Rumen Tissue Research Articles

Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model

BackgroundThis study aimed to elucidate the molecular mechanisms of solid diet introduction initiating the cellular growth and maturation of rumen tissues and characterize the shared and unique biological processes upon different solid diet regimes.MethodsTwenty-four Hu lambs were randomly allocated to three groups fed following diets: goat milk powder only (M, n = 8), goat milk powder + alfalfa hay (MH, n = 8), and goat milk powder + concentrate starter (MC, n = 8). At 42 days of age, the lambs were slaughtered. Ruminal fluid sample was collected for analysis of concentration of volatile fatty acid (VFA) and microbial crude protein (MCP). The sample of the rumen wall from the ventral sac was collected for analysis of rumen papilla morphology and transcriptomics.ResultsCompared with the M group, MH and MC group had a higher concentration of VFA, MCP, rumen weight, and rumen papilla area. The transcriptomic results of rumen wall showed that there were 312 shared differentially expressed genes (DEGs) between in “MH vs. M” and “MC vs. M”, and 232 or 796 unique DEGs observed in “MH vs. M” or “MC vs. M”, respectively. The shared DEGs were most enriched in VFA absorption and metabolism, such as peroxisome proliferator-activated receptor (PPAR) signaling pathway, butanoate metabolism, and synthesis and degradation of ketone bodies. Additionally, a weighted gene co-expression network analysis identified M16 (2,052 genes) and M18 (579 genes) modules were positively correlated with VFA and rumen wall morphology. The M16 module was mainly related to metabolism pathway, while the M18 module was mainly associated with signaling transport. Moreover, hay specifically depressed expression of genes involved in cytokine production, immune response, and immunocyte activation, and concentrate starter mainly altered nutrient transport and metabolism, especially ion transport, amino acid, and fatty acid metabolism.ConclusionsThe energy production during VFA metabolism may drive the rumen wall development directly. The hay introduction facilitated establishment of immune function, while the concentrate starter enhanced nutrient transport and metabolism, which are important biological processes required for rumen development.

Longitudinal assessment revealed the shifts in rumen and colon mucosal-attached microbiota of dairy calves during weaning transition

The objectives of this study were to investigate the shifts in rumen and colon mucosa-associated microbiota in dairy calves fed a high milk replacer feeding rate before and after weaning and to determine whether such shifts are associated with tissue physiological measures. Longitudinal biopsy was performed to collect rumen and colon mucosal tissues of 4 ruminally cannulated Holstein dairy bull calves (weaned at 6 wk of age) at the end of wk 5 (before weaning), 7 (weaning adaptation) and 12 (after weaning), and were used to assess mucosa-associated microbiota and their changes using amplicon sequencing. Both rumen and colon mucosa-associated bacterial communities shifted during the weaning process, as evidenced by their clear separation among 3 different weaning periods and increased α diversity (Shannon and Chao1 indices) during weaning transition. Among the 3 dominant bacterial phyla identified (relative abundance >1.0%), the relative abundance of Proteobacteria and Bacteroidetes decreased in the rumen mucosa, whereas the relative abundance of Firmicutes increased in both rumen and colon mucosa during weaning transition. In the rumen mucosa, Campylobacter (0.6-22.1%) gradually became prevalent during weaning transition, whereas Succinivibrio (6.2-10.3%) and Prevotella 1 (4.7-10.5%) were dominant regardless of weaning transition. In the colon mucosa, Bacteroides (12.8-25.4%) was dominant during weaning transition, although its relative abundance decreased after weaning. In the meantime, relative abundance of uncultured Lachnospiraceae increased from 2.2% to 25.7% during this period. In addition, genera Pyramidobacter (in the rumen mucosa) and Lachnoclostridium (in the colon mucosa) were positively correlated with rumen papilla surface area and colon mucosal thickness, respectively. Moreover, genera Ruminococcaceae UCG-005 and Sharpea in the rumen mucosa were positively correlated with the molar proportion of propionate and butyrate, respectively. Overall, our findings revealed that rumen and colon mucosa-associated bacterial communities altered in response to the weaning transition, and some bacterial taxa in these communities may have positive effects on rumen and colon mucosa development during this period.

Rumen morphometry and sorting behavior of fattening male goat fed pelleted and unpelleted TMR with two levels of wheat straw

Abstract The physical form of the diet and level of straw in fattening total mixed rations (TMR) can influence sorting behavior and rumen morphometry. Therefore, the objectives of this experiment were to evaluate two levels of wheat straw (WS) in conventional and pelleted TMR on feed sorting behavior, rumen morphometry, the thickness of stratum corneum (SC), and color of reticulorumen mucosa. Thirty-two Beetle male goats (8 goats/treatment) were assigned to one of the four treatments in a 2 × 2 factorial arrangement: CTMR15 and CTMR 25 (conventional TMR containing 15 and 25 % WS, respectively), the PTMR15 and PTMR25 (pelleted TMR containing 15 and 25 % WS, respectively). In PTMR, the WS was ground to 8 mm and then pelleted. Feed sorting behavior of goats fed conventional TMR was evaluated twice weekly using Penn State Particle Separator (PSPS). At the end of the experiment, goats (n = 8/treatment) were slaughtered and rumen tissues preserved for further rumen morphometric examination. The CTMR25 fed goats consumed more medium ( 8 mm) and short (> 1.18) particles. There was a significant interaction (P 0.05) by the PF or the SL in the diet. The thickness of stratum corneum (SC) (18.55 μm) was highest (P

Influence of two rumen cannulation techniques on postoperative recovery in sheep.

To determine the influence of two methods of rumen cannulation on postoperative animal welfare. Experimental study. Twelve commercial wethers (n = 6 per group). Group 1 wethers underwent a one-step procedure to place a cannula immediately after fistulation of the rumen to the skin. Group 2 wethers underwent a two-step procedure in which a portion of the rumen was externalized and held with a clamp for 9 days, after which the cannula was placed into the fistula created by removal of the clamped rumen tissue. Feed intake and vital signs were monitored daily for 24 days postoperatively. Plasma fibrinogen and serum cortisol were measured daily for 14 days postoperatively to estimate inflammatory and stress responses, respectively. Change in body weight was also assessed. Cannulation method did not affect (P > .05) body weight, temperature, heart rate, respiratory rate, fibrinogen level, or cumulative cortisol level. Feed intake was lower (0.82 vs 1.2 kg/d; P < .0001), and mean cortisol level was greater (124.2 vs 121.5 ng/mL; P = .038) in group 2 compared with group 1. Although both cannulation methods mostly elicited similar physiological responses, animals seemed to experience more discomfort and stress when undergoing the two-step procedure. Rumen cannulation performed in one step is recommended to improve postoperative welfare.

PSVI-17 Evaluating the impact of a high-starch and high-forage diet on the ruminal solid, liquid, and epimural microbiota of dairy cows

Abstract Ruminants harbor a rumen microbial community that convert their host-indigestible diet into nutrients. This rumen microbiome is known to contain three distinct communities: luminal solids, luminal liquids, and the epithelial, or epimural, communities. Currently, there is little research examining the diet-dependent responses of all three microbial communities within the same animals. To address this, we used next-generation 16S rRNA sequencing to characterize the bacterial communities associated with the ruminal solids, liquids, and epimural tissue of 13 lactating and cannulated Holstein dairy cows fed high-starch (diet A) and high-forage (diet B) diets in a crossover experimental design. This crossover design consisted of two groups, two diets, and two sampling periods, with animals receiving a single diet for 8 weeks. Ruminal solids and liquids were collected by separating whole rumen contents through cheesecloth, while rumen epithelial tissue was collected from the ventral-sac via biopsy. Samples were collected at the end of each diet-treatment period. Independent of diet, all sample-types were dominated by bacteria in the phyla Firmicutes and Bacteroidetes. Proteobacteria and Epsilonbacteraeota were also highly abundant, but only in epimural samples. Overall, the epimural microbiota was more diverse, relative to both luminal communities, and diet was found to impact community diversity in solids only. We also found that sample-type, diet-treatment, and their interactions, significantly impacted community structure (Bray-Curtis; PERMANOVA P &amp;lt; 0.05) and composition (Jaccard; PERMANOVA P &amp;lt; 0.05). Of the genera which differed in abundance according to diet and sample-type, Succiniclasticum was highly abundant in epimural samples only, and increased in abundance under a high-forage diet (P &amp;lt; 0.05). In contrast, Saccharofermentans was highly abundant in luminal samples only, but also increased in abundance under a high-forage diet (P &amp;lt; 0.05). These sample-type and diet-dependent differences in specific bacteria likely reflect the overall dietary and environmental factors shaping the heterogeneity of all three ruminal communities.

224 Epimural microbiota and rumen epithelial gene expression in healthy and liver-abscessed animals

Abstract Different dietary and feed additive strategies have been developed to reduce the liver abscess in feedlot cattle, but liver abscesses are still a major problem in beef production. We have limited knowledge about how rumen microbial communities interact with host epithelial gene expression in healthy and liver-abscessed animals. The objective of this study was to investigate the associations between the rumen content associated and rumen epimural microbiome and epithelial gene expression in liver-abscessed and healthy animals. To this end, we collected the ruminal contents and tissue samples from healthy (N=30; score=0, steers n=19 and heifers n=11) and liver-abscessed (N=30; score=A+, steers n=21 and heifers n=9) feedlot cattle at harvest. The bacterial community compositions in the ruminal contents and papillae were evaluated via 16S rDNA sequencing of the V4 region using the Illumina MiSeq platform. Additionally, total RNA was extracted from rumen epithelial tissues and sequenced using the Illumina NextSeq platform. The permutational analysis (PERMANOVA) on Bray Curtis distances matrices showed the microbial community in the ruminal contents was significantly different (P&amp;lt; 0.001) from the bacterial community observed in rumen papillae. The ruminal contents contained a higher abundance of Bacteroidetes and Proteobacteria while papillae contained higher abundance of Firmicutes. The epimural microbiota was different (P&amp;lt; 0.01) between healthy and liver abscessed animals while ruminal contents microbiome was not different between the two groups. The DeSeq2 algorithm identified differentially expressed genes (221) related to MAPK, NF-kappa B signaling pathway, immune and inflammatory response in liver-abscessed animals. Additionally, a wide range of epimural bacterial taxa were correlated (-0.52 to 0.67) with differentially expressed genes. These data demonstrate the interaction between epimural microbiota and the host and its effect on liver abscesses, and indicate the need to study the epimural microbiome for its impact on liver abscesses in feedlot cattle. USDA is an equal opportunity provider and employer.

Short communication: Molecular markers for epithelial cells across gastrointestinal tissues and fecal RNA in preweaning dairy calves

The objective of this study was to compare the transcription of gene markers for gastrointestinal (GI) epithelial cells, including fatty acid binding protein 2 (FABP2) and cytokeratin 8 (KRT8), and tight junction complex genes (TJP1, CLDN1, CLDN4) in fecal RNA against several GI tract tissue sections in dairy calves. Eight healthy Jersey calves were euthanized at 5 wk of age, and postmortem samples were collected from rumen, duodenum, jejunum, ileum, large intestine, cecum, and feces for total RNA isolation. Tissues and fecal samples were immediately frozen in liquid nitrogen until RNA isolation. A real-time quantitative PCR analysis was performed using a single standard curve composited of equal amounts of all samples, including cDNA from fecal and GI tract tissues. The mRNA expression of the tight junctions TJP1, CLDN1, and CLDN4 was greater in fecal RNA compared with lower GI tract tissues (i.e., duodenum, jejunum, ileum, large intestine, and cecum). Similar to fecal RNA, rumen tissue had greater expression of tight junctions CLDN1 and CLDN4 than lower GI tract tissues. Similarly, rumen tissue had greater expression of TPJ1 than all lower GI tract tissues except duodenum. The expression of TJP1 and CLDN4 was greater in fecal RNA than in rumen tissue; in contrast, CLDN1 mRNA expression was greater in rumen tissue than in the fecal RNA. The expression of FABP2 was greater in duodenum in comparison to all tissue except ileum. The mRNA expression of FABP2 in fecal samples was similar to jejunum and ileum. The expression of KRT8 in fecal samples was similar to duodenum, large intestine, and cecum. The fecal RNA had a greater expression of KRT8 in comparison to jejunum and ileum. The rumen tissue had the lowest mRNA expression of KRT8. The expression levels of FABP2, KRT8, and tight junction genes observed in fecal transcripts suggest that a considerable amount of RNA derived from GI tract epithelial cells can be detected in fecal RNA, which is in agreement with previous data in neonatal dairy calves and other biological models including humans, rodents, and primates. The greater expression of tight junctions in fecal RNA in comparison to sections of the low GI remains to be understood, and due to the importance of tight junctions in GI physiology, further clarification of this effect is warranted. The similarities in mRNA expression of FABP2 and KRT8 between fecal RNA and intestinal sections add up to the accumulating evidence that fecal RNA can be used to investigate molecular alterations in the GI tract of neonatal dairy calves. Further research in this area should include high-throughput transcriptomic analysis via RNA-seq to uncover novel molecular markers for specific sections of the GI tract of neonates.

Effects of diets with different levels of fennel (Foeniculum vulgare) seed powder on DLK1 gene expression in brain, adipose tissue, femur muscle and rumen of Kermani lambs

Abstract DLK1 (protein delta homolog 1) plays an important role in production of adipocytes, muscle development, wound healing, pancreas, liver and lung cells development and also in the development of meat quality, digestion and growth performance. Therefore, the goal of this research was to investigate the effects of different levels of fennel seed power in the diet on growth performance and on DLK1 gene expression in brain, adipose, femur (leg) muscle and rumen muscle tissues of Kermani lambs. Dietary treatments including different levels of fennel seed powder (0, 1 and 2 % of diet DM) were fed to 3 groups of lambs (each group contained 10 animals) for three months. Some physiological parameters relating to muscle and adipose development were measured. Tissues including brain, adipose tissue, femur (leg) muscle and rumen muscle were collected for expression analysis of the DLK1 gene. In this study, increasing the level of fennel seed powder in diets of lambs, increased the amount of DLK1 gene expression in the femur muscle and rumen tissues. Feeding 2 % fennel in comparison to the control diet (0 %) resulted in a significant difference in the amount of DLK1 gene expression in the femur (leg) muscle and in the rumen muscle (P

Evaluation of various barley processing methods on rumen microbial population, histomorphometry, and fermentation characteristics in fattening lamb

Barley deserves a top place in the farm for feeding livestock. It is irreplaceable by any other grain in sheep diets for producing capacious rumen microbial yields. The present study was conducted to investigatethe effect of different methods of barley processing on a number of microbes, fermentation parameters, and the rumen tissue characteristics of fattening lambs. For this purpose, 20 fattening male lambs with a mean weight of 25 ± 1.1 kg were tested for 80 daysbasedon a completely randomized design with four treatments (GRB: ground barley, SRB: steam-rolled barley, GEB: germinated barley, SOB: soaked barley) and five replicates. Three lambs from each treatment were slaughtered and sampling was done on the rumen liquid and tissue to determine their pH and volatile fatty acid (VFA), amylolytic bacteria, proteolytic, cellulolytic, heterophilic, and protozoa contents. The findings showed that the number of cellulolytic bacteria in ground barley treatment was lower than that of soaked barley treatment. In addition, there existed fewer heterophilic bacteria in germinated barley groups compared with other treatments. The lactic acid level in the GRB was increased compared to that in SRB and GEB treatments (P &lt; 0.05). The GRB further reduced the thickness of the rumen wall in comparison with SRB. In general, replacing GRB with SOB improved certain thickness of the epithelial tissue and cellulolytic bacteria of the rumen.

Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats.

Simple SummaryIn ruminants, the rumen epithelium plays an important role in nutrient absorption, metabolism and transport. MicroRNAs (miRNAs) have been reported to regulate the proliferation of diverse epithelial cells. In this study, we profiled the miRNA transcriptomes of goat rumens at four development stages and screened for candidate miRNAs related to rumen development. MiR-148a-3p was found to be highly expressed in the rumen tissues and induced the proliferation of GES-1 cells by targeting QKI. Our findings provide some insights into the functional roles of miRNAs in rumen growth and functional development in ruminants.The rumen is an important digestive organ of ruminants. From the fetal to adult stage, the morphology, structure and function of the rumen change significantly. However, the knowledge of the intrinsic genetic regulation of these changes is still limited. We previously reported a genome-wide expression profile of miRNAs in pre-natal goat rumens. In this study, we combined and analyzed the transcriptomes of rumen miRNAs during pre-natal (E60 and E135) and post-natal (D30 and D150) stages. A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the pre-weaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites of miR-148a-3p in the 3′-UTR of QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI through in situ hybridization was observed in the rumen tissues but not in the intestinal tracts. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers of the rumen, suggesting that miR-148a-3p is involved in the development of the rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells. Taken together, our study identified DEMs involved in the development of the rumen and provides insights into the regulation mechanism of rumen development in goats.

Gene co-expression and alternative splicing analysis of key metabolic tissues to unravel the regulatory signatures of fatty acid composition in cattle

ABSTRACT Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.

Exploring the Rumen and Cecum Microbial Community from Fetus to Adulthood in Goat.

Simple SummaryThe rumen and cecum are two important fermentation organs in ruminants. The acquisition and development of the neonatal microbiome, as well as the difference between these two organs, was important. We performed 16S rRNA gene sequencing to study the diversity, structure and composition of the goat microbial communities between the rumen and cecum from fetus to adulthood. The results revealed the microbial transmission routes from the mother to fetus, and also revealed the establishment and dynamic fluctuations of the gut microbiome from fetus to adulthood in goats.The present study aimed to investigate the colonization process of epithelial bacteria attached to the rumen and intestinal tract tissue during the development of goats after birth. However, this process from fetus to adulthood was very limited. In goats, the rumen and cecum are two important fermentation organs, and it is important to study the acquisition and development of the neonatal microbiome, as well as the difference between these two organs. To characterize the microbial establishment and dynamic changes in the rumen and cecum from fetus to adulthood, we performed 16S rRNA gene sequencing for 106 samples from 47 individuals of nine pregnant mother–fetus pairs and 16 kids from birth up to 6 months. The diversity, structure and composition of the microbial communities were distinct between the rumen and cecum after birth, while they were similar in the fetal period. The study showed a rapid loss and influx of microbes at birth, followed by slight selection after drinking colostrum, and then a strong selection after weaning, suggesting that the establishment and dynamic fluctuations of the gut microbiome undergoes three distinct phases of microbiome progression in life: a conserved phase (during late pregnancy in the fetus), a transitional phase (newborn until weaning), and a stable phase (from weaning to adulthood). The results supported the view that microbes exist in the fetus, and revealed the establishment and dynamic fluctuations of the gut microbiome from fetus to adulthood in goats.

The functional development of the rumen is influenced by weaning and associated with ruminal microbiota in lambs

Rumen development is critical for the development of early lambs. This work aims to evaluate the effects of abrupt weaning at day 21 on rumen fermentation, histomorphological traits and the ruminal microbiota compared with continuous suckling. Twelve pairs of artificially reared full-sib neonatal male Hu lambs were allocated to two groups, one of which was weaned at day 21 (EW group) and the other which was not weaned (CON group). At day 26 and day 49, six lambs from each group were randomly selected and sacrificed to collect ruminal contents and rumen tissue samples. Results showed that weaning influenced the fermentation parameters in the rumen, and altered the microbial community composition on day 49 (p < 0.05). Several genera were associated with rumen fermentation parameters (p < 0.05). Volatile fatty acid (VFA) concentration is the key parameter impacting microbiota composition. Weaning influenced the expression of genes associated with VFA metabolism and regulation of cell proliferation (p < 0.05). In conclusion, weaning significantly influenced the morphological and functional development of the rumen, and bacterial community composition. The microbial community composition was strongly associated with rumen weight and fermentation profiles, but not with morphological development.

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs.

Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes correlated negatively with propionate and TVFA (P < 0.05); and Elusimicrobia correlated negatively with propionate and butyrate (P < 0.05). Actinobacteria and Verrucomicrobia correlated positively correlated with NH3-N. In conclusion, supplementary feeding of lambs before weaning promoted the development of rumen tissue morphology and rumen microorganisms.

Establishment and transcriptomic analyses of a cattle rumen epithelial primary cells (REPC) culture by bulk and single-cell RNA sequencing to elucidate interactions of butyrate and rumen development

As a critical and high-value tool to study the development of rumen, we established a stable rumen epithelial primary cell (REPC) culture from a two-week-old Holstein bull calf rumen epithelial tissue. The transcriptomic profiling of the REPC and the direct effects of butyrate on gene expression were assessed. Correlated gene networks elucidated the putative roles and mechanisms of butyrate action in rumen epithelial development. The top networks perturbed by butyrate were associated with epithelial tissue development. Additionally, two critical upstream regulators, E2F1 and TGFB1, were identified to play critical roles in the differentiation, development, and growth of epithelial cells. Significant expression changes of upstream regulators and transcription factors provided further evidence in support that butyrate plays a specific and central role in regulating genomic and epigenomic activities influencing rumen development. This work is the essential component to obtain a complete global landscape of regulatory elements in cattle and to explore the dynamics of chromatin states in rumen epithelial cells induced by butyrate at early developmental stages.

Impacts of Time-Fed Concentrate-Based Diets on Plasma Metabolites, Rumen Histology, and mRNA Expression of Hepatic Enzymes of Wethers.

Simple SummaryIn modern ruminant meat production systems, wethers and steers are commonly fed diets containing 80% grain, or more. These diets are commonly fed to increase fat deposition in meat-producing ruminants. However, when wethers and steers are not appropriately transitioned to grain-based diets, they can experience metabolic and inflammatory conditions that negatively affect health and production. It is still unclear how meat-producing ruminants adapt to grain-based diets over time. This study evaluated the effects of an abrupt dietary change, from 80% forage to 80% grain, on rumen, plasma, and liver metabolism in growing wethers and monitored their ability to adapt over time. The results of the study suggest that wethers fed an 80% grain diet adapt over time by altering the expression of key enzymes involved in the systemic inflammation, iron metabolism, and cholesterol and glucose synthesis. This study provides novel insight into the physiology of fattening ruminants that have been abruptly fed grain-based diets and highlights the fact that meat-producing animals can be fed grain-based diets to meet increasing human meat requirements.Transition to grain increases inflammation and causes parakeratosis, which can decrease growth performance in fattening animals. It is unknown if ruminants adapt to these inflammatory responses over time. In a three-phase, 49-day experiment, all wethers (n = 13, BW = 50.6 ± 4.7 kg; 4.9 ± 0.3 months of age) were fed an 80% forage diet during P1(day 0 to 21). On day 21, 4 wethers were slaughtered to obtain baseline liver and rumen tissue. During P2 (day 22 to 25), the remaining wethers were fed an 80% concentrate diet. Four wethers were slaughtered on day 25 to obtain P2 liver and rumen tissue. During P3 (day 22 to 49), the remaining five wethers were fed 80% concentrate diets and were slaughtered on day 49 to obtain P3 liver and rumen tissue. Rumen parakeratosis was greater (p ≤ 0.02) in wethers sampled in P2 and P3 when compared to those sampled in P1. Among positive acute phase reactants, expression of serum α-amyloid (SAA) and haptoglobin (HPT) tended (p ≤ 0.12) to be 6- and 10-fold greater, respectively, in wethers sampled in P2 compared to wethers sampled in P1; however, SAA and HPT expression was not different between wethers sampled in P3 and P1. Plasma glucose and β-hydroxybutyric acid (BHBA) increased (p ≤ 0.03) in wethers sampled in both P2 and P3 compared to the wethers sampled in P1, while total protein and cholesterol decreased (p ≤ 0.06) only in wethers sampled from P2 compared to those sampled in P1. Hepatic acute phase responses suggest that the wethers adapted to an 80% concentrate diet over time.

Ruminal transcript abundance of the centromere-associated protein E gene may influence residual feed intake in beef steers.

A better understanding regarding the mechanisms by which the rumen processes feed may assist us in identifying animals with superior feed efficiency. Studies to evaluate the gene expression of rumen tissue have previously been performed to analyze their relationship with feed efficiency. Continuing this research is critical to determine whether the expression of the genes identified is associated with feed efficiency in additional populations of beef cattle to ensure that they are robust across breed and environment. A previous rumen-transcriptome study on Hereford×Angus steers identified 122 differentially expressed genes (PFDR <0.05) associated with residual feed intake (RFI), a measure of feed efficiency. The purpose of our study was to test the most divergent, up- and down-regulated genes in the rumen tissue of an unrelated population of Hereford×Angus steers that included two contemporary groups. A total of 13 genes were evaluated by quantitative real-time PCR. The centromere-associated protein E (CENPE) gene was expressed in lower concentrations in the rumen epithelium of steers in the more efficient (low RFI) group in both contemporary groups of animals, which was the same as the previous study. In addition, CENPE, a gene involved in chromosome alignment during mitosis, has also been associated with growth traits in cattle and pigs. There was no relationship between the expression of the other 12 genes tested with RFI in the population of steers in this study, which illustrates the importance of validating gene expression data in additional populations.

Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue.

Simple SummaryEconomics of feedlot beef production dictate that beef cattle must gain weight at their maximum potential rate; this involves getting them quickly onto a full feed of high fermentable diet which can induce the ruminal acidosis disease. The molecular host mechanisms that occur as a response to the acidosis, are mostly unknown. For answering this question, the rumen epithelial transcriptome in acidosis and control fattening steers were obtained. By RNA sequencing we found the different expression profiles of genes in normal and acidosis induced steers. Then we constructed two metabolic networks for normal and acidosis tissue based on gene expression profile. Our results suggest that rapid shifts to diets rich in fermentable carbohydrates cause an increased concentration of ruminal volatile fatty acids (VFA) and toxins and significant changes in transcriptome profiles and metabolites of rumen epithelial tissue, with negative effects on economic consequences of poor performance and animal health.The objective of this study was to develop a system-level understanding of acidosis biology. Therefore, the genes expression differences between the normal and acidosis rumen epithelial tissues were first examined using the RNA-seq data in order to understand the molecular mechanisms involved in the disease and then their corresponding metabolic networks constructed. A number of 1074 genes, 978 isoforms, 1049 transcription start sites (TSS), 998 coding DNA sequence (CDS) and 2 promoters were identified being differentially expressed in the rumen tissue between the normal and acidosis samples (p < 0.05). The functional analysis of 627 up-regulated genes revealed their involvement in ion transmembrane transport, filament organization, regulation of cell adhesion, regulation of the actin cytoskeleton, ATP binding, glucose transmembrane transporter activity, carbohydrate binding, growth factor binding and cAMP metabolic process. Additionally, 111 differentially expressed enzymes were identified between the rumen epithelial tissue of the normal and acidosis steers with 46 up-regulated and 65 down-regulated ones in the acidosis group. The pathways and reactions analyses associated with the up-regulated enzymes indicate that most of these enzymes are involved in the fatty acid metabolism, biosynthesis of amino acids, pyruvate and carbon metabolism while most of the down-regulated ones are involved in purine and pyrimidine, vitamin B6 and antibiotics metabolisms. The degree distribution of both metabolic networks follows a power-law one, hence displaying a scale-free property. The top 15 hub metabolites were determined in the acidosis metabolic network with most of them involved in the fatty acid oxidation, VFA biosynthesis, amino acid biogenesis and glutathione metabolism which plays an important role in the stress condition. The limitations of this study were low number of animals and using only epithelial tissue (ventral sac) for RNA-seq.

Transcriptomic Changes in the Rumen Epithelium of Cattle after the Induction of Acidosis.

The transition from normal forage to a highly fermentable diet to achieve rapid weight gain in the cattle industry can induce ruminal acidosis. The molecular host mechanisms that occur in acidosis are largely unknown. Therefore, the histology and transcriptome profiling of rumen epithelium was investigated in normal and acidosis animals to understand the molecular mechanisms involved in the disease. The rumen epithelial transcriptome from acidosis (n=3) and control (n=3) Holstein steers was obtained using RNA-sequencing. The mean values of clean reads were 70,975,460&amp;plusmn;984,046 and 71,142,189&amp;plusmn;834,526 in normal and acidosis samples, respectively. In total, 1,074 differentially expressed genes were identified in the two groups (P&amp;lt;0.05), of which 624 and 450 genes were up- and down-regulated in the acidosis samples, respectively. Functional analysis indicated that the majority of the up-regulated genes had a function in filament organization, positive regulation of epithelial and muscle fiber concentration, biomineral tissue development, negative regulation of fat cell differential, regulation of ion transmembrane transport, regulation of cell adhesion and butyrate, as well as short-chain fatty acid absorption that was metabolized as an energy source. Functional analysis of the down-regulated genes revealed effects in immune response, positive regulation of T-cell migration, regulation of metabolic processes, and localization. Furthermore, the results showed a differential expression of genes involved in the Map Kinase and Toll-like receptor signaling pathways. The IL1B, CXCL5, IL36A, and IL36B were significantly down-regulated in acidosis rumen tissue samples. The results suggest that rapid shifts to rich fermentable carbohydrates diets cause an increase in the concentration of ruminal volatile fatty acids, tissue damage, and significant changes in transcriptome profiles of rumen epithelial.

The bovine epimural microbiota displays compositional and structural heterogeneity across different ruminal locations

Dairy cattle are globally important agricultural animals. Central to their biology is the rumen, which houses an essential microbial community, or microbiome, important for providing nutrition from otherwise host-inaccessible dietary components. The rumen environment is noted for its substantial spatial heterogeneity, as illustrated by the stratification into ruminal solid and liquid phases. A third microbiota found directly attached to the ruminal epithelium (the epimural microbiota) also exists but is less well understood because of challenges in sampling the ruminal epithelium. As a result, our understanding of the epimural microbiota is based on analyses of cannulated animals sampled at a single location-the ventral sac-and does not account for other ruminal locations, which may have importance for overall rumen function. To address this knowledge gap, we hypothesize that the epimural microbiota at different ruminal locations differs due to known morphological, physiological, and functional differences across the geographic spread of the rumen epithelium. Here, we characterized bacterial epimural communities at different sites within 8 lactating Holstein dairy cows using 16S rRNA gene sequencing. Four different sites were sampled via rumen tissue biopsy: cranial sac (CS), ventral sac (VS), caudodorsal blind sac (CDBS), and caudoventral blind sac (CVBS). We found that locations differed in both epimural bacterial community structure and composition, with the CDBS community displaying the greatest diversity. Across all sampling sites, epimural bacterial communities were dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. Bacteria within Prevotellaceae, Butyrivibrio, Campylobacter, Mogibacterium, and Desulfobulbus all showed high relative sequence abundance and differential distributions according to sample location. There appears to be a core epimural microbiota present across all locations in all cows, although relative abundance was highly variable. The difference in relative abundance in epimural microbial communities, perhaps influenced by host physiology and the diversity within rumen contents, likely has important consequences for nutrition acquisition and general health. To the best of our knowledge, this work represents the first characterization of the ruminal epimural microbiota across different epithelial locations for any bovine ruminant.