Milk Microbiome in dairy cows
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB87653 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14821300.fastq.gz | Fastqsanger.gz | |||
| ERR14821400.fastq.gz | Fastqsanger.gz | |||
| ERR14821301.fastq.gz | Fastqsanger.gz | |||
| ERR14821401.fastq.gz | Fastqsanger.gz | |||
| ERR14821302.fastq.gz | Fastqsanger.gz |
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Project description:The molecular and cellular mechanisms underlying the adaption of the mammary gland (MG) to increased ambient heat, and which account for changes in milk composition and immunity are not known yet. This study aimed to elucidate the expression of MG proteins and differences in milk composition and ruminal short-chain fatty acid concentrations of dairy cows experiencing 7 days of heat stress (28°C, THI = 76), pair-feeding (PF) or ad libitum feeding (CON) at thermoneutrality (16°C, THI = 60; each n=10). The feed intake of PF cows were matched to the intake of HS cows. The portion of ruminal acetate, the acetate:propionate ratio, and milk urea concentration were greater whereas milk protein yield and lactose yield were lower in HS than CON cows on day 3 and 6 of the challenge, whilst energy and fat corrected milk were lower in HS than CON and PF cows. The proteome analysis revealed induced bacterial invasion of epithelial cells, leukocyte transendothelial migration, reduction of the pyruvate and carbon metabolism, and platelet activation in the MG of HS compared to CON and/or PF cows. These results highlight adaptive metabolic and immune responses to mitigate the negative effects of ambient heat in the mammary gland.
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Project description:Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks. Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis. Comparison between three weekly means (n=4 for each week, 12 arrays in total)
2009-08-28 | E-GEOD-17849 | biostudies-arrayexpress
Project description:Four mature, non-lactating dairy cattle were transitioned from a high forage diet (HF; 0% grain) to a high grain diet (HG; 65% grain) that was fed for three weeks. Rumen papillae biopsies were performed during the HF baseline (week 0) and after the first (week 1) and third week (week 3) of the grain challenge to create a transcript profile for the the short and long-term adaption of the rumen epithelium during ruminal acidosis.
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Project description:Ruminal microbiota in dairy cows Raw sequence reads
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Project description:Peripheral blood mononuclear cells (PBMC) from cows with experimentally induced hypocalcaemia or spontaneous milk fever were subject of an oligo-microarray analysis following quantitative real-time reverse transcription PCR (q-PCR). In experimental hypocalcaemia induced by 10 % Na2EDTA infusion (n = 4), the microarray revealed that 32 genes were significantly up- or down-regulated compared to control treatment by 11 % CaEDTA infusion (n = 4). In milk fever cases (n = 8), the microarray demonstrated that 98 genes were expressed differentially higher or lower compared to healthy parturient cows (n = 5). From both data, five genes were selected to be strongly related to both experimental hypocalcaemia and milk fever. Additionally, another gene was judged to be specific for milk fever independent of hypocalcaemia. The mRNA expressions of these six genes in milk fever cases were verified by q-PCR, which were significantly higher or lower than those in healthy parturient cows. In the experimental hypocalcemia study, four healthy nonpregnant, non-lactating ovariectomised Holstein cows were used. The experiment was performed according to a 2 M-CM-^W 2 crossover design with 2 weeks intervals. Cows were infused with either Na2EDTA (hypocalcaemic treatment) or CaEDTA (control treatment) solution during a period of 4 h. The animals were monitored for clinical signs of hypocalcaemia (dry nose, staggering, astasia, reduced ruminal activity, increased heart rate, increased respiratory frequency, sweating, and ear cold). Infusion of EDTA solution was temporarily suspended when hypocalcaemia induced astasia was represent. If affected cow stood again, EDTA infusion was resumed. PBMC samples were collected before the start of infusion (0 h; pre-treatment) and at 4 and 24 h after the start of infusion 24h and utilized for gene expression analysis of PBMC. In the spontaneous milk fever study, a total of 13 Holstein dairy cows, which were 8 parturient cows diagnosed with milk fever within 2 days postpartum and 5 clinically healthy parturient cows within 2 days after parturition (Group H), were used. All spontaneous milk fever cases showed hypocalcaemia (< 1.8 mmol/l) in the blood samples obtained before the first treatment, and were treated by an intravenous infusion of a 20 % Ca borogluconate solution (500 ml). The milk fever cases were divided into two categories according to the reponse of the cows to the first Ca treatment: an immediate response in which the cow could stand within 1 day after a single Ca treatment (Group A, n = 4) and a requirement further treatment over 1 day after a single Ca treatment (Group B, n = 4). PBMC samples were collected vein just before the first Ca treatment in groups A and B and within 2 days postpartum in group H and utilized for gene expression analysis of PBMC.
2013-06-16 | E-GEOD-46901 | biostudies-arrayexpress
Project description:The study investigated the acute and simultaneous response of the mammary and liver transcriptome to an intra-mammary lipopolysaccharide (LPS) challenge in early-lactating cows, and its consequences on metabolic biomarkers and liver composition. At 7 days of lactation, 7 cows served as controls (CTR) and 7 cows (LPS) received an intra-mammary E. coli LPS challenge. The mammary and liver tissues were sampled at 2.5 h from challenge for transcriptomic profiling. Liver composition was evaluated at 2.5 h and 7 d after challenge and blood biomarkers were analized at -2, 3, 7 and 14 d from challenge. In mammary tissue, the LPS challenge resulted in 189 differentially expressed gene (DEG), with 20 downregulated and 169 upregulated, while in the liver were found 107 DEG with 42 downregulated and 65 upregulated in LPS vs CTR. In the udder, the Dynamic Impact Approach (DIA) highlighted the activation of NOD-like receptor signaling, Toll-like receptor signaling, RIG-I-like receptor signaling and Apoptosis pathways, while in the liver were inhibited the Fatty acid elongation in mitochondria and activated the p53 signaling pathway. The LPS induced the alteration of liver lipid metabolism (rise of total lipid and triglyceride concentration), a systemic inflammation (rise of blood ceruloplasmin and bilirubin) and an increase of body fat mobilization. In cows subjected to intra-mammary LPS, the mammary gland responds activating mechanisms of pathogen recognition. In the liver the response likely depends by mediators coming from udder and affects the liver functionality and mainly the fatty acid metabolism.
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Project description:Mastitis remains one of the most prevalent and costly diseases impacting the dairy industry worldwide. Escherichia coli is an environmental bacterium that frequently causes intramammary infections, the outcome of which depends on the capacity of the host to recognize and clear the bacterial pathogen. E. coli intramammary infection elicits localized and systemic responses, some of which have been characterized in mammary secretory tissue. However, nothing is known about early transcriptome-wide responses to infection that occur within regions of the teat and mammary parenchyma. Therefore, the objective of the current study was to use microarray analysis to characterize gene expression patterns and process networks that become activated in different regions of the mammary gland during the acute phase of experimentally induced intramammary infection with E. coli. Tissues evaluated were from Furstenberg’s rosette, teat cistern, gland cistern, and lobulo-alveolar regions of control and infected mammary glands, 12 and 24 h after bacterial (or control) infusions. For selected genes, quantitative RT-PCR was performed to confirm the microarray findings (Toll-like receptors; TLR1, TLR2, TLR4, TLR6) and evaluate the correspondence between mRNA level in tissues and protein level in milk (interleukin 8, tumor necrosis factor-alpha, haptoglobin, lipopolysaccharide-binding protein). The main networks activated by E. coli infection pertained to immune and inflammatory response, with marked induction of genes encoding proteins that function in chemotaxis, leukocyte activation and signaling. Genomic response was greatest in tissues of the teat and gland cisterns at 12 h post-infection, while tissue of the lobulo-alveolar region responded only, and most strongly of the regions, 24 h following the infection. Up regulation of TLR2, TLR4, IL8, TNF-alpha and bactericidal/permeability-increasing protein peaked at 12 h post infection in tissues of the teat and in the gland cistern, while the highest level of lipopolysaccharide-binding protein was reached at 24 h in the lobular alveoli region of infected quarters. Very few genes were down–regulated within the timeframe of this study. Similar genetic networks were impacted in all regions during early phases of E. coli intramammary infection, although regional differences throughout the gland were noted. Importantly, the tissues of the teat, which are first to encounter invading bacteria during a natural infection, responded rapidly and intensely, suggesting an important sentinel function for this region. Both resident mammary cells and infiltrating immune cells likely play an important role in recognition of pathogens and production of inflammatory mediators during mastitis. Three healthy lactating Holstein cows were used in this study. All mammary glands were bacteria-free. Immediately following the morning milking, 4 mL of E. coli suspension (100 colony forming units/mL) were infused into one mammary gland of the udder and the contralateral gland was infused with PBS (control gland). After the PM milking 12 h later, the remaining ipsilateral quarter was infused with E. coli. Cows were euthanized 24 h after initial infusions and tissues were collected from 4 regions of each mammary gland: Furstenburg’s rosette, teat cistern, gland cistern and lobuloalveolar regions. Tissues were snap frozen in liquid nitrogen, stored at -80C until processing.
2009-08-18 | E-GEOD-15441 | biostudies-arrayexpress