Pig gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA474940 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7275040.fastq.gz | Fastqsanger.gz | |||
| SRR7275050.fastq.gz | Fastqsanger.gz | |||
| SRR7275041.fastq.gz | Fastqsanger.gz | |||
| SRR7275051.fastq.gz | Fastqsanger.gz | |||
| SRR7275042.fastq.gz | Fastqsanger.gz |
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Project description:The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR.
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Project description:This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function, the immune system and systemic physiology. We used casein (CAS), partially delactosed whey powder (DWP), spray dried porcine plasma (SDPP), soybean meal (SBM), wheat gluten meal (WGM) and yellow meal worm (YMW) as protein sources. We investigated the effects of feeding mice during a period of four weeks on semi-synthetic diets containing 30% of six different protein sources. Microarrays were used to detail the global gene expression in the ileal mucosae of mice. Male C57BL/6J mice were stratified according to bodyweight and litter of origin into six dietary treatment groups. These mice were fed for four weeks with semi-synthetic diets containing one of the following protein sources. At the end of four weeks, mice were sacrificed by euthenesia and ileal tissue samples (scrapings) were collected for RNA extraction and hybridization on Affymetrix microarrays. Soybean meal (SBM) diet group served as reference to make comparisons with other experimental diets.
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Project description:Variations in the estimation of basal endogenous losses (BEL) of amino acids in the ileum, as determined by different methods could affect the accuracy of estimating the nutritional value of dietary ingridients. This study used a quantitative proteomic approach to identify variations in BEL in the ileal digesta of growing pigs fed a nitrogen free diet (NFD) or a casein diet (CAS)
2025-06-09 | PXD052560 | Pride
Project description:The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR. Experiment Overall Design: Animals were reared on the sow at an outdoor or indoor facility. Additional piglets from the indoor facility were transferred to individual isolator units at 24 hours of age, and given a daily dose of antibiotic cocktail for the duration of the study. Piglets were weaned at day 28. From day 29 onwards, piglets were fed creep feed ad libitum. Ileal tissue samples were excised from N=6 piglets per group at day 5, 28 and 56.
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Project description:Pig ileal and cecal digesta raw sequence reads
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Project description:An experiment was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 days of age on immune competence related parameters and performance of broiler. A total number of 960 one-day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to one of three experimental diets including graded levels, 0%, 5%, and 10% of rye. Tested immune competence related parameters were composition of the intestinal microbiota, genes expression in gut tissue, and gut morphology. The inclusion of 5% or 10% rye in the diet (d14-28) resulted in decreased performance and litter quality, but in increased villus height and crypt depth in the small intestine (jejunum) of the broilers. Relative bursa and spleen weights were not affected by dietary inclusion of rye. In the jejunum, no effects on number and size of goblet cells, and only trends on microbiota composition in the digesta were observed. Dietary inclusion of rye affected expression of genes involved in cell cycle processes of the jejunal enterocyte cells, thereby influencing cell growth, cell differentiation and cell survival, which in turn were consistent with the observed differences in the morphology of the gut wall. In addition, providing rye-rich diets to broilers affected the complement and coagulation pathways, which are parts of the innate immune system. These pathways are involved in eradicating invasive pathogens. Overall, it can be concluded that inclusion of 5% or 10% rye to the grower diet of broilers had limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue, however, were affected by dietary rye inclusion level, indicating that rye supplementation to broiler diets might affect immune competence of the birds.
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Project description:<p>Dietary glycerol supplementation in aquaculture feed is seen as an alternative and inexpensive way to fuel fish metabolism, attenuate metabolic utilization of dietary proteins and, subsequently reduce nitrogen excretion. In this study, we evaluated the impact of dietary glycerol supplementation has on nitrogen excretion of European seabass (Dicentrarchus labrax) and its effects on metabolite profile and bacterial community composition of gut digesta. These effects were evaluated in a 60-day trial with fish fed diets supplemented with 0, 2.5 or 5% (w/w) refined glycerol. Nuclear magnetic resonance spectroscopy and high-throughput 16S rRNA sequencing characterized the effects of glycerol supplementation of digesta metabolite and bacterial community composition of 6h postprandial fish. Our results showed ammonia excretion was not altered by dietary glycerol supplementation and the highest glycerol dosage was associated with significant increases in amino acids and a significant decrease of ergogenic creatine in digesta metabolome. Concomitantly, significant decreases in putative amino acid degradation pathways were detected in the predicted metagenome analysis, suggesting a metabolic shift. Taxon-specific analysis revealed significant increases in abundance of some specific genera (e.g. Burkholderia and Vibrio) and bacterial diversity. Overall, our results indicate glycerol supplementation may decrease amino acid catabolism without adversely affecting fish gut bacterial communities.</p>
2020-07-30 | MTBLS870 | MetaboLights