Milk Replacer - Calf microbiota study
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33625 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3477400_1.fastq.gz | Fastqsanger.gz | |||
| ERR3477400_2.fastq.gz | Fastqsanger.gz | |||
| ERR3477410_1.fastq.gz | Fastqsanger.gz | |||
| ERR3477410_2.fastq.gz | Fastqsanger.gz | |||
| ERR3477420_1.fastq.gz | Fastqsanger.gz |
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2022-12-11 | E-MTAB-11581 | biostudies-arrayexpress
Project description:Feed restriction during the early life of ewe lambs (F0) triggers the transfer of epigenetic marks to the next generation, thus impairing the reproductive performance of F1. However, the effects of this factor on milk production and composition, including its abundance in regulatory miRNA (many of which are contained in exosomes, small vesicles of endocytic origin that play a role in the modulation of immune response of the offspring), has not been tested so far. Therefore, in this study, the replacement ewe lambs (F0) obtained in a previous project (a group of ewes fed milk replacer ad libitum –ADL– vs. a group of ewes restricted –RES– to 62.5% the intake level of milk replacer during the suckling period) were raised under similar post-weaning conditions and mated to obtain the progeny (F1). The F1 dairy ewes were also mated, and six of these F1 dairy ewes were selected and divided into two groups: the F1-ADL group (n=3) born from F0-ADL and the F1-RES group (n=3), born from F0-RES animals. Milk production was controlled during the peak lactation period, and milk samples were obtained for each gland separately to measure chemical composition, somatic cell counts, and bacteriology. Exosomes were also isolated for each gland separately to define the miRNA content. The miRNAome was determined following a Next Generation Sequencing approach. The first preliminary results indicate significant differences in the abundance of five miRNAs in the milk obtained during the peak of lactation. Thus, oar-miR-150, oar-miR-221, oar-miR-23a, oar-miR-27a, oar-miR-376c were all down modulated in F1-RES when compared to F0-ADL. Most of these miRNAs have been found to play a role in biological functions such as development, apoptosis, muscle differentiation, reproduction, or milk production. Moreover, somatic cell count (SCC) was reduced significantly in milk samples during the peak of lactation of F1-RES dairy sheep. No significant differences were found in milk production, the chemical composition of milk (fat, protein, lactase), or bacteriology (colony forming units, CFU). This study's results provide some evidence of the effects of nutritional programming events on the milk's bioactive components.
2024-11-19 | GSE266266 | GEO
Project description:The objectives of the study were to use RNA-Seq to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1) and 8 days after weaning (d 8). RNA-seq analysis was carried out on RNA extracted from whole blood. Gradual weaning had no effect on gene expression (P>0.05).There were 550 differentially expressed genes at a false discovery rate of 10% and with a â¥1.5-fold change, between Holstein-Friesian and Jersey calves on d -14, 490 on d 1, and 411 on d 8. GOseq/KEGG pathway analysis showed that the cytokine-cytokine receptor interaction pathway and the neuroactive ligand-receptor interaction pathway were over-represented between breeds on all days (P<0.01; Qâ¤0.1). These results demonstrate that the gradual weaning practiced here does not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of expression changes in any genes in response to gradual weaning. These data also suggest differences in cell signalling and immune responses between breeds. Eight Holstein-Friesian and eight Jersey bull calves were group housed indoors and individually fed milk replacer and concentrate using an automatic feeder. Calves were gradually weaned by reducing milk-replacer from 6 litres to 0 litres over 14 days (d) (d -13 to d 0). Calves were blood sampled on d -14, 1, and 8, relative to weaning (d 0). RNA-seq analysis was carried out on RNA extracted from whole blood.
2016-08-19 | E-GEOD-76841 | biostudies-arrayexpress
Project description:We show here the transcriptional response in the distal small intestine of piglets fed either normal milk replacer, or milk replacer with added starch.
2020-04-07 | GSE148110 | GEO
Project description:To investigate the molecular bases of diet induced differences in milk composition, we collected milk from mid lactation dairy ewes and after 3 weeks of diet supplementation with extruded linseed. RNAs were isolated from milk somatic cells isolated from milk of 3 sheep and Illumina RNA sequencing was performed to analyze RNA synthesis in these cells.
2017-02-08 | GSE89163 | GEO
Project description:In dairy cows, milk production and composition are affected by numerous factors, including diet. Milk is the body fluid with the highest RNA concentration, including numerous microRNA. These microRNA presence in the different milk compartments is still poorly documented and the effect of feed restriction on milk miRNome has not been described yet. The aim of this study was to describe the effects of feed restrictions of different intensitizes on milk compartment miRNome composition. Two feed restriction trials were performed on lactating dairy cows, one of high intensity and one of moderate intensity. 2 896 mature microRNA were identified in milk, including 1 493 that were already known in bovine specie. Among the 1 095 miRNA that were abundant enough to be informative, 10% were exclusive to one milk compartment and the abundance of 155 varied between compartments, revealing a specific miRNome for each milk fraction. Feed restriction affected differently these miRNome, with microRNA in whole milk and milk extracellular vesicles being the most affected and microRNA in fat globules and exfoliated mammary epithelial cells being relatively or completely unaffected. Target prediction of known microRNA that varied under feed restriction reflected modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle and stress responses. These findings open up opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows.
2023-05-31 | GSE207759 | GEO
Project description:Assessing Faecalibacterium prausnitzii as a Psychobiotic in Pre-weaning Dairy Calves
| PRJNA1085263 | ENA
Project description:Background: To reduce costs of rearing replacement heifers, researchers have focused on decreasing age at breeding and first calving, and to increase returns upon initiation of lactation the focus has been on increasing mammary development prior to onset of first lactation. Enhanced plane of nutrition pre-weaning may benefit the entire replacement heifer operation by promoting mammary gland development and greater future production. Methods: Twelve Holstein heifer calves (<1 wk old) were reared on 1 of 2 dietary treatments (n = 6/group) for 8 wk: a control group fed a restricted milk replacer at 0.45 kg/d (R, 20% crude protein, 20% fat), or an accelerated group fed an enhanced milk replacer at 1.13 kg/d (EH, 28% crude protein, 25% fat). At weaning (8 wk), calves were euthanized and sub-samples of mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested upon removal from the body. Total RNA from both tissues was extracted and sequenced using the Illumina HiSeq2500 platform. The Dynamic Impact Approach (DIA) and Ingenuity Pathway Analysis (IPA) were used for pathway analysis and functions, gene networks, and cross-talk analyses of the two tissues. Results: When comparing EH vs R 1,561 genes (↑895, and ↓666) and 970 genes (↑506, and ↓464) were found differentially expressed in PAR and MFP, respectively. DIA and IPA results highlight a greater proliferation and differentiation activity in both PAR and MFP, supported by an increased metabolic activity. When calves were fed EH, the PAR displayed transcriptional signs of greater overall organ development, with higher ductal growth and branching, together with a supportive blood vessel and nerve network. These activities were mediated by intracellular cascades, such as AKT, SHH, MAPKs, and Wnt, probably activated by hormones, growth factors, and endogenous molecules. The analysis also revealed strong communication between MFP and PAR, with the first enhancing the development of PAR through secreted growth factors and the recruitment of immune cells. Conclusion: The transcriptomics and bioinformatics approach highlighted the mechanisms that mediate the mammary gland response to a higher plane of nutrition in the pre-weaning period.
2018-05-01 | GSE102435 | GEO
Project description:The aim of the present study was to correlate lipid metabolism genes in the mammary gland tissue affected by stage of lactation and nutrition to the resulting milk fatty acids composition in grazing dairy cows, and to classify milk fatty acid (FA) groups based on variations in lipid metabolism gene expression patterns. Identifying the relationship between lipid metabolism genes in the mammary gland tissue and the resulting milk fatty acid composition is expected to greatly contribute to our understanding of milk fatty acid metabolism and to enhance opportunities to improve milk fat composition through nutrition. In fact, SNCA, SCD5, and PNPLA2 lipid metabolism-related genes affected by unsaturated fatty acids supplementation, were found to strongly correlated to different milk FA groups, but also contributed most to the classification of these FA groups, suggesting a significant role in mediating the lipid metabolism in the mammary gland tissue and determining the milk fatty acids composition. A total of 28 Holstein-Friesian dairy cows in mid-lactation were blocked according to parity (2.4 ± 0.63 years), days in milk (DIM; 153 ± 32.8 days), milk yield (25.7 ± 3.08 kg/d) and fat content (4.3 ± 0.12%). Cows were then randomly assigned to four UFA-sources based on rapeseed, soybean, linseed or a mixture of the three oils for 23 days (Period I) after which, all 28 cows were switched to a control diet for an additional 28 days (Period II). On the last day of both periods, mammary gland biopsies were taken to study genome-wide differences in lipid metabolism gene expression.
2011-01-01 | E-GEOD-20908 | biostudies-arrayexpress
Project description:The aim of the present study was to correlate lipid metabolism genes in the mammary gland tissue affected by stage of lactation and nutrition to the resulting milk fatty acids composition in grazing dairy cows, and to classify milk fatty acid (FA) groups based on variations in lipid metabolism gene expression patterns. Identifying the relationship between lipid metabolism genes in the mammary gland tissue and the resulting milk fatty acid composition is expected to greatly contribute to our understanding of milk fatty acid metabolism and to enhance opportunities to improve milk fat composition through nutrition. In fact, SNCA, SCD5, and PNPLA2 lipid metabolism-related genes affected by unsaturated fatty acids supplementation, were found to strongly correlated to different milk FA groups, but also contributed most to the classification of these FA groups, suggesting a significant role in mediating the lipid metabolism in the mammary gland tissue and determining the milk fatty acids composition.
2011-01-01 | GSE20908 | GEO