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Bovine gut metagenome

ABSTRACT: Effects of forage type and age at which forage provision is started on bacteria associated with digesta throughout the gastro-intestinal tract of pre-weaned Holstein calves

PROVIDER: PRJNA320709 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3478800.fastq.gz	Fastqsanger.gz
	SRR3478800_1.fastq.gz	Fastqsanger.gz
	SRR3478800_2.fastq.gz	Fastqsanger.gz
	SRR3481811.fastq.gz	Fastqsanger.gz
	SRR3481811_1.fastq.gz	Fastqsanger.gz

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bovine gut metagenome

Project description:Bacteria associated with digesta throughout the gastro-intestinal tract of pre-weaned Holstein calves

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Effects of dietary forage and calf starter on ruminal pH and transcriptomic adaptation of the rumen epithelium in Holstein calves during the weaning transition

Project description:We assessed the transcriptomic adaptation of the calf rumen epithelium to changes in ruminal pH caused by feeding calf starter with and without forage during weaning transition. The calves were divided into a gorage provision group (HAY group, n = 3) and forage non-provision group (CON group, n = 4) 3 weeks after weaning.

2016-06-29 | E-GEOD-83813 | biostudies-arrayexpress

Characterisation of the whole blood mRNA transcriptome in Holstein-Friesian and Jersey calves in response to gradual weaning

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:Rumen microbiota in weaned Holstein bull calves

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Project description:Rectal microbiota in weaned Holstein bull calves

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Transcriptome anlaysis of gastrointestinal tract of pre-weaned cavles

Project description:In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.

2016-05-01 | GSE74329 | GEO

Characterisation of the whole blood mRNA transcriptome in Holstein-Friesian and Jersey calves in response to gradual weaning

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 ≥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; Q≤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.

2016-08-19 | GSE76841 | GEO

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Project description:This study aimed to investigate the effect of postbiotic from dead cell Lactobacillus ingluviei CR37 on growth performance, antioxidant capacity, and liver transcriptional response of calves. Fourteen Holstein bull calves were assigned to 2 treatment groups: CON (n = 7) or DCLI (n = 7, fed 1 g/d of dead cell Lactobacillus ingluviei CR37 strain, containing 108 CFU/g). Calves received milk replacer (MR) at 1.75% of BW (based on air-dry weight) and the amount was adjusted weekly according to body weight, while fresh and clean water was provided ad libitum. All calves had free access to starter starting on day 33. On day 82, the MR solution was reduced to 50% of the previous week's allocation, and calves were completely weaned by day 89. Liver samples were collected after slaughter on day 90. Transcriptome analysis identified 33 DEGs, including 16 upregulated DEGs such as Endothelial lipase (LIPG), Peroxisomal Acyl-CoA oxidase 1 (ACOX1), Solute carrier family 27 member 6 (SLC27A6), and 17 downregulated DEGs such as Family with sequence similarity 107 member A (FAM107A), 4-Hydroxy-2-oxoglutarate aldolase 1 (HOGA1), Farnesyl diphosphate synthase (FDPS). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 significant pathways, including the PPAR signaling pathway and Pentose phosphate pathway. Taken together, postbiotic supplementation demonstrated potential benefits in improving lipid metabolism and mitigating oxidative stress in weaning calves.

2025-04-03 | GSE293736 | GEO

bovine liver iTRAQ - Integrative hepatic metabolomics and proteomics reveal insights into the mechanism of different feed efficiency with high or low dietary forage levels in Holstein heifers

Project description:12 Holstein dairy heifers were limit-fed with high or low forage diets, and integrative hepatic metabolomics and proteomics were used to reveal insights into the mechanism of different feed efficiency behind that.

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