Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle

Integrated Blood Transcriptome and Multi-Tissue Trace Mineral Analyses of Healthy Stocker Cattle Fed Complexed or Inorganic Trace Mineral Supplement

Supplementing trace minerals is common in managing bovine respiratory disease (BRD) in post-weaned cattle; however, its influence on host immunity and metabolism in high-risk cattle remains unclear. We aimed to assess the impact of three supplementation programs on liver and serum trace element concentrations and blood gene expression. Fifty-six high-risk beef steers were randomly assigned to one of three groups over 60 days: (1) sulfate-sourced Cu, Co, Mn, and Zn (INR), (2) amino acid-complexed Cu, Mn, Co, and Zn (AAC), or (3) AAC plus trace mineral and vitamin drench (COMBO). Serum and liver biopsies for Cu, Co, Mn, and Zn at d0, d28, and d60 were analyzed from cattle free of BRD (n = 9 INR; n = 6 AAC; n = 10 COMBO). Differences and correlations of mineral concentrations were analyzed via generalized linear mixed models and Spearman's rank coefficients, respectively (p < 0.05). Whole blood RNA samples from healthy cattle (n = 4 INR; n = 4 AAC; n = 4 COMBO) at d0, d13, d28, d45, and d60 were sequenced and analyzed for differentially expressed genes (DEGs) via glmmSeq (FDR < 0.05), edgeR (FDR < 0.10), and Trendy (p < 0.10). Serum and liver Cu and Co concentrations increased over time in all groups, with higher liver Cu in COMBO (487.985 μg/g) versus AAC (392.043 μg/g) at d60 (p = 0.013). Serum and liver Cu concentrations (ρ = 0.579, p = 6.59 × 10-8) and serum and liver Co concentrations (ρ = 0.466, p = 2.80 × 10-5) were linearly correlated. Minimal gene expression differences were found between AAC versus COMBO (n = 2 DEGs) and INR versus COMBO (n = 0 DEGs) over time. AAC versus INR revealed 107 DEGs (d13-d60) with increased traits in AAC including metabolism of carbohydrates/fat-soluble vitamins, antigen presentation, ATPase activity, and B- and T-cell activation, while osteoclast differentiation and neutrophil degranulation decreased in AAC compared to INR. Our study identifies gene expression differences in high-risk cattle fed inorganic or amino acid-complexed mineral supplements, revealing adaptive immune and metabolic mechanisms that may be improved by organically sourced supplementation.

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.

Longitudinal characterization of the metabolome of dairy cows transitioning from one lactation to the next: Investigations in blood serum

The objective of this study was to characterize changes in the serum metabolome and various indicators of oxidative balance in dairy cows starting 2 wk before dry-off and continuing until wk 16 of lactation. Twelve Holstein dairy cows (body weight 745 ± 71 kg, body condition score 3.43 ± 0.66; mean ± SD) were housed in a tiestall barn from 10 wk before to 16 wk after parturition. Cows were dried off 6 wk before the expected calving date (mean dry period length = 42 d). From 8 wk before calving to 16 wk after calving, blood samples were taken weekly to study redox metabolism by determining antioxidant capacity, measured as the ferric-reducing ability of plasma, reactive oxidative metabolites, oxidative stress index, oxidative damage of lipids, measured as thiobarbituric acid reactive substances, and glutathione peroxidase activity. According to these results, dairy cows had the lowest serum antioxidant capacity and greater levels of oxidative stress during the dry-off period and the early postpartum period. For metabolomics, a subset of serum samples including wk -7 (before dry-off), -5 (after dry-off), -1, 1, 5, 10, and 15 relative to calving were used. A targeted metabolomics approach was performed using liquid chromatography and flow injection with electrospray ionization triple quadrupole mass spectrometry using the MxP Quant 500 kit (Biocrates Life Sciences AG). A total of 240 metabolites in serum were used in the final data analysis. Principal component analysis revealed a clear separation by days of sampling, indicating a remarkable shift in metabolic phenotype between the dry period and late and early lactation. Changes in many non-lipid metabolites associated with one-carbon metabolism, the tricarboxylic acid cycle, the urea cycle, and AA catabolism were observed in the study, with changes in AA serum concentrations likely related to factors such as energy and nitrogen balance, digestive efficiency, and changing diets. The study confirmed an extensive remodeling of the serum lipidome in peripartum dairy cows, highlighting the importance of changes in acylcarnitine (acylCN), phosphatidylcholines (PC), and triacylglycerols (TG), as they play a crucial role in lipid metabolism. Results showed that short-chain acylCN increased after dry-off and decreased thereafter, whereas lipid-derived acylCN increased around parturition, suggesting that more fatty acids could enter mitochondria. Phospholipids and sphingolipids in serum showed changes during lactation. In particular, concentrations of sphingomyelins, PC, and lysoPC decreased around calving but increased in mid- and late lactation. In contrast, concentrations of TG remained consistently low after parturition. The serum concentrations of bile acids fluctuated during the dry period and lactation, with glycocholic acid, cholic acid, glycodeoxycholic acid, and taurocholic acid showing the greatest concentrations. These changes are likely due to the interplay of diet, liver function, and the ability of the gut microbiota to convert primary to secondary bile acids. Overall, these descriptive results may aid in hypothesis generation and in the design and interpretation of future metabolite-based studies in dairy cows. Furthermore, they contribute to our understanding of the physiological ranges in serum metabolites relative to the lactation cycle of the dairy cow.

Pasture-finishing of bison improves animal metabolic health and potential health-promoting compounds in meat

BACKGROUND

With rising concerns regarding the effects of red meat on human and environmental health, a growing number of livestock producers are exploring ways to improve production systems. A promising avenue includes agro-ecological practices such as rotational grazing of locally adapted ruminants. Additionally, growing consumer interest in pasture-finished meat (i.e., grass-fed) has raised questions about its nutritional composition. Thus, the goal of this study was to determine the impact of two common finishing systems in North American bison-pasture-finished or pen-finished on concentrates for 146 d-on metabolomic, lipidomic, and fatty acid profiles of striploins (M. longissimus lumborum).

RESULTS

Six hundred and seventy-one (671) out of 1570 profiled compounds (43%) differed between pasture- and pen-finished conditions (n = 20 animals per group) (all, P < 0.05). Relative to pasture-finished animals, the muscle of pen-finished animals displayed elevated glucose metabolites (~ 1.6-fold), triglycerides (~ 2-fold), markers of oxidative stress (~ 1.5-fold), and proteolysis (~ 1.2-fold). In contrast, pasture-finished animals displayed improved mitochondrial (~ 1.3-fold higher levels of various Krebs cycle metabolites) and carnitine metabolism (~ 3-fold higher levels of long-chain acyl carnitines) (all P < 0.05). Pasture-finishing also concentrated higher levels of phenolics (~ 2.3-fold), alpha-tocopherol (~ 5.8-fold), carotene (~ 2.0-fold), and very long-chain fatty acids (~ 1.3-fold) in their meat, while having lower levels of a common advanced lipoxidation (4-hydroxy-nonenal-glutathione; ~ 2-fold) and glycation end-product (N6-carboxymethyllysine; ~ 1.7-fold) (all P < 0.05). In contrast, vitamins B₅, B₆, and C, gamma/beta-tocopherol, and three phenolics commonly found in alfalfa were ~ 2.5-fold higher in pen-finished animals (all P < 0.05); suggesting some concentrate feeding, or grazing plants rich in those compounds, may be beneficial.

CONCLUSIONS

Pasture-finishing (i.e., grass-fed) broadly improves bison metabolic health and accumulates additional potential health-promoting compounds in their meat compared to concentrate finishing in confinement (i.e., pen-finished). Our data, however, does not indicate that meat from pen-finished bison is therefore unhealthy. The studied bison meat-irrespective of finishing practice-contained favorable omega 6:3 ratios (< 3.2), and amino acid and vitamin profiles. Our study represents one of the deepest meat profiling studies to date (> 1500 unique compounds), having revealed previously unrecognized differences in animal metabolic health and nutritional composition because of finishing mode. Whether observed nutritional differences have an appreciable effect on human health remains to be determined.

Prokaryotic Diversity of Ruminal Content and Its Relationship with Methane Emissions in Cattle from Kazakhstan

In this study, we analyzed the microbial composition of the rumen contents of cattle from Kazakhstan. Specifically, samples of the liquid and solid fractions of the rumen were collected to determine the quantitative and qualitative composition of methanogenic archaea. Cattle were six steers receiving hay-concentrate feeding. Methane emission was determined by repeated measurements for each animal. Rumen samples were then taken from fistulas and analyzed using 16S metabarcoding via Next-Generation Sequencing (NGS). The difference between the rumen fractions was investigated, resulting in differential distribution of the families Streptococccaceae, Lactobacillaceae, Desulfobulbaceae, and Succinivibrionaceae, which were more abundant in the liquid fraction, while Thalassospiraceae showed a higher presence in the solid fraction. These differences can be explained by the fact that fibrolytic bacteria are associated with the solid fraction compared to the liquid. A relationship between methane emission and methanogenic microbiota was also observed. Steers producing more methane showed microbiota richer in methanogens; specifically, most Mathanobacteriaceae resided in the liquid fraction and solid fraction of animals 1 and 6, respectively. The same animals carried most of the Methanobrevibacter and Methanosphaera genera. On the contrary, animals 2, 3, and 5 hosted a lower amount of methanogens, which also agreed with the data on methane emissions. In conclusion, this study demonstrated a relationship between methane emission and the content of methanogenic archaea in different rumen fractions collected from cattle in Kazakhstan. As a result of the studies, it was found that the solid fraction of the rumen contained more genera of methanogens than the liquid fraction of the rumen. These results prove that taking rumen contents through a fistula is more useful than taking it through a probe. The presented data may be of interest to scientists from all over the world engaged in similar research in a comparative aspect.

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.

Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle

The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle's rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R2 = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis

Methane (CH₄) is an important greenhouse gas (GHG). Enteric methane emissions from farmed ruminant livestock account for approximately 15% of global GHG emissions, with approximately 44% of livestock emissions in the form of methane. The purpose of the research is to study the influence of feeding types and regional characteristics of Kazakhstan on the microbiota of feces and the number of methane-forming archaea of beef and meat-and-dairy cattle productivity. For this purpose, fecal samples were taken rectally from 37 cattle heads from four regions of Kazakhstan (Western, Southern, Northern and Southeast). The taxonomic composition of the community in all samples was determined by 16S metabarcoding; additionally alpha and beta diversities were calculated. The dominant phyla were: Firmicutes (57.30%), Bacteroidetes (17.00%), Verrucomicrobia (6.88%), Euryarchaeota (6.49%), Actinobacteria (4.77%) and Patescibacteria (3.38%). Significant differences with regard to methanogens bacteria were found: Euryarchaeota were less present in animals from Western Kazakhstan (2.40%), while Methanobacteriales and Methanobrevibacter were prevalent in Southeast, and less abundant in Western region. Western Kazakhstan differs from the other regions likely because animals are mainly grazed in the pasture. Thus, grazing animals has an impact on their microbiota thus leading to a decrease in methane emissions.

Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits

The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.

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.

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.

Multi-Omics Analysis Reveals a Dependent Relationship Between Rumen Bacteria and Diet of Grass- and Grain-Fed Yaks

Current information on the differences between rumen bacteria and metabolites of the grass-fed and grain-fed yaks is limited. Understanding the composition and alterations of rumen microbial metabolites is important to clarify its potential role in grass-fed and grain-fed systems. The aim of this research was to explore the influence of different production systems on the functional attributes and metabolites in the rumen microbiota of yak using genomics (Illumina MiSeq sequencing of the 16S rRNA gene) and untargeted metabolomics (UHPLC-QTOF-MS). Rumen samples were obtained from grass-fed (C), grain-fed for 3-month (G3), and grain-fed for 6-month yaks (G6). Results showed that the grain-fed yaks presented a lower rumen bacterial richness and diversity when compared to grass-fed yaks. Bacteroidota, Firmicutes, and Fibrobacterota were the main bacterial phyla. At the phylum and genus level, the grass-fed yaks significantly increased the abundance of Fibrobacterota and Fibrobacter (p < 0.05), respectively. The metabolomics analysis revealed that the metabolite profiles differed among the three groups. Compared with the grass-fed group, grain feeding significantly increased azelaic acid, hypoxanthine, uridine, L-phenylalanine, anserine, and decreased alpha-linolenic acid, adenine. Pathway enrichment analysis showed significant differences in metabolic pathways among all comparison groups, but the glycerophospholipid metabolism and alpha-linolenic acid metabolism pathway were common key metabolic pathways. This study showed that the combined analysis of microbiota and metabolites could distinguish different production systems and the fattening time of yaks, providing novel insights for us to understand the function of the rumen bacteria.

Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis

Diet-induced acidosis imposes a health risk to young calves. In this study, we aimed to investigate the host jejunum transcriptome changes, along with its microbial community variations, using our established model of feed-induced ruminal acidosis in young calves. Eight bull calves were randomly assigned to two diet treatments beginning at birth (a starch-rich diet, Aci; a control diet, Con). Whole-transcriptome RNA sequencing was performed on the jejunum tissues collected at 17 weeks of age. Ribosomal RNA reads were used for studying microbial community structure variations in the jejunum. A total of 853 differentially expressed genes were identified (402 upregulated and 451 downregulated) between the two groups. The cell cycle and the digestion and absorption of protein in jejunal tissue were affected by acidosis. Compared to the control, genera of Campylobacter, Burkholderia, Acidaminococcus, Corynebacterium, and Olsenella significantly increased in abundance in the Aci group, while Lachnoclostridium and Ruminococcus were significantly lower in the Aci group. Expression changes in the AXL gene were associated with the abundance variations of a high number of genera in jejunum. Our study provided a snapshot of the transcriptome changes in the jejunum and its associated meta-transcriptome changes in microbial communities in young calves with feed-induced acidosis.