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International Journal of Molecular... Aug 2022The weaning transition in calves is characterized by major structural changes such as an increase in the rumen capacity and surface area due to diet changes. Studies...
The weaning transition in calves is characterized by major structural changes such as an increase in the rumen capacity and surface area due to diet changes. Studies evaluating rumen development in calves are vital to identify genetic mechanisms affected by weaning. This study aimed to provide a genome-wide characterization of CTCF-binding sites and differentially CTCF-binding sites (DCBS) in rumen tissue during the weaning transition of four Holstein calves to uncover regulatory elements in rumen epithelial tissue using ChIP-seq. Our study generated 67,280 CTCF peaks for the before weaning (BW) and 39,891 for after weaning (AW). Then, 7401 DCBS were identified for the AW vs. BW comparison representing 0.15% of the cattle genome, comprising ~54% of induced DCBS and ~46% of repressed DCBS. Most of the induced and repressed DCBS were in distal intergenic regions, showing a potential role as insulators. Gene ontology enrichment revealed many shared GO terms for the induced and the repressed DCBS, mainly related to cellular migration, proliferation, growth, differentiation, cellular adhesion, digestive tract morphogenesis, and response to TGFβ. In addition, shared KEGG pathways were obtained for adherens junction and focal adhesion. Interestingly, other relevant KEGG pathways were observed for the induced DCBS like gastric acid secretion, salivary secretion, bacterial invasion of epithelial cells, apelin signaling, and mucin-type O-glycan biosynthesis. IPA analysis further revealed pathways with potential roles in rumen development during weaning, including TGFβ, Integrin-linked kinase, and Integrin signaling. When DCBS were further integrated with RNA-seq data, 36 putative target genes were identified for the repressed DCBS, including , , , , and This study successfully identified DCBS in cattle rumen tissue after weaning on a genome-wide scale and revealed several candidate target genes that may have a role in rumen development, such as , , , and . The information generated in this preliminary study provides new insights into bovine genome regulation and chromatin landscape.
Topics: Animal Feed; Animals; Binding Sites; Cattle; Diet; Genome; Rumen; Transforming Growth Factor beta; Weaning
PubMed: 36012336
DOI: 10.3390/ijms23169070 -
Journal of Animal Science Oct 2021Rumen epithelium plays an essential role in absorption, transport, and metabolism of short-chain fatty acids, the main products of rumen fermentation, and in preventing...
Rumen epithelium plays an essential role in absorption, transport, and metabolism of short-chain fatty acids, the main products of rumen fermentation, and in preventing microbes and other potentially harmful rumen contents from entering the systemic circulation. The objective of this study was to generate an immortal rumen epithelial cell line that can be used as a convenient model of rumen epithelial cells in vitro. We isolated primary rumen epithelial cells from a steer through trypsin digestion and transduced them with lentiviruses expressing the Simian Virus (SV) 40 T antigen. We cloned the transduced cells by limiting dilution. Western blotting analysis confirmed the expression of the SV40 T antigen in two single-cell clones. Cells from one clone, named bovine rumen epithelial clone 1 (BREC1), displayed a flat and squamous morphology in culture. RNA sequencing revealed that BREC1 cells expressed many markers of epithelial cells, including keratins, the epidermal growth factor receptor, and the short-chain fatty acid transporters monocarboxylic acid transporter (MCT) 1 (MCT-1) and MCT-4. RNA sequencing revealed that BREC1 cells expressed key enzymes such as 3-hydroxymethyl-3-methylglutaryl-CoA lyase and 3-hydroxy-3-methylglutaryl-CoA synthase 1 involved in ketogenesis, a unique function of rumen epithelial cells. RNA sequencing also revealed the expression of genes encoding tight junctions, desmosomes, anchoring junctions, and polarized plasma membranes, structures typical of epithelial cells, in BREC1 cells. Cell proliferation assays indicated that BREC1 cells were similar to primary rumen epithelial cells in response to insulin-like growth factor 1, insulin, and butyrate. In conclusion, BREC1 is not only a convenient but an appropriate model for studying the factors and mechanisms that control proliferation, apoptosis, differentiation, nutrient transport, metabolism, and barrier function in rumen epithelium.
Topics: Animals; Cattle; Epithelial Cells; Epithelium; Fatty Acids, Volatile; Fermentation; Rumen
PubMed: 34570883
DOI: 10.1093/jas/skab273 -
BMC Veterinary Research Nov 2023Dietary selenium (Se) sources affects the structure of the rumen microbial community and rumen fermentation. This study evaluated the effects of sodium selenite (SS) and...
Dietary selenium (Se) sources affects the structure of the rumen microbial community and rumen fermentation. This study evaluated the effects of sodium selenite (SS) and bio-nanostructured selenium (SeNSM) on rumen fermentation and structure of rumen microbial community of lactating Barki ewes. Twenty one lactating Barki ewes were assigned into three groups based on their body weight and milk yield. The experiment lasted for 50 days, whenever, the control group was fed basal diet; group SS received basal diets plus sodium selenite as inorganic source of Se; and group SeNSM received basal diet plus organic selenium bio-nanostructured. Ruminal pH and volatile Fatty Acids (VFA) was lower (P < 0.05) in SeNSM group compared to control. Principle Coordinate Analysis separated the microbial communities into three clusters based on feeding treatment. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes that were affected (P < 0.05) by Se sources. Specifically Bacteriodetes was higher (P < 0.05) in SS and SeNSM groups; and Firmicutes was higher (P < 0.05) in the control group. Moreover, the predominant bacterial genera were Prevotella, Rikenellaceae RC9 gut group, Unclassified_Bacteroidales, which were higher (P < 0.05) in SeNSM group. The methanogenic community belonged to phylum Euryarchaeota and was significantly decreased (P < 0.05) by Se supplementation. Principal component analysis based on rumen fermentation parameters, and relative abundances of bacteria and methanogens revealed three distinct clusters. These findings suggest that Se supplementation affected the relative abundances of dominant bacterial groups, declined rumen methanogens and SeNSM supplementation showed some positive impacts on some fibrolytic bacteria.
Topics: Sheep; Animals; Female; Sodium Selenite; Dietary Supplements; Selenium; Rumen; Lactation; Fermentation; Diet; Microbiota; Bacteria; Firmicutes
PubMed: 38008716
DOI: 10.1186/s12917-023-03799-7 -
Veterinary Research Nov 2023Ruminants play a vital economic role as livestock, providing high-quality protein for humans. At present, 3D-cultured ruminant abomasum and intestinal organoids have...
Ruminants play a vital economic role as livestock, providing high-quality protein for humans. At present, 3D-cultured ruminant abomasum and intestinal organoids have been successfully established to study host and pathogen interaction. The rumen is a unique digestive organ of ruminants that occupies 70% of the volume of the digestive tract and its microbiota can decompose lignocellulose to support animal growth. Here we report a method for culturing rumen epithelial organoids. We found that single rumen epithelial cells form self-organized 3D structures representative of typical stratified squamous epithelium, which is similar to rumen epithelium. EGF, Noggin, Wnt3a, IGF-1, and FGF-10 significantly enhanced the seeding efficiency of organoids. Moreover, the inclusion of CHIR-99021, A83-01, SB202190, and Y-27632 is crucial for organoid formation and maintenance. Importantly, we demonstrate that rumen epithelial cells retain their ability to form organoids after passage, cryopreservation, and resuscitation. The rumen epithelial organoids express rumen cell type-specific genes, uptake fatty acids, and generate 2D cultures. In summary, our data demonstrate that it is feasible to establish organoids from single rumen epithelial cells, which is a novel in vitro system that may reduce the use of experimental animals.
Topics: Humans; Sheep; Animals; Rumen; Epithelial Cells; Cells, Cultured; Organoids; Ruminants
PubMed: 37946298
DOI: 10.1186/s13567-023-01234-1 -
Journal of Dairy Science Aug 2022Quantifying digestive and fermentative processes within the rumen environment has been the subject of decades of research; however, our existing research methodologies... (Review)
Review
Quantifying digestive and fermentative processes within the rumen environment has been the subject of decades of research; however, our existing research methodologies preclude time-sensitive and spatially explicit investigation of this system. To better understand the temporal and spatial dynamics of the rumen environment, real-time and in situ monitoring of various chemical and physical parameters in the rumen through implantable microsensor technologies is a practical solution. Moreover, such sensors could contribute to the next generation of precision livestock farming, provided sufficient wireless data networking and computing systems are incorporated. In this review, various microsensor technologies applicable to real-time metabolic monitoring for ruminants are introduced, including the detection of parameters for rumen metabolism, such as pH, temperature, histamine concentrations, and volatile fatty acid concentrations. The working mechanisms and requirements of the sensors are summarized with respect to the selected target parameters. Lastly, future challenges and perspectives of this research field are discussed.
Topics: Animals; Farms; Fatty Acids, Volatile; Livestock; Rumen; Ruminants
PubMed: 35773034
DOI: 10.3168/jds.2021-20576 -
Animal : An International Journal of... Dec 2022Compared with maize silage- and concentrate-based diets, herbage-based diets were repeatedly shown to favourably influence the milk fatty acid (FA) profile. However, it...
Compared with maize silage- and concentrate-based diets, herbage-based diets were repeatedly shown to favourably influence the milk fatty acid (FA) profile. However, it is unclear how the herbage feeding mode (grazing vs indoor green-feeding) and conservation (fresh herbage vs hay vs silage) modify the milk FA profile. Therefore, the aim of the present experiment was to investigate the effect of different herbage utilisation methods (including herbage feeding mode and herbage conservation method) on the ruminal biohydrogenation of dietary FA and the consequences on the milk FA composition in cows of two breeds (Holstein and Montbéliarde). Concomitant effects of botanical composition and phenological stage of the herbage on milk FA profile were controlled for by harvesting barn-dried hay and silage simultaneously as first cut from the same ryegrass-dominated grassland in a semi-mountainous region. Seven weeks later, the first regrowth of the same plot was used as fresh herbage, either grazed or fed indoor (indoor green-feeding). Twenty-four Montbéliarde and 24 Holstein cows were randomly allocated to four groups of 12 cows balanced by breed, parity, and milk yield. In a free-stall barn, three groups were given ad libitum access to hay, silage, or fresh herbage, respectively. The fourth group was strip-grazing. All cows were supplemented with 3 kg DM/day of the same energy-rich concentrate. After 2 weeks of adaptation to the forage, samples of forage, concentrate, milk, blood, and rumen fluid were collected. Fatty acid composition of forages, rumen fluid, and milk was analysed by gas chromatography. Haymaking reduced total FA content of the herbage, in particular that of linoleic acid (LA) and α-linolenic acid (ALA). Still, rumen fluid lipids of hay-fed cows had the highest proportion of rumenic acid, LA, ALA, and total polyunsaturated fatty acids (PUFAs). Milk fat from hay-fed cows had the highest proportion of LA, and the apparent transfer rates from feed to milk of LA and ALA were higher in hay-fed cows than in silage-fed cows. The proportion of PUFAs was highest in milk fat from grazing and indoor green-fed Montbéliarde cows and lowest in silage-fed cows of both breeds. In conclusion, the herbage utilisation method affects the ruminal biohydrogenation of LA and ALA, whereby herbage drying particularly increases their transfer from herbage to milk.
Topics: Female; Animals; Cattle; Fatty Acids; Milk; Rumen; Lactation; Plant Breeding; Diet; Linoleic Acid; Silage; Fatty Acids, Unsaturated
PubMed: 36434984
DOI: 10.1016/j.animal.2022.100674 -
FEMS Microbiology Reviews Jul 2019The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting... (Review)
Review
The herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.
Topics: Anaerobiosis; Animal Nutritional Physiological Phenomena; Animals; Dietary Fiber; Ecosystem; Rumen; Ruminants
PubMed: 31050730
DOI: 10.1093/femsre/fuz007 -
The ISME Journal Feb 2021The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates...
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
Topics: Anaerobiosis; Animals; Cattle; Female; Fungi; Glycoside Hydrolases; Proteome; Rumen
PubMed: 32929206
DOI: 10.1038/s41396-020-00769-x -
Journal of Veterinary Internal Medicine 2023Rumen juice analysis (RJA) involves analysis of a 10mL sample within minutes after sampling. However, it can be challenging to collect 10 mL of rumen juice (RJ) from...
BACKGROUND
Rumen juice analysis (RJA) involves analysis of a 10mL sample within minutes after sampling. However, it can be challenging to collect 10 mL of rumen juice (RJ) from some ruminants, and clinical circumstances can delay RJA.
OBJECTIVES
Quantify the effect of sample volume (2, 5, 10, 50, and 100 mL), and time-to-analysis (0, 30, and 60 minutes) on RJA.
ANIMALS
Cannulated cow.
METHODS
Observational experimental study. Two liters of RJ were collected at 26 separate times. The samples were subdivided into 2 duplicates of each sample volume at each sampling time; and analyzed at 0, 30, and 60 minutes after collection. Rumen juice analysis included pH measurement, methylene blue reduction time (MBRT), and protozoal motility.
RESULTS
The pH of 2 and 5 mL samples was significantly (P = .01) higher than the pH of 50 and 100 mL samples at all time points. The MBRT was significantly lower (faster bacterial reduction) for 100 mL samples compared to all other samples at 0 minute and to 2, 5, and 50 mL samples at 30 min. The pH and MBRT at 60 minutes were significantly higher than at 0 minute for all volumes (P < .05 and P < .01, respectively). For large protozoa, small sample volumes (2 and 5 mL) had significantly lower protozoal motility (scores of 5 and 4.5, respectively) compared to 100 mL samples at 60 minutes (score of 4; P < .05).
CONCLUSIONS AND CLINICAL IMPORTANCE
Interpretation of RJA could be affected by small sample volumes and delays to analysis. Sample volumes of ≥10 mL analyzed within 30 minutes after collection are recommended.
Topics: Female; Animals; Cattle; Rumen; Bacteria
PubMed: 37026411
DOI: 10.1111/jvim.16697 -
Microbiome Oct 2022The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are...
BACKGROUND
The rumen is an ecosystem with a complex microbial microflora in which microbes initiate biofilm formation by attaching to plant surfaces for plant degradation and are capable of converting feed to nutrients and energy via microbial processes. Quorum sensing (QS) is a cell-to-cell communication mechanism that allows microbes to synchronize the expression of multiple genes in the group to perform social behaviors such as chemotaxis and biofilm formation using self-synthesized QS signaling molecules. Whereas QS has been extensively studied in model microorganisms under pure culture conditions, QS mechanisms are poorly understood in complex bacterial communities, such as the rumen microflora, in which cell-to-cell communication may be common.
RESULTS
Here, we analyzed 981 rumens bacterial and archaeal genomes from the Joint Genome Institute (JGI) and GenBank databases and identified 15 types of known QS signaling molecule-related genes. The analysis of the prevalence and abundance of genes involved in QS showed that 767 microbial genomes appeared to possess QS-related genes, including 680 bacterial genomes containing autoinducer-2 (AI-2) synthase- or receptor-encoding genes. Prevotella, Butyivibrio, Ruminococcus, Oribacterium, Selenomonas, and Treponema, known abundant bacterial genera in the rumen, possessed the greatest numbers of AI-2-related genes; these genes were highly expressed within the metatranscriptome dataset, suggesting that intra- and interspecies communication mediated by AI-2 among rumen microbes was universal in the rumen. The QS processes mediated by the dCache_1-containing AI-2 receptors (CahRs) with various functional modules may be essential for degrading plants, digesting food, and providing energy and nutrients to the host. Additionally, a universal natural network based on QS revealed how rumen microbes coordinate social behaviors via the AI-2-mediated QS system, most of which may potentially function via AI-2 binding to the extracellular sensor dCache_1 domain to activate corresponding receptors involved in different signal transduction pathways, such as methyl-accepting chemotaxis proteins, histidine kinases, serine phosphatases, c-di-GMP synthases and phosphodiesterases, and serine/threonine kinases in the rumen.
CONCLUSIONS
The exploration of AI-2-related genes, especially CahR-type AI-2 receptors, greatly increased our insight into AI-2 as a potentially "universal" signal mediating social behaviors and will help us better understand microbial communication networks and the function of QS in plant-microbe interactions in complex microecosystems. Video Abstract.
Topics: Animals; Bacteria; Bacterial Proteins; Histidine; Homoserine; Lactones; Methyl-Accepting Chemotaxis Proteins; Microbiota; Phosphoric Diester Hydrolases; Phosphoric Monoester Hydrolases; Rumen; Serine; Threonine
PubMed: 36203182
DOI: 10.1186/s40168-022-01367-z