Chicken gut microbiota samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1034760 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Differentially expressed proteins in the liver and ovary of two different breeds of chickens were characterized to investigate the reasons for the differences in laying performance between local breeds and commercial laying hens in the later laying period.
2023-09-05 | PXD045098 |
Project description:The intestinal mucosa is the main organ that exerts nutrient absorption, which will further influence laying performance and egg nutrition in hens. Previously, we have screened out three strains of Lactobacillus (L. sa., L. ag. and L. av.) from a native chicken breed in China. However, the optimal regulation of Lactobacillus combination on poultry products needs to be verified. In this study, a total of 120 HyLine hens (n = 30) at the period of laying peak were randomly divided into four groups: (1) control, (2) L. sa. + L. ag., (3) L. sa. + L. av. and (4) L. ag. + L. av. groups, which were fed with corresponding Lactobacillus (10e8 CFUs/hen/day) for 30 consecutive days. Compared with the control group, feeding of L. sa. + L. ag. could improve the laying rate, egg weight, especially for higher amino acids level in albumen. The mechanism study showed that, in the intestine lumen, feeding of L. sa. + L.ag. could up-regulate the Lactobacillus abundance and down-regulate the Escherichia coli abundance. Meanwhile, the tryptophan metabolism pathway was up-regulated, the primary bile acid biosynthesis pathway was down-regulated. In the crypt, up-regulated genes involved the oxidative phosphorylation pathway and the ROS level were appeared in L. sa. + L.ag. feeding group. Our study further proved that the amount of Paneth cells and the mRNA abundance of Wnt3a and Dll1 in the crypt were up-regulated upon L. sa. + L. ag. feeding. Correspondingly, the mRNA abundance of Lgr5, CCND1 and CDK2 in the crypt were enhanced upon L. sa. + L. ag. feeding. In conclusion, co-feeding of L. sa. and L. ag. in hens could improve the gut microflora and altered the microflora metabolism profile in the intestine. Further, promote the crypt’s local energy metabolism and enhancing ROS level in the crypt, thereby enhance the activity of Paneth cell and regulate the activity of ISCs. Ultimately, the intestinal mucosal renewal and the laying performance were improved.
2021-12-31 | GSE176247 | GEO
Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients that are linked to a wide set of biological processes. In laying hens there is still uncertainty about the optimal Ca/P ratio in feed and further strategies for the reliable mineral restriction in poultry diets are required. The dataset is based on Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens sampled at peak performance. The experimental design comprises four dietary groups differed in Ca (recommended vs. 15 % reduction) and mineral P (adequate vs. 20 % reduction) levels; 1) control diet (Con; Ca=34.4g/kg, P=5.3 g/kg and Ca/P ratio=7.45), 2) Low Ca and P diet (LCaP), 3) low Ca diet (LCa), and low P diet (LP). Jejunal transcriptome profiles were assessed by mRNA sequencing in a total of 80 animals (10 hens per experimental group for each laying line) at sampling age of 31 weeks) to approximate the consequences of variable Ca and P supply.
2021-06-14 | E-MTAB-9109 | biostudies-arrayexpress
Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide variety of tissues has been discovered. The aim of this study are to perform uterine transcriptome profiling (RNA-seq) to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Uterine mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least two-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 32 million reads from layers and 28 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 616 were differentially expressed between layer and non-layer hens. 229 DEGs were significantly up-regulated and 286 were significantly down-regulated in the laying hens when compared to the non-laying hens. Twelve candiate genes, linked to calcium remodeling, were identified by gene function analysis and validated using qPCR. MEPE, CALCB, OTOP2, STC2 and ATP2C2 were confirmed to be highly expressed in laying hens as compared to molting and non-laying hens. RNA-seq and qPCR data for relative gene expression were highly correlated (R2 =0.99). Conclusions: Our study reports the expression of four novel genes that are speculated to transport calcium ions across the uterine epithellium for eggshell mineralization. These genes can be used as quantitative basis of selecting hens with an improved eggshell quality.
2018-12-06 | GSE114103 | GEO
Project description:Purpose: With the advent of Next-generation sequencing (NGS), several novel genes/proteins and cellular pathways in wide varitey of tissues has discovered. The aim of this study are to perform transcriptome profiling (RNA-seq) of magnum to determine differently expressed genes in laying and non-laying hens and to further validate the expression of candidate genes using real-time quantitative reverse transcription polymerase chain reaction (qRT–PCR) in laying, non-laying and molting hens. Methods: Magnum mRNA profiles of 35-60 weeks-old laying and non-laying hens, three each, were generated with NextSeq 500 sequencer in single-end mode with a read length of 1x76 bp. Raw sequencing reads were cleaned and trimmmed with Prinseq tool and good reads were aligned against the chicken reference gemone (Galgal 5.0) in Array Studio. Differential gene expression analysis was performed by the DESeq2 algorithm as implemented in Array Studio. The genes with at least three-fold change (FC) and Benjamini and Hochberg q-value < 0.05 were called differentially expressed. Results: Using an optimized data analysis workflow, we mapped about 30.5 million reads from layers and 33.4 million reads from non-layers to the chicken genome. A total of 19,152 gene transcripts were annotated from Ensembl alignment which represents 50.24% of the chicken genome assembly. Differential gene expression analysis showed 540 were differentially expressed between layer and non-layer hens. 152 DEGs were significantly up-regulated and 388 were significantly down-regulated in the laying hens when compared to the non-laying hens. Conclusions: Our study reports the expression of several pre-discovered and many novel genes that may be involved in the transport of precurosor molecules for biosynthesis and secretion of the egg-white proteins in the magnum. These genes can be used as quantitative basis of selecting hens with an improved egg quality.
2021-03-22 | GSE123588 | GEO
Project description:Broiler breeder hens given ad libitum access to feed have excessive ovarian follicle development with poor reproductive outcome. One strategy to improve their reproductive capacity is by restricting their feed intake. In this study, we sequenced the liver transcriptomes of hens fed ad libitum (FF, n=3) and hens given a restricted fed diet (RF, n=3) to get insight into possible signaling pathways affected by dietary treatment. Hens were reared according to commercial guidelines until 38 weeks of age, when they were assigned to either FF or continued on RF for 6 weeks. Liver mRNA samples from three hens in each group were sequenced using the Illumina HiSeq 2000/2500 technology at a depth of 100 bp. The sequencing quality of the data was determined using FastQC. Reads were aligned to UCSC Galgal4 using Tophat (v2.0.13) and transcripts were counted using cuffdiff (v.2.2.1). A multidimensional scaling plot (MDS plot) was generated to evaluate the variance among biological replicates and identified one FF hen as a sample outlier and this animal was removed from the analysis. Differential gene expression analysis was conducted using edgeR and yielded 120 differentially expressed genes. This study identified transcriptional differences in the livers of FF and RF hens which may signal metabolic status to the ovary.
2022-02-03 | GSE175780 | GEO
Project description:Precision Glycan Supplementation Improves Gut Microbiota Diversity, Performance, and Disease Outbreak Resistance in Broiler Chickens
| PRJNA1054663 | ENA
Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ⤠0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ⥠2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ⤠0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ⤠0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver. The liver expression profile of juvenile hens and laying hens were generated by RNA-seq.
2016-01-08 | E-GEOD-70010 | biostudies-arrayexpress
Project description:The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. The study was performed using two complementary approaches: a descriptive study of standard laying hens and then a differential study performed with hens from experimental lines expressing broad variations of achieved fertility (approximately 20 per cent). A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance. Keywords: oocyte competence, fertility
2008-03-01 | GSE10231 | GEO
Project description:In this study, RNA-Seq technology was adopted to investigate the differences in expression profiles of the hepatic lipid metabolism-related genes and the associated pathways between juvenile and laying hens. RNA-Seq analysis was carried out to estimate total RNA harvested from the liver of juvenile hens (n = 3) and laying hens (n = 3). Compared with juvenile hens, 2574 differentially expressed (DE) genes (1487 down and 1087 up) with P ≤ 0.05 were obtained, and 955 of these genes were significantly DE (SDE) at a false discovery rate (FDR) of 0.05 and fold-change ≥ 2 in laying hens. There were 198 SDE novel genes (107 down-regulated and 91 up-regulated) (FDR ≤ 0.05) that were obtained from the transcriptome, and most of them were highly expressed. Moreover, 332 SDE isoforms were identified. Gene Ontology (GO) enrichment and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that SDE genes were significantly associated with steroid biosynthesis, PPAR signaling pathway, biosynthesis of unsaturated fatty acids, glycerophospholipid metabolism, three amino acid pathways, and pyruvate metabolism (P ≤ 0.05). The top significantly enriched GO terms included lipid biosynthesis, cholesterol and sterol metabolic, and oxidation reduction suggesting the principal lipogenesis in the liver of laying hens. This study suggests that the major changes at the level of transcriptome in laying hen liver are closely related to fat metabolism. Some highly differentially expressed uncharacterized novel genes and alternative splicing isoforms detected might also take part in lipid metabolism, though it needs investigation. Therefore, this study provides valuable information of mRNA of chicken liver, and deeper functional investigations on the mRNAs could help explore or provide new insights into molecular networks of lipid metabolism in chicken liver.
2016-01-08 | GSE70010 | GEO