composition and functionality of the rumen microbiome and economically advantageous traits in cattle. Consequently, the development of innovative strategies to enhance cattle feed efficiency, while curbing environmental and financial burdens, becomes imperative. The advent of omics technologies has yielded fresh insights into metabolic health fluctuations in dairy cattle, consequently enhancing nutritional management practices. The pivotal role of the rumen microbiome in augmenting feeding efficiency by transforming low-quality feedstuffs into energy substrates for the host is underscored. This microbial community assumes focal importance within gut microbiome studies, contributing indispensably to plant fiber digestion, as well as influencing production and health variability in ruminants. Instances of compromised animal welfare can substantially modulate the microbiological composition of the rumen, thereby influencing production rates. A comprehensive global approach that targets both cattle and their rumen microbiota is paramount for enhancing feed efficiency and optimizing rumen fermentation processes. This review article underscores the factors that contribute to the establishment or restoration of the rumen microbiome post perturbations and the intricacies of host-microbiome interactions. We accentuate the elements responsible for responsible host-microbiome interactions and practical applications in the domains of animal health and production. Moreover, meticulous scrutiny of the microbiome and its consequential effects on cattle production systems greatly contributes to forging more sustainable and resilient food production systems, thereby mitigating the adverse environmental impact.

Effects of perinatal stress on the metabolites and lipids in plasma of dairy goats

Dairy goats experience metabolic stress during the peripartal period, and their ability to navigate this stage of lactation is related to the occurrence and development of metabolic diseases. Unlike dairy cows, there is a lack of comprehensive analysis of changes in the plasma profiles of peripartal dairy goats, particularly using high-throughput techniques. A subset of 9 clinically-healthy dairy goats were used from a cohort of 96 primiparous Guanzhong dairy goats (BCS, 2.75 ± 0.15). Blood samples were collected at seven time points around parturition (d 21, 14, 7 before parturition, the day of kidding, and d 7, 14, 21 postpartum), were analyzed using untargeted metabolomics and targeted lipidomics. The orthogonal partial least squares discriminant analysis model revealed a total of 31 differential metabolites including p-cresol sulfate, pyruvic acid, cholic acid, and oxoglutaric acid. The pathway enrichment analysis identified phenylalanine metabolism, aminoacyl-tRNA biosynthesis, and citrate cycle as the top three significantly-altered pathways. The Limma package identified a total of 123 differentially expressed lipids. Phosphatidylserine (PS), free fatty acids (FFA), and acylcarnitines (ACs) were significantly increased on the day of kidding, while diacylglycerols (DAG) and triacylglycerols (TAG) decreased. Ceramides (Cer) and lyso-phosphatidylinositols (LPI) were significantly increased during postpartum period, while PS, FFA, and ACs decreased postpartum and gradually returned to antepartum levels. Individual species of FFA and phosphatidylcholines (PC) were segregated based on the differences in the saturation and length of the carbon chain. Overall, this work generated the largest repository of the plasma lipidome and metabolome in dairy goats across the peripartal period, which contributed to our understanding of the multifaceted adaptations of transition dairy goats.

Characterizing ruminal acidosis risk: A multiherd, multicountry study

A multicenter observational study was conducted on early lactation Holstein cows (n = 261) from 32 herds from 3 regions (Australia, AU; California, CA; and Canada, CAN) to characterize their risk of acidosis into 3 groups (high, medium, or low) using a discriminant analysis model previously developed. Diets ranged from pasture supplemented with concentrates to total mixed ration (nonfiber carbohydrates = 17 to 47 and neutral detergent fiber = 27 to 58% of dry matter). Rumen fluid samples were collected <3 h after feeding and analyzed for pH, and ammonia, d- and l-lactate, and volatile fatty acid (VFA) concentrations. Eigenvectors were produced using cluster and discriminant analysis from a combination of rumen pH, and ammonia, d-lactate, and individual VFA concentrations and were used to calculate the probability of the risk of ruminal acidosis based on proximity to the centroid of 3 clusters. Bacterial 16S ribosomal DNA sequence data were analyzed to characterize bacteria. Individual cow milk volume, fat, protein, and somatic cell count values were obtained from the closest herd test to the rumen sampling date (median = 1 d before rumen sampling). Mixed model analyses were performed on the markers of rumen fermentation, production characteristics, and the probability of acidosis. A total of 26.1% of the cows were classified as high risk for acidosis, 26.8% as medium risk, and 47.1% as low risk. Acidosis risk differed among regions with AU (37.2%) and CA (39.2%) having similar prevalence of high-risk cows and CAN only 5.2%. The high-risk group had rumen phyla, fermentation, and production characteristics consistent with a model of acidosis that reflected a rapid rate of carbohydrate fermentation. Namely, acetate to propionate ratio (1.98 ± 0.11), concentrations of valerate (2.93 ± 0.14 mM), milk fat to protein ratio (1.11 ± 0.047), and a positive association with abundance of phylum Firmicutes. The medium-risk group contains cows that may be inappetant or that had not eaten recently or were in recovery from acidosis. The low-risk group may represent cattle that are well fed with a stable rumen and a slower rumen fermentation of carbohydrates. The high risk for acidosis group had lower diversity of bacteria than the other groups, whereas CAN had a greater diversity than AU and CA. Rumen fermentation profile, abundance of ruminal bacterial phyla, and production characteristics of early lactation dairy cattle from 3 regions were successfully categorized in 3 different acidosis risk states, with characteristics differing between acidosis risk groups. The prevalence of acidosis risk also differed between regions.

Effects of hindgut acidosis on production, metabolism, and inflammatory biomarkers in previously immune-activated lactating dairy cows

Previous stressors and systemic inflammation may increase the intestine's susceptibility to hindgut acidosis (HGA). Therefore, our experimental objectives were to evaluate the effects of isolated HGA on metabolism, production, and inflammation in simultaneously immune-activated lactating cows. Twelve rumen-cannulated Holstein cows (118 ± 41 d in milk; 1.7 ± 0.8 parity) were enrolled in a study with 3 experimental periods (P). Baseline data were collected during P1 (5 d). On d 1 of P2 (2 d), all cows received an i.v. lipopolysaccharide (LPS) bolus (0.2 µg/kg of body weight; BW). During P3 (4 d), cows were randomly assigned to 1 of 2 abomasal infusion treatments: (1) control (LPS-CON; 6 L of H₂O/d; n = 6) or (2) starch infused (LPS-ST; 4 kg of corn starch + 6 L of H₂O/d; n = 6). Treatments were allocated into 4 equal doses (1.5 L of H₂O or 1 kg of starch and 1.5 L of H₂O, respectively) and administered at 0000, 0600, 1200, and 1800 h daily. Additionally, both treatments received i.v. LPS on d 1 and 3 of P3 (0.8 and 1.6 µg/kg of BW, respectively) to maintain an inflamed state. Effects of treatment, time, and their interaction were assessed. Repeated LPS administration initiated and maintained an immune-activated state, as indicated by increased circulating white blood cells (WBC), serum amyloid A (SAA), and LPS-binding protein (LBP) during P2 and P3 (29%, 3-fold, and 50% relative to P1, respectively) for both abomasal infusion treatments. Regardless of abomasal treatment, milk yield and dry matter intake were decreased throughout P2 and P3 but with lesser severity following each LPS challenge (54, 44, and 37%, and 49, 42, and 40% relative to baseline on d 1 of P2, d 1 and d 3 of P3, respectively). As expected, starch infusions markedly decreased fecal pH (5.56 at nadir vs. 6.57 during P1) and increased P3 fecal starch relative to LPS-CON (23.7 vs. 2.4% of dry matter). Neither LPS nor starch infusions altered circulating glucose, insulin, nonesterified fatty acids, or β-hydroxybutyrate, although LPS-ST cows had decreased blood urea nitrogen throughout P3 (16% relative to LPS-CON). Despite the striking reduction in fecal pH, HGA had no additional effect on circulating WBC, SAA, or LBP. Thus, in previously immune-activated dairy cows, HGA did not augment the inflammatory state, as indicated by a lack of perturbations in production, metabolism, and inflammatory biomarkers.

Effects of abomasally infused rumen fluid from corn-challenged donor cows on production, metabolism, and inflammatory biomarkers in healthy recipient cows

Subacute rumen acidosis may cause postruminal intestinal barrier dysfunction, but this does not appear to be due to increased hindgut fermentation. Alternatively, intestinal hyperpermeability may be explained by the plethora of potentially harmful substances (e.g., ethanol, endotoxin, and amines) produced in the rumen during subacute rumen acidosis, which are difficult to isolate in traditional in vivo experiments. Therefore, objectives were to evaluate whether abomasal infusion of acidotic rumen fluid collected from donor (Donor) cows elicits systemic inflammation or alters metabolism or production in healthy recipients. Ten rumen-cannulated lactating dairy cows [249 ± 63 d in milk; 753 ± 32 kg of body weight (BW)] were randomly assigned to 1 of 2 abomasal infusion treatments: (1) healthy rumen fluid (HF; 5 L/h; n = 5) or (2) acidotic rumen fluid (AF; 5 L/h; n = 5) infused. Eight rumen-cannulated cows [4 dry, 4 lactating (lactating = 391 ± 220 d in milk); 760 ± 70 kg of BW] were used as Donor cows. All 18 cows were acclimated to a high-fiber diet (46% neutral detergent fiber; 14% starch) during an 11-d prefeeding period during which rumen fluid was collected for the eventual infusion into HF cows. During period (P) 1 (5 d), baseline data were obtained and on d 5 Donor were corn-challenged (2.75% BW ground corn after 16 h of 75% feed restriction). Cows were fasted until 36 h relative to rumen acidosis induction (RAI), and data were collected through 96 h RAI. At 12 h RAI, an additional 0.50% BW of ground corn was added, and acidotic fluid collections began (7 L/Donor every 2 h; 6 M HCl was added to collected fluid until pH was between 5.0 and 5.2). On d 1 of P2 (4 d), HF/AF cows were abomasally infused with their respective treatments for 16 h, and data were collected for 96 h relative to the first infusion. Data were analyzed in SAS (SAS Institute Inc.) using PROC MIXED. Following the corn challenge in the Donor cows, rumen pH only mildly decreased at nadir (pH = 5.64 at 8 h RAI) and remained above the desired threshold for both acute (5.2) and subacute (5.6) acidosis. In contrast, fecal and blood pH markedly decreased to acidotic levels (nadir = 4.65 and 7.28 at 36 and 30 h RAI, respectively), and fecal pH remained below 5 from 22 to 36 h RAI. In Donor cows, dry matter intake remained decreased through d 4 (36% relative to baseline) and serum amyloid A and lipopolysaccharide-binding protein markedly increased by 48 h RAI in Donor cows (30- and 3-fold, respectively). In cows that received the abomasal infusions, fecal pH decreased in AF from 6 to 12 h relative to the first infusion (7.07 vs. 6.33) compared with HF; however, milk yield, dry matter intake, energy-corrected milk, rectal temperature, serum amyloid A, and lipopolysaccharide-binding protein were unaffected. Overall, the corn challenge did not cause subacute rumen acidosis but markedly decreased fecal and blood pH and stimulated a delayed inflammatory response in the Donor cows. Abomasal infusion of rumen fluid from corn-challenged Donor cows decreased fecal pH but did not cause inflammation, nor did it create an immune-activated phenotype in recipient cows.

Untargeted metabolomics and lipidomics to assess plasma metabolite changes in dairy goats with subclinical hyperketonemia

Subclinical hyperketonemia (SCHK) is the major metabolic disease observed during the transition period in dairy goats, and is characterized by high plasma levels of nonesterified fatty acids (NEFA) and β-hydroxybutyrate (BHB). However, no prior study has comprehensively assessed metabolomic profiles of dairy goats with SCHK. Plasma samples were collected within 1 h after kidding from SCHK goats (BHB concentration >0.8 mM, n = 7) and clinically healthy goats (BHB concentration <0.8 mM, n = 7) with similar body condition score (2.75 ± 0.15, mean ± standard error of the mean) and parity (primiparous). A combination of targeted and untargeted mass spectrometric approaches was employed for analyzing the various changes in the plasma lipidome and metabolome. Statistical analyses were performed using the GraphPad Prism 8.0, SIMCA-P software (version 14.1), and R packages (version 4.1.3). Plasma aminotransferase, nonesterified fatty acids, and BHB concentrations were greater in the SCHK group, but plasma glucose concentrations were lower. A total of 156 metabolites and 466 lipids were identified. The analysis of untargeted metabolomics data by principal component analysis and orthogonal partial least squares discriminant analysis revealed a separation between SCHK and clinically healthy goats. According to the screening criteria (unpaired t-test, P < 0.05), 30 differentially altered metabolites and 115 differentially altered lipids were detected. Pathway enrichment analysis identified citrate cycle, alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine metabolism as significantly altered pathways. A greater concentration of plasma isocitric acid and cis-aconitic acid levels was observed in SCHK goats. In addition, AA such as lysine and isoleucine were greater, whereas alanine and phenylacetylglycine were lower in SCHK dairy goats. Dairy goats with SCHK also exhibited greater oleic acid, acylcarnitine, and phosphatidylcholine and lower choline and sphingomyelins. Acylcarnitines, oleic acid, and tridecanoic acid displayed positive correlations with several lipid species. Alanine, hippuric acid, and histidinyl-phenylalanine were negatively correlated with several lipids. Overall, altered metabolites in SCHK dairy goats indicated a more severe degree of negative energy balance. Data also indicated an imbalance in the tricarboxylic acid (TCA) cycle, lipid metabolism, and AA metabolism. The findings provide a more comprehensive understanding of the pathogenesis of SCHK in dairy goats.

Filling gaps in animal welfare assessment through metabolomics

Sustainability has become a central issue in Italian livestock systems driving food business operators to adopt high standards of production concerning animal husbandry conditions. Meat sector is largely involved in this ecological transition with the introduction of new label claims concerning the defense of animal welfare (AW). These new guarantees referred to AW provision require new tools for the purpose of authenticity and traceability to assure meat supply chain integrity. Over the years, European Union (EU) Regulations, national, and international initiatives proposed provisions and guidelines for assuring AW introducing requirements to be complied with and providing tools based on scoring systems for a proper animal status assessment. However, the comprehensive and objective assessment of the AW status remains challenging. In this regard, phenotypic insights at molecular level may be investigated by metabolomics, one of the most recent high-throughput omics techniques. Recent advances in analytical and bioinformatic technologies have led to the identification of relevant biomarkers involved in complex clinical phenotypes of diverse biological systems suggesting that metabolomics is a key tool for biomarker discovery. In the present review, the Five Domains model has been employed as a vademecum describing AW. Starting from the individual Domains-nutrition (I), environment (II), health (III), behavior (IV), and mental state (V)-applications and advances of metabolomics related to AW setting aimed at investigating phenotypic outcomes on molecular scale and elucidating the biological routes most perturbed from external solicitations, are reviewed. Strengths and weaknesses of the current state-of-art are highlighted, and new frontiers to be explored for AW assessment throughout the metabolomics approach are argued. Moreover, a detailed description of metabolomics workflow is provided to understand dos and don'ts at experimental level to pursue effective results. Combining the demand for new assessment tools and meat market trends, a new cross-strategy is proposed as the promising combo for the future of AW assessment.

Effects of hindgut acidosis on production, metabolism, and inflammatory biomarkers in feed-restricted lactating dairy cows

Study objectives were to evaluate the effects of hindgut acidosis (HGA) on production, metabolism, and inflammation in feed-restricted (FR) dairy cows. Twelve rumen-cannulated cows were enrolled in a study with 3 experimental periods (P). During P1 (5 d), baseline data were collected. During P2 (2 d), all cows were FR to 40% of their baseline feed intake. During P3 (4 d), cows remained FR and were assigned to 1 of 2 abomasal infusion treatments: (1) control (FR-CON; 6 L of H₂O/d; n = 6) or (2) starch (FR-ST; 4 kg of corn starch + 6 L of H₂O/d; n = 6). Respective treatments were partitioned into 4 equal doses (1 kg of corn starch/infusion) and were abomasally infused daily at 0000, 0600, 1200, and 1800 h. All 3 P were analyzed independently and the effects of treatment, time, and treatment × time were assessed using PROC MIXED, and P1 and P2 data were analyzed using the treatments cows were destined to be assigned to during P3. Hallmark production and metabolic responses to feed restriction were observed in both treatments, including decreased milk yield (39%) and energy-corrected milk (32%), circulating glucose (12%), insulin (71%), and increased circulating nonesterified fatty acids (3.2-fold) throughout both P2 and P3, relative to P1. However, despite a marked reduction in fecal pH (0.96 units), the aforementioned metrics were unaltered by HGA. During P3, starch infusions increased circulating β-hydroxybutyrate, with the most pronounced increase occurring on d 2 (81% relative to FR-CON). Further, feed restriction decreased blood urea nitrogen during P2 (17% relative to P1) in both treatments, and this was exacerbated by starch infusions during P3 (31% decrease relative to FR-CON). In contrast to our hypothesis, neither feed restriction nor HGA increased circulating acute-phase proteins (serum amyloid A and lipopolysaccharide binding protein) relative to P1 or FR-CON, respectively. Thus, despite marked reductions in fecal pH, prior feed restriction did not appear to increase the susceptibility to HGA.

Effects of inoculation with active microorganisms derived from adult goats on growth performance, gut microbiota and serum metabolome in newborn lambs

This study evaluated the effects of inoculation with adult goat ruminal fluid on growth, health, gut microbiota and serum metabolism in lambs during the first 15 days of life. Twenty four Youzhou dark newborn lambs were selected and randomly distributed across 3 treatments (n = 8/group): autoclaved goat milk inoculated with 20 mL sterilized normal saline (CON), autoclaved goat milk inoculated with 20 mL fresh ruminal fluid (RF) and autoclaved goat milk inoculated with 20 mL autoclaved ruminal fluid (ARF). Results showed that RF inoculation was more effective at promoting recovery of body weight. Compared with CON, greater serum concentrations of ALP, CHOL, HDL and LAC in the RF group suggested a better health status in lambs. The relative abundance of Akkermansia and Escherichia-Shigella in gut was lower in the RF group, whereas the relative abundance of Rikenellaceae_RC9_gut_group tended to increase. Metabolomics analysis shown that RF stimulated the metabolism of bile acids, small peptides, fatty acids and Trimethylamine-N-Oxide, which were found the correlation relationship with gut microorganisms. Overall, our study demonstrated that ruminal fluid inoculation with active microorganisms had a beneficial impact on growth, health and overall metabolism partly through modulating the gut microbial community.

Creep Feeding and Weaning Influence the Postnatal Evolution of the Plasma Metabolome in Neonatal Piglets

Data on the evolution of blood metabolites and metabolic markers in neonatal piglets are scarce, although this information is vital to detect physiological aberrations from normal development. We aimed to characterize age- and nutrition-related changes in the plasma metabolome and serum biochemistry of suckling and newly weaned piglets and assess metabolite patterns as physiological markers for the two phases. In two replicate batches (n = 10 litters/group), piglets either received sow milk alone or were additionally offered creep feed from day 10 until weaning (day 28). Blood was collected from one piglet/litter on days 7, 14, 21, 28, 31 and 35 of life, totaling five females and five males/group/day. Signature feature ranking identified plasma triglycerides (TG) as discriminative for age and nutrition during the suckling phase. Influential TG 20:4_36:5, TG 17:0_34:2 and TG 18:2_38:6 were higher in creep-fed piglets on days 14, 21 and 28 of life, respectively, compared to only sow milk-fed piglets. Metabolites belonging to pathways within histidine, D-glutamine and D-glutamate metabolism as well as hippuric acid were distinctive for the postweaning compared to the suckling period. In conclusion, plasma lipid profiles especially corresponded to the type of nutrition in the suckling phase and showed a strong weaning effect.

Effects of Different Dietary Protein Level on Growth Performance, Rumen Fermentation Characteristics and Plasma Metabolomics Profile of Growing Yak in the Cold Season

This experiment was aimed to compare the effects of two diets with different protein content on the growth performance, immune indexes, rumen fermentation characteristics and plasma metabolomics of growing yak in the cold season. A total of 24, 2-year-old healthy yaks with similar body weight (142.9 ± 3.56 kg) were randomly allocated to two isoenergetic diets with different protein content (10 vs 14%) according to a non-paired experimental design, and the protein of the diets was increased by increasing soybean meal, rapeseed meal and cottonseed meal. The growth performance experiment lasted 56 days. Four days before the end of the growth experiment, the digestion trial was conducted, and the rumen fluid and plasma was collected for measurement. The results showed that the average daily feed intake (p < 0.001) and average daily gain (p = 0.006) of yak fed a high-protein diet was significantly greater, while the feed conversion ratio was lower (p = 0.021) than that of yaks fed a low-protein diet. Plasma aspartate aminotransferase (p = 0.002), alanine aminotransferase (p < 0.001), malondialdehyde (p = 0.001), tumor necrosis factor-α (p = 0.032) and interferon-γ (p = 0.017) of the high-protein group were significantly lesser, whereas superoxide dismutase (p = 0.004) and interleukin-2 (p = 0.007) was significantly greater than that of the low-protein group. The rumen microbial crude protein (p < 0.047) and crude protein digestibility (p = 0.015) of yak fed a high-protein diet was significantly greater than that of the low-protein group. The metabolomics results showed that yaks fed a high-protein diet were elevated in protein digestion and absorption, arginine and proline metabolism, tryptophan metabolism, purine metabolism, butanoate metabolism, taste transduction, pyrimidine metabolism, pantothenate and CoA biosynthesis, glutathione metabolism and renin secretion pathways. It is concluded that a high-protein diet in the cold season can promote rumen microbial crude protein synthesis, enhance antioxidant and immune function and promote growth performance of yaks.

Cow's microbiome from antepartum to postpartum: A long-term study covering two physiological challenges

Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.

Prevalence and Implications of Shiga Toxin-Producing E. coli in Farm and Wild Ruminants

Shiga-toxin-producing Escherichia coli (STEC) is a food-borne pathogen that causes human gastrointestinal infections across the globe, leading to kidney failure or even death in severe cases. E. coli are commensal members of humans and animals' (cattle, bison, and pigs) guts, however, may acquire Shiga-toxin-encoded phages. This acquisition or colonization by STEC may lead to dysbiosis in the intestinal microbial community of the host. Wildlife and livestock animals can be asymptomatically colonized by STEC, leading to pathogen shedding and transmission. Furthermore, there has been a steady uptick in new STEC variants representing various serotypes. These, along with hybrids of other pathogenic E. coli (UPEC and ExPEC), are of serious concern, especially when they possess enhanced antimicrobial resistance, biofilm formation, etc. Recent studies have reported these in the livestock and food industry with minimal focus on wildlife. Disturbed natural habitats and changing climates are increasingly creating wildlife reservoirs of these pathogens, leading to a rise in zoonotic infections. Therefore, this review comprehensively surveyed studies on STEC prevalence in livestock and wildlife hosts. We further present important microbial and environmental factors contributing to STEC spread as well as infections. Finally, we delve into potential strategies for limiting STEC shedding and transmission.

Higher Concentration of Dietary Selenium, Zinc, and Copper Complex Reduces Heat Stress-Associated Oxidative Stress and Metabolic Alteration in the Blood of Holstein and Jersey Steers

This study investigated the influence of high concentrations of dietary minerals on reducing heat stress (HS)-associated oxidative stress and metabolic alterations in the blood of Holstein and Jersey steers. Holstein steers and Jersey steers were separately maintained under a 3 × 3 Latin square design during the summer conditions. For each trial, the treatments included Control (Con; fed basal TMR without additional mineral supplementation), NM (NRC recommended mineral supplementation group; [basal TMR + (Se 0.1 ppm + Zn 30 ppm + Cu 10 ppm) as DM basis]), and HM (higher than NRC recommended mineral supplementation group; [basal TMR + (Se 3.5 ppm + Zn 350 ppm + Cu 28 ppm) as DM basis]). Blood samples were collected at the end of each 20-day feeding trial. In both breeds, a higher superoxide dismutase concentration (U/mL) along with lower HSP27 (μg/L) and HSP70 (μg/L) concentrations were observed in both mineral-supplemented groups compared to the Con group (p < 0.05). The HM group had significantly higher lactic acid levels in Jersey steers (p < 0.05), and tended to have higher alanine levels in Holstein steers (p = 0.051). Based on star pattern recognition analysis, the levels of succinic acid, malic acid, γ-linolenic acid, 13-methyltetradecanoic acid, and tyrosine decreased, whereas palmitoleic acid increased with increasing mineral concentrations in both breeds. Different treatment groups of both breeds were separated according to the VIP scores of the top 15 metabolites through PLS−DA analysis; however, their metabolic trend was mostly associated with the glucose homeostasis. Overall, the results suggested that supplementation with a higher-than-recommended concentration of dietary minerals rich in organic Se, as was the case in the HM group, would help to prevent HS-associated oxidative stress and metabolic alterations in Holstein and Jersey steers.

Mastitis: What It Is, Current Diagnostics, and the Potential of Metabolomics to Identify New Predictive Biomarkers

Periparturient diseases continue to be the greatest challenge to both farmers and dairy cows. They are associated with a decrease in productivity, lower profitability, and a negative impact on cows’ health as well as public health. This review article discusses the pathophysiology and diagnostic opportunities of mastitis, the most common disease of dairy cows. To better understand the disease, we dive deep into the causative agents, traditional paradigms, and the use of new technologies for diagnosis, treatment, and prevention of mastitis. This paper takes a systems biology approach by highlighting the relationship of mastitis with other diseases and introduces the use of omics sciences, specifically metabolomics and its analytical techniques. Concluding, this review is backed up by multiple studies that show how earlier identification of mastitis through predictive biomarkers can benefit the dairy industry and improve the overall animal health.

Rumen fermentative metabolomic and blood insights into the effect of yeast culture supplement on growing bulls under heat stress conditions

This study was conducted to investigate the effects of yeast culture supplements on the physiological state and growth performance of growing bulls under heat stress conditions and the underlying mechanism. A total of 14 (6.0 ± 1.0 months old) growing bulls with similar body weight were randomly assigned into the control group (YC_0g/d) and yeast culture supplement group (YC_40g/d). YC_0g/d contained three replicates, with two bulls in each replicate, which were fed a basal diet. Meanwhile, the YC_40g/d treatment contained four replicates, with two bulls in each replicate, which were fed a basal diet supplemented with 40 g/day of yeast culture per cattle. Growth performance, nutrient digestibility, rumen fermentable metabolites, serum immunity, serum hormones, and serum antioxidant parameters were measured. Results showed that the average daily gain significantly increased (P < 0.05), while the feed-to-gain ratio significantly decreased (P < 0.01) after YC supplementation compared with the YC_0g/d. The digestibility of neutral detergent fiber (P < 0.05) was higher in YC_40g/d. There were no significant differences in ruminal pH, NH₃-N, butyrate, or acetate/propionate (P > 0.05). Besides, the rumen MCP, acetate, propionate, and total VFA content remarkably increased with the supplement of YC (P < 0.05). Yeast culture supplementation increased the concentration of nicotinamide riboside, neuromedin B, peptides, and formyl-5-hydroxykynurenamine. The YC_40g/d group had a significantly (P < 0.05) higher serum triiodothyronine level, serum glutathione peroxidase levels, and total antioxidant capacity while having a lower serum malondialdehyde level than the YC_0g/d group. In conclusion, the addition of yeast culture in the diet improves the growth performance of growing bulls under heat stress by increasing nutrient digestibility, rumen fermentation function, antioxidant capacity, and rumen metabolites.

Effects of Barley Starch Level in Diet on Fermentation and Microflora in Rumen of Hu Sheep

This study aimed to explore the effects of different levels of barley starch instead of corn starch on the rumen fermentation and microflora when feeding a corn-based diet to Hu sheep. Thirty-two male Hu sheep equipped with permanent rumen fistulas were selected and fed in individual metabolic cages. All sheep were randomly divided into four groups (eight sheep in each group) and fed with four diets containing a similar starch content, but from different starch sources, including 100% of starch derived from corn (CS), 33% of starch derived from barley + 67% of starch derived from corn (33 BS), 67% of starch derived from barley + 33% of starch derived from corn (67 BS) and 100% of starch derived from barley (100 BS). The experimental period included a 14 d adaptation period and a 2 d continuous data collection period. The results showed that the molar proportions of acetate, isobutyrate, butyrate and isovalerate and the ratio of acetate to propionate in the 67 BS and 100 BS groups decreased compared with the CS and 33 BS groups (p < 0.001), while the molar proportions of propionate and valerate increased (p < 0.001). The combination of 33% barley starch and 67% corn starch in the diet improved the production of TVFAs (p = 0.007). The OTUs and Shannon indexes of the CS and 33 BS groups were higher than the 67 BS and 100 BS groups (p < 0.001), and the Chao1 and Ace indexes were higher than the 100 BS group (p < 0.05). In addition, the 33 BS group had increased the relative abundances of Bacteroidetes, Prevotella and Ruminococcus and the abundances of Fibrobacter succinogenes, Ruminococcus flavefaciens, Streptococcus bovis, Selenomonas ruminantium and Prevotella brevis relative to the CS group (p < 0.05). These results indicate that the substitution of 33% of the CS with BS did not change the rumen fermentation pattern relative to the CS group, and increased the richness and diversity of the rumen microbes in Hu sheep compared with other two starch substitute groups.

Invited review: Effect of subacute ruminal acidosis on gut health of dairy cows

Subacute ruminal acidosis (SARA) is assumed to be a common disease in high-yielding dairy cows. Despite this, the epidemiological evidence is limited by the lack of survey data. The prevalence of SARA has mainly been determined by measuring the pH of ruminal fluid collected using rumenocentesis. This may not be sufficiently accurate, because the symptoms of SARA are not solely due to ruminal pH depression, and ruminal pH varies among sites in the rumen, throughout a 24-h period, and among days. The impact of SARA has mainly been studied by conducting SARA challenges in cows, sheep, and goats based on a combination of feed restriction and high-grain feeding. The methodologies of these challenges vary considerably among studies. Variations include differences in the duration and amount of grain feeding, type of grain, amount and duration of feed restriction, number of experimental cows, and sensitivity of cows to SARA challenges. Grain-based SARA challenges affect gut health. These effects include depressing the pH in, and increasing the toxin content of, digesta. They also include altering the taxonomic composition of microbiota, reducing the functionality of the epithelia throughout the gastrointestinal tract (GIT), and a moderate inflammatory response. The effects on the epithelia include a reduction in its barrier function. Effects on microbiota include reductions in their richness and diversity, which may reduce their functionality and reflect dysbiosis. Changes in the taxonomic composition of gut microbiota throughout the GIT are evident at the phylum level, but less evident and more variable at the genus level. Effects at the phylum level include an increase in the Firmicutes to Bacteroidetes ratio. More studies on the effects of a SARA challenge on the functionality of gut microbiota are needed. The inflammatory response resulting from grain-based SARA challenges is innate and moderate and mainly consists of an acute phase response. This response is likely a combination of systemic inflammation and inflammation of the epithelia of the GIT. The systemic inflammation is assumed to be caused by translocation of immunogenic compounds, including bacterial endotoxins and bioamines, through the epithelia into the interior circulation. This translocation is increased by the increase in concentrations of toxins in digesta and a reduction of the barrier function of epithelia. Severe SARA can cause rumenitis, but moderate SARA may activate an immune response in the epithelia of the GIT. Cows grazing highly fermentable pastures with high sugar contents can also have a low ruminal pH indicative of SARA. This is not accompanied by an inflammatory response but may affect milk production and gut microbiota. Grain-based SARA affects several aspects of gut health, but SARA resulting from grazing high-digestible pastures and insufficient coarse fiber less so. We need to determine which method for inducing SARA is the most representative of on-farm conditions.

Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation

Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.

The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau

Ruminal microbiota and metabolites play crucial roles in animal health and productivity. Exploring the dynamic changes and interactions between microbial community composition and metabolites is important for understanding ruminal nutrition and metabolism. Tibetan sheep (Ovis aries) are an important livestock resource on the Qinghai-Tibetan Plateau (QTP), and the effects of various dietary protein levels on ruminal microbiota and metabolites are still unknown. The aim of this study was to investigate the response of ruminal microbiota and metabolites to different levels of dietary protein in Tibetan sheep. Three diets with different protein levels (low protein 10.1%, medium protein 12.1%, and high protein 14.1%) were fed to Tibetan sheep. 16S rRNA gene sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) were used to study the profile changes in each group of ruminal microbes and metabolites, as well as the potential interaction between them. The rumen microbiota in all groups was dominated by the phyla Bacteroidetes and Firmicutes regardless of the dietary protein level. At the genus level, Prevotella_1, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-001 were dominant. Under the same forage-to-concentrate ratio condition, the difference in the dietary protein levels had no significant impact on the bacterial alpha diversity index and relative abundance of the major phyla and genera in Tibetan sheep. Rumen metabolomics analysis revealed that dietary protein levels altered the concentrations of ruminal amino acids, carbohydrates and organic acids, and significantly affected tryptophan metabolism (p < 0.05). Correlation analysis of the microbiota and metabolites revealed positive and negative regulatory mechanisms. Overall, this study provides detailed information on rumen microorganisms and ruminal metabolites under different levels of dietary protein, which could be helpful in subsequent research for regulating animal nutrition and metabolism through nutritional interventions.

Evaluating Starter Feeding on Ruminal Function in Yak Calves: Combined 16S rRNA Sequencing and Metabolomics

For young ruminants, starter feeding can effectively facilitate the growth and development of rumen in ruminants, but the development of rumen is an important physiological challenge as it remains unclear for the mechanism of starter feeding stimulating. In this study, we performed an analysis of ruminal microbiota and their metabolites in yak calves to explore how the ruminal microbiota and their metabolites stimulate the ruminal function. This study associated 16S rRNA sequencing with liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to evaluate the effects of starter feeding on ruminal microbiota diversity and metabolites in yak calves. We designed the experiment using 20 yak calves that were assigned equally into 2 groups, based on feeding milk replacer; the control (RA) group was fed with alfalfa hay while the treatment (RAS) group was fed with alfalfa hay and starter. After the experiment, we investigated the ruminal microbiota and metabolites through 16S rRNA sequencing and LC-MS-based metabolomics. During the preweaning period, the RAS group significantly promoted the growth performance and ruminal development in yak calves, including increases in body weight, chest girth, and development of rumen (P &lt; 0.05). The RAS group increased the relative abundance of Bacteroidota, Proteobacteria, Chloroflexi, Synergistota, and Spirochaetota and decreased the abundance of Firmicutes, Desulfobacterota, Actinobacteriota, and Actinobacteriota at the phylum level (P &lt; 0.05). At the genus level, the ruminal content of the RAS group was significantly enriched for Rikenellaceae_RC9_gut_group and Ruminococcus, while depleted for Prevotella, Christensenellaceae_R-7_group, and NK4A214_group (P &lt; 0.05). A total of 37 metabolites were identified between the RA group and the RAS group, of which 15 metabolites were upregulated and 22 metabolites were downregulated compared with the RA group. Metabolic pathway analyses indicated that upregulated the metabolites of the RAS group yak calves were related to carbohydrate metabolism, ubiquinone, and other terpenoid-quinone biosynthesis, while the downregulated metabolic pathway was relevant to xenobiotic biodegradation, metabolism, and nucleotide metabolism. In summary, starter feeding before weaning significantly increased the dry matter intake and body weight of yak calves, changed the diversity and abundance of ruminal microbiota, and positively regulated the good development of ruminal morphology and function, providing an important basis for high-quality cultivation and the nutritional level of nutrition of yak calves in the Qinghai Tibet plateau. This study is based on the availability of 16S rRNA sequencing and LC-MS-based metabolomics in clarifying the function of starter feeding in the yak calves.

Metabolomics Analysis Across Multiple Biofluids Reveals the Metabolic Responses of Lactating Holstein Dairy Cows to Fermented Soybean Meal Replacement

This experiment was performed to reveal the metabolic responses of dairy cows to the replacement of soybean meal (SBM) with fermented soybean meal (FSBM). Twenty-four lactating Chinese Holstein dairy cattle were assigned to either the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] or the FSBM group (the experimental TMR diet containing 5.55% FSBM), in a completely randomized design. The entire period of this trial consisted of 14 days for the adjustment and 40 days for data and sample collection, and sampling for rumen liquid, blood, milk, and urine was conducted on the 34th and 54th day, respectively. When SBM was completely replaced by FSBM, the levels of several medium-chain FA in milk (i.e., C13:0, C14:1, and C16:0) rose significantly (p < 0.05), while the concentrations of a few milk long-chain FA (i.e., C17:0, C18:0, C18:1n9c, and C20:0) declined significantly (p < 0.05). Besides, the densities of urea nitrogen and lactic acid were significantly (p < 0.05) higher, while the glucose concentration was significantly (p < 0.05) lower in the blood of the FSBM-fed cows than in the SBM-fed cows. Based on the metabolomics analysis simultaneously targeting the rumen liquid, plasma, milk, and urine, it was noticed that substituting FSBM for SBM altered the metabolic profiles of all the four biofluids. According to the identified significantly different metabolites, 3 and 2 amino acid-relevant metabolic pathways were identified as the significantly different pathways between the two treatments in the rumen fluid and urine, respectively. Furthermore, glycine, serine, and threonine metabolism, valine, leucine, and isoleucine biosynthesis, and cysteine and methionine metabolism were the three key integrated different pathways identified in this study. Results mainly implied that the FSBM replacement could enhance nitrogen utilization and possibly influence the inflammatory reactions and antioxidative functions of dairy cattle. The differential metabolites and relevant pathways discovered in this experiment could serve as biomarkers for the alterations in protein feed and nitrogen utilization efficiency of dairy cows, and further investigations are needed to elucidate the definite roles and correlations of the differential metabolites and pathways.

Defining Fatty Acid Changes Linked to Rumen Development, Weaning and Growth in Holstein-Friesian Heifers

After birth, as effectively monogastric animals, calves undergo substantial physiological changes to become ruminants by 3 months of age and reach sexual maturity at approximately 15 months of age. Herein, we assess longitudinal metabolomic changes in Holstein-Friesian (HF) heifers from birth until sexual maturity during this developmental process. Sera from 20 healthy, HF heifers were sampled biweekly from 2 weeks of age until 13 months of age and then monthly until 19 months of age. Sera were assessed using flow infusion electrospray high-resolution mass spectrometry (FIE-HRMS) on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer for high-throughput, sensitive, non-targeted metabolite fingerprinting. Partial least squares discriminant analysis (PLS-DA) and unsupervised hierarchical clustering analysis (HCA) of the derived metabolomes indicated changes detectable in heifers’ sera over time. Time series analyses identified 30 metabolites that could be related to rumen development and weaning at ~3 months of age. Further time series analysis identified 40 metabolites that could be correlated with growth. These findings highlight the role of acetic acid and 3-phenylpropionate (3-PP) in rumen development and growth, suggest that weaning induces elevated levels of fatty acyls in response to a post-weaning stress-induced innate immune response and demonstrate the utilization of fatty acyls in growth. The identified metabolites offer serum metabolites which could inform the nutrition and healthy development of heifers.

Prenatal Supplementation in Beef Cattle and Its Effects on Plasma Metabolome of Dams and Calves

This study investigated the effect of different prenatal nutrition on the plasma metabolome of Nellore dams and their offspring. For that purpose, three nutritional treatments were used in 126 cows during pregnancy: NP—(control) only mineral supplementation; PP—protein-energy supplementation in the final third; and FP—protein-energy supplementation during the entire pregnancy. Targeted metabolomics were analyzed in plasma at the beginning of pregnancy and in pre-delivery of cows (n = 27) as well as in calves (n = 27, 30 ± 9.6 days of age). Data were analyzed by the analysis of variance, partial least squares discriminant analysis, and the principal component analysis (PCA). The PCA showed a clear clustering in the periods investigated only in cows (early gestation and pre-delivery). We found significant metabolites in both supervised analyses (p < 0.05 and VIP score > 1) for cows (Taurine, Glutamic acid, Histidine, and PC aa C42:2) and for calves (Carnosine, Alanine, and PC aa C26:0). The enrichment analysis revealed biological processes (p < 0.1) common among cows and calves (histidine metabolism and beta-alanine metabolism), which may be indicative of transgenerational epigenetic changes. In general, fetal programming affected mainly the metabolism of amino acids.

Methane emissions and rumen metabolite concentrations in cattle fed two different silages

In this study, 18 animals were fed two forage-based diets: red clover (RC) and grass silage (GS), in a crossover-design experiment in which methane (CH4) emissions were recorded in respiration chambers. Rumen samples obtained through naso-gastric sampling tubes were analysed by NMR. Methane yield (g/kg DM) was significantly lower from animals fed RC (17.8 ± 3.17) compared to GS (21.2 ± 4.61) p = 0.008. In total 42 metabolites were identified, 6 showing significant differences between diets (acetate, propionate, butyrate, valerate, 3-phenylopropionate, and 2-hydroxyvalerate). Partial least squares discriminant analysis (PLS-DA) was used to assess which metabolites were more important to distinguish between diets and partial least squares (PLS) regressions were used to assess which metabolites were more strongly associated with the variation in CH4 emissions. Acetate, butyrate and propionate along with dimethylamine were important for the distinction between diets according to the PLS-DA results. PLS regression revealed that diet and dry matter intake are key factors to explain CH4 variation when included in the model. Additionally, PLS was conducted within diet, revealing that the association between metabolites and CH4 emissions can be conditioned by diet. These results provide new insights into the methylotrophic methanogenic pathway, confirming that metabolite profiles change according to diet composition, with consequences for CH4 emissions.

Goat Milk Foodomics. Dietary Supplementation of Sunflower Oil and Rapeseed Oil Modify Milk Amino Acid and Organic Acid Profiles in Dairy Goats

The dietary supplementation of vegetable oils is known to improve the dietary energy density as well as milk fatty acid profile; however, the impacts on the milk foodome is largely unknown. This study investigated the effect of two different sources of unsaturated fatty acids, rapeseed oil and sunflower oil, as a feeding supplement on the milk foodome from dairy goats. Nine Danish Landrace goats at 42 ± 5 days in milk were allocated to three treatment groups for 42 days with three animals per group. A control group received a basal diet made of forage and concentrate at an 85:15 ratio. On top of the basal diet, the second and third groups received rapeseed oil or sunflower oil supplements at 4% of dry matter, respectively. Goat milk was sampled on days 14, 21, and 42. The milk foodome was measured using gas chromatography–mass spectrometry and proton nuclear magnetic resonance spectroscopy. The milk levels of 2-hydroxyisovaleric acid, oxaloacetic acid, and taurine were higher in the milk from goats fed with sunflower oil compared to the control group. More glucose-1-phosphate was found in the milk from goats fed with rapeseed oil compared to the control group. Amino acids, valine and tyrosine, and 2-hydroxyisovaleric acid and oxaloacetic acid were higher in the sunflower group compared to the rapeseed group, while the milk from the rapeseed-fed goats had greater levels of ethanol and 2-oxoglutaric acid compared to the sunflower group. Thus, results show that foodomics is suitable for studying how milk chemistry changes as a function of feeding regime.

Performance of dairy cows fed normal- or reduced-starch diets supplemented with an exogenous enzyme preparation

The objective of this study was to investigate the effects of supplementation of an exogenous enzyme preparation (EEP) on performance, total-tract digestibility of nutrients, plasma AA profile, and milk fatty acids composition in lactating dairy cows fed a reduced-starch diet compared with a normal-starch diet (i.e., positive control). Forty-eight Holstein cows (28 primiparous and 20 multiparous) were enrolled in a 10-wk randomized complete block design experiment with 16 cows per treatment. Treatments were as follows: (1) normal-starch diet (control) containing (% dry matter basis) 24.8% starch and 33.0% neutral detergent fiber (NDF), (2) reduced-starch diet (RSD) containing 18.4% starch and 39.1% NDF, or (3) RSD supplemented with 10 g/cow per day of an EEP (ENZ). The EEP contained amylolytic and fibrolytic activities and was top-dressed on the total mixed ration at the time of feeding. Compared with normal-starch diet, dry matter intake and milk and energy-corrected milk (ECM) yields were lower (on average by 7.1, 9.5, and 7.2%, respectively) for cows on the RSD treatments. Concentrations, but not yields, of milk fat and total solids were increased by RSD. Energy-corrected milk feed efficiency did not differ among treatments. Total-tract digestibility of NDF tended to increase by RSD treatments. Plasma AA concentrations were not affected by treatment, except that of 3-methylhistidine was increased by ENZ, compared with RSD. Blood glucose concentration tended to be lower in cows on the RSD treatments, but ENZ increased glucose and tended to increase insulin concentrations at 4 h after feeding when compared with RSD. Cows on the RSD treatments had decreased concentrations of de novo fatty acids and tended to have increased concentrations of preformed fatty acids in milk. Overall, decreasing dietary starch concentration by 26% decreased dry matter intake, milk, and ECM yields, but ECM feed efficiency was not different among treatments. The negative effects of reducing dietary starch on production were not attenuated by the EEP.

Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows

Subacute ruminal acidosis (SARA) is a major metabolic disease in lactating dairy cows caused by the excessive intake of high-concentrate diets. Here, we investigated the synergistic responses of rumen bacteria and epithelium to high-grain (HG)-induced SARA. Eight ruminally cannulated lactating Holstein cows were randomly assigned to 2 groups for a 3-week experiment and fed either a conventional (CON) diet or an HG diet. The results showed that the HG-feeding cows had a thickened rumen epithelial papilla with edge injury and a decreased plasma β-hydroxybutyrate concentration. The 16S rRNA gene sequencing results demonstrated that HG feeding caused changes in rumen bacterial structure and composition, which further altered rumen fermentation and metabolism. Cooccurrence network analysis revealed that the distribution of the diet-sensitive bacteria responded to the treatment (CON or HG) and that all diet-sensitive amplicon sequence variants showed low to medium degrees of cooccurrence. Metabolomics analysis indicated that the endothelial permeability-increasing factor prostaglandin E1 and the polyamine synthesis by-product 5′-methylthioadenosine were enriched under HG feeding. Transcriptome analysis suggested that cholesterol biosynthesis genes were upregulated in the rumen epithelium of HG cows. The gene expression changes, coupled with more substrate being available (total volatile fatty acids), may have caused an enrichment of intracellular cholesterol and its metabolites. All of these variations could coordinately stimulate cell proliferation, increase membrane permeability, and trigger epithelial inflammation, which eventually disrupts rumen homeostasis and negatively affects cow health.

IMPORTANCE Dairy cows are economically important livestock animals that supply milk for humans. The cow’s rumen is a complex and symbiotic ecosystem composed of diverse microorganisms, which has evolved to digest high-fiber diets. In modern dairy production, SARA is a common health problem due to overfeeding of high-concentrate diets for an ever-increasing milk yield. Although extensive studies have been conducted on SARA, it remains unclear how HG feeding affects rumen cross talk homeostasis. Here, we identified structural and taxonomic fluctuation for the rumen bacterial community, an enrichment of certain detrimental metabolites in rumen fluid, and a general upregulation of cholesterol biosynthesis genes in the rumen epithelium of HG-feeding cows by multi-omics analysis. Based on these results, we propose a speculation to explain cellular events of coordinated rumen bacterial and epithelial adaptation to HG diets. Our work provides new insights into the exploitation of molecular regulation strategies to treat and prevent SARA.

Development of a novel chromophore reaction-based fluorescent probe for biogenic amines detection

Biogenic amines (BAs) are important biomarkers to monitor meat spoilage. However, the design of efficient BA fluorescent probes with distinct colorimetric and ratiometric fluorescent dual-channels is still a critical challenge because of similar chemical properties and basicity between BAs and other amines. Herein, pyrrolopyrrole cyanine (PPCy-1) is reported to display distinctly high reactivity toward BAs through an ultrasensitive irreversible chromophore reaction for the first time. The reaction mechanism is ascribed to synergistic aza-Michael addition and B-N detachment, followed by hydrolysis to produce low-conjugated diketopyrrolopyrrole and heteroaromatic acetonitrile compounds. As a result, colorimetric and ratiometric fluorescent dual-channel (Δλ_ab = 188 nm and Δλ_em = 151 nm) signals and a limit of detection up to 62.1 nM level for BA solution are acquired. In addition, the colorimetric detection of volatile amine vapor using the PPCy-1-loaded filter paper, showing a color change from green to yellow, is feasible. A simple and cost-effective fluorescence "turn on" method using the filter paper or the CAD-40 resin loaded with PPCy-1 to detect TVB (total volatile bases) originating from shrimp spoilage is further demonstrated.

Effect of aspirin to intentionally induce leaky gut on performance, inflammation, and carcass characteristics of feedlot cattle

The negative impacts of stress on gastrointestinal tract (GIT) barrier function can result in compromised animal growth and health. Aspirin is known to cause mucosal injury leading to increased gut permeability and tight junction damage and can be used as a model to study leaky gut in cattle. The objective of this study was to determine the long-term impact of aspirin-induced chronic leaky gut on cattle growth and carcass attributes. Two treatments were evaluated in two studies: control (no aspirin) or 0.25% of the diet dry matter (DM) aspirin fed daily. Diets consisted of 50% corn, 24% dried distillers grains, 20% corn silage, and 6% supplement on a DM basis. In experiment 1, sixteen Angus × Simmental heifers, allotted by body weight (BW) and breed composition, were fed diets for 154 d. On day 155, heifers were dosed with 1 liter of a 180-mM Cr-ethylenediaminetetraacetic acid solution using an esophageal tube and had urine collected every 1.5 to 3 h for 48 h for analysis of Cr as a measure of gut leakiness. In experiment 2, ninety-six Simmental × Angus steers (355.0 ± 14.8 kg) were allotted by BW and breed composition and fed treatment diets for 159 d. Weight was recorded monthly and serum was collected on day 159 and analyzed for lipopolysaccharide-binding protein (LBP), interleukin-6 (IL-6), serum amyloid A (SAA), haptoglobin, and aspartate aminotransferase (AST). Data were analyzed using the MIXED procedure of SAS. Heifers fed 0.25% aspirin in experiment 1 excreted more Cr into urine compared with heifers not fed aspirin (overall treatment effect, P = 0.01). In experiment 2, aspirin tended to increase serum LBP (P = 0.06) but had no effect on concentrations of IL-6, haptoglobin, SAA, or AST (P ≥ 0.25). Aspirin tended to decrease average daily gain (P = 0.10), decreased hot carcass weight and rib-eye area (P ≤ 0.05), and increased fat thickness, marbling score, and yield grade (P ≤ 0.02). Aspirin tended to increase kidney, pelvic, and heart fat percentage (P = 0.10) and had no effect on liver abscesses (P ≥ 0.80). This study indicates that leaky gut induced by long-term administration of aspirin has negative impacts on feedlot performance and carcass composition. The negative impact of aspirin-induced leaky gut on animal performance suggests that chronic leaky gut caused by other factors (subacute acidosis, stress) may be a significant problem for the feedlot industry.

Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle

Metabolomics has been applied to measure the dynamic metabolic responses, to understand the systematic biological networks, to reveal the potential genetic architecture, etc., for human diseases and livestock traits. For example, the current published results include the detected relevant candidate metabolites, identified metabolic pathways, potential systematic networks, etc., for different cattle traits that can be applied for further metabolomic and integrated omics studies. Therefore, summarizing the applications of metabolomics for economic traits is required in cattle. We here provide a comprehensive review about metabolomic analysis and its integration with other omics in five aspects: (1) characterization of the metabolomic profile of cattle; (2) metabolomic applications in cattle; (3) integrated metabolomic analysis with other omics; (4) methods and tools in metabolomic analysis; and (5) further potentialities. The review aims to investigate the existing metabolomic studies by highlighting the results in cattle, integrated with other omics studies, to understand the metabolic mechanisms underlying the economic traits and to provide useful information for further research and practical breeding programs in cattle.

Mucosal Microbiota and Metabolome in the Ileum of Hu Sheep Offered a Low-Grain, Pelleted or Non-pelleted High-Grain Diet

Alterations in mucosal microbiota and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC/MS) to investigate mucosal microbiota and their metabolic profiles in the ileum of Hu sheep fed different diets. Here, we randomly allocated 15 Hu sheep to three diets, a non-pelleted low-grain diet (control diet; CON), a non-pelleted high-grain diet (HG), and a pelleted high-grain diet (HP). After 60 days of treatment, ileal mucosal samples were collected for microbiome and metabolome analysis. The results of principal coordinate analysis and permutation multivariate analysis showed that there was a tendency for microbial differentiation between the CON and HG groups (P < 0.1), although no significant difference between the HG and HP groups was observed (P > 0.05). Compared with the CON diet, the HG diet decreased (P < 0.05) the abundance of some probiotic species (e.g., Sphingomonas and Candidatus Arthromitus) and increased (P < 0.05) the abundance of acid-producing microbiota (e.g., Succiniclasticum, Nesterenkonia, and Alloprevotella) in the ileal mucosa. Compared with the HG diet, the HP diet decreased (P < 0.05) the abundance of Alloprevotella and increased (P < 0.05) the abundance of Mycoplasma in the ileal mucosa. Furthermore, partial least squares discriminant analysis and orthogonal partial least-squared discriminant analysis indicated that different dietary treatments resulted in different metabolic patterns in the ileal mucosa of the CON, HG, and HP groups. The HG diet altered (VIP > 1 and P < 0.05) the metabolic patterns of amino acids, fatty acids, and nucleotides/nucleosides (such as increased amounts of ornithine, tyrosine, cis-9-palmitoleic acid, and adenosine) compared with the CON diet. However, 10 differential metabolites (VIP > 1 and P < 0.05; including tyrosine, ornithine, and cis-9-palmitoleic acid) identified in the HG group exhibited a diametrically opposite trend in the HP group, suggesting that the HP diet could partially eliminate the changes brought upon by the HG diet. Collectively, our findings demonstrate that different diets altered the ileal mucosal microbiota and metabolites and provide new insight into the effects of high-grain diets on the intestinal health of ruminant animals.

Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau

To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli

Cattle are the main reservoirs of Shiga toxin producing Escherichia coli (STEC), a major foodborne pathogen associated with acute enteric disease and hemolytic-uremic syndrome in humans. A total of 397 beef and dairy cattle from 5 farms were included in this study, of which 660 samples were collected for 16S rRNA gene sequencing. The microbiota of farms with a high-STEC prevalence (HSP) had greater richness compared to those of farms with a low-STEC prevalence (LSP). Longitudinal analyses showed STEC-shedders from LSP farms had higher microbiome diversity; meanwhile, changes in the microbiome composition in HSP farms were independent of the STEC shedding status. Most of the bacterial genera associated with STEC shedding in dairy farms were also correlated with differences in the percentage of forage in diet and risk factors of STEC carriage such as days in milk, number of lactations, and warm temperatures. Identifying factors that alter the gut microbiota and enable STEC colonization in livestock could lead to novel strategies to prevent fecal shedding and the subsequent transmission to humans.

Systematic review and meta-analysis of probiotic use on inflammatory biomarkers and disease prevention in cattle

The aim of this study was to appraise the available evidence on the effectiveness of probiotic treatment on mature cattle immunity, inflammation, and disease prevention. A systematic review with meta-analysis was conducted to analyse studies that were eligible to answer the following research question: "in cattle of at least 6-months of age, is the use of probiotics associated with immunomodulatory and inflammatory responses, and clinical disease outcomes?" Our literature search yielded 25 studies that fit the inclusion criteria. From these studies, only 19 were suitable for inclusion in the meta-analysis due to data limitations and differences in study population characteristics. Included studies were assessed for bias using a risk assessment tool adapted from the Cochrane Collaboration's tool for assessing risk of bias in randomised trials. GRADE guidelines were used to assess the quality of the body of evidence at the outcome level. The meta-analysis was performed using Review Manager and R. The overall quality of evidence at the outcome level was assessed as being very low. On average, the treatment effect on immunoglobulin G (IgG), serum amyloid A (SAA), haptoglobin (Hp) and β-hydroxybutyrate (BoHB) for cows receiving probiotics did not differ from control cows. Exposure to probiotics was not associated with reduced risk of reproductive disorders (pooled RR = 1.02 95 % CI = 0.81-1.27, P = 0.88). There is insufficient evidence to support any significant positive effects of probiotics on cattle immunity and disease prevention. This lack of consistent evidence could be due to dissimilarities in the design of the included studies such as differences in dosage, dose schedule, diet composition and/or physiological state of the host at the time of treatment.

Comparative untargeted metabolome analysis of ruminal fluid and feces of Nelore steers (Bos indicus)

We conducted a study to identify the fecal metabolite profile and its proximity to the ruminal metabolism of Nelore steers based on an untargeted metabolomic approach. Twenty-six Nelore were feedlot with same diet during 105 d. Feces and rumen fluid were collected before and at slaughter, respectively. The metabolomics analysis indicated 49 common polar metabolites in the rumen and feces. Acetate, propionate, and butyrate were the most abundant polar metabolites in both bio-samples. The rumen presented significantly higher concentrations of the polar compounds when compared to feces (P < 0.05); even though, fecal metabolites presented an accentuated representability of the ruminal fluid metabolites. All fatty acids present in the ruminal fluid were also observed in the feces, except for C20:2n6 and C20:4n6. The identified metabolites offer information on the main metabolic pathways (higher impact factor and P < 0.05), as synthesis and degradation of ketone bodies; the alanine, aspartate and glutamate metabolisms, the glycine, serine; and threonine metabolism and the pyruvate metabolism. The findings reported herein on the close relationship between the ruminal fluid and feces metabolic profiles may offer new metabolic information, in addition to facilitating the sampling for metabolism investigation in animal production and health routines.