Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097045 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28616511_1.fastq.gz | Fastqsanger.gz | |||
| SRR28616511_2.fastq.gz | Fastqsanger.gz | |||
| SRR28616512_1.fastq.gz | Fastqsanger.gz | |||
| SRR28616512_2.fastq.gz | Fastqsanger.gz | |||
| SRR28616513_1.fastq.gz | Fastqsanger.gz |
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Project description:The increasing aquaculture production volumes have caused an escalating demand for alternative protein feed ingredients. Agro-industrial by-products such as sunflower meal are relatively abundant and cheap, but the inclusion levels are limited due to the presence of antinutritional factors and fiber. Solid state fermentation is a processing method with the aim of reducing the content of fiber and antinutritional factors and improving nutritional value in plant protein raw materials. In this study, Atlantic salmon (Salmo salar) at two commercial-like fish farms were fed diets containing 5% non-fermented sunflower meal (as a control diet) and two experimental diets with 5% or 10% fermented sunflower meal. The field trial lasted for eight and 11 months in a coastal and fjord location, respectively with the aim of comparing the effect of fermented diets on growth performance, gut microbiota, distal intestine histology and gene expression of Atlantic salmon under different environmental conditions. The findings revealed that diets with fermented sunflower meal sustained growth performance, improved intestinal health by reducing the prevalence of prominent inflammation and ectopic goblet cells and promoted gut lactic acid bacteria Lactiplantibacillus and Lactobaccilaceae after long-term feeding. Our results suggest that fermented sunflower meal is suitable as a protein source for Atlantic salmon when included at a level of up to 10% in the diet.
2025-04-01 | GSE267194 | GEO
Project description:The goal of this study is to find out the exact mechanisms of action of silymarin (SM), a complex mixture of flavonolignans structures isolated from milk thistle (Silybum marianum), on the biological behavior (phenotype) of human HaCaT keratinocytes.
2022-12-21 | GSE162336 | GEO
Project description:Human breast milk contains a diverse community of bacteria but factors that produce variation in the breast milk microbiome are largely unknown. We evaluated if 1) maternal factors including breastfeeding practices modified the diversity and abundance of bacterial communities in breast milk and 2) if subclinical mastitis (SCM), an asymptomatic inflammatory condition occurring during lactation, induced a distinctive microbiota signature.
| EGAS00001003044 | EGA
Project description:Lactic acid bacteria have been used as starter strains in the production of fermented dairy products for centuries. Lactobacillus acidophilus is a widely recognized probiotic bacteria commonly added to yogurt and used in dietary supplements. In this study, a whole genome microarray was employed to monitor gene expression of L. acidophilus cells propagated in 11% skim milk (SM) during early, mid and late logarithmic phase, and stationary phase. Approximately 21% of 1,864 ORFs were differentially expressed at least in one time point. Genes differentially expressed in SM included several members of the proteolytic enzyme system. Expression of prtP (proteinase precursor) and prtM (maturase) increased over time as well as several peptidases and transport systems. Expression of Opp1 (oligopeptide transport system 1) was highest at 4h, while gene expression of Opp2 increased over time reaching its highest level at 12h, suggesting that the two systems have different specificities. Expression of a two-component regulatory system (2CRS), previously shown to regulate acid tolerance and proteolytic activity, also increased during the early log and early stationary phases of growth. Expression of the genes involved in lactose utilization increased immediately (5 min) upon exposure to milk. The acidification activity, survival under storage conditions, and adhesion to mucin and Caco-2 tissue culture cells of selected mutants containing insertionally inactivated genes differentially expressed in the wild-type strain during growth in milk were examined for any potential links between probiotic properties and bacterial growth and survival in milk. Some of the most interesting genes found to be expressed in milk were correlated with signaling (AI-2) and adherence to mucin and intestinal epithelial cells, in vitro.
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Project description:In this study we conducted a randomized, controlled, cross-over single-meal study
comparing a meal with highly fermented yogurt and cheese, and a meal with beef
and pork meatballs. Postprandial urine samples from 17 subjects were collected
sequentially after each meal up to 24 hr and analyzed by untargeted metabolomics
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Project description:The survival of probiotics could be strongly enhanced by delivery vehicles, but the mechanism was unknown. In this study, whole genome microarray technology was used to detect the gene expression profiles of probiotic Lactobacillus casei Zhang in the absence and presence of fermented milk in simulated gastrointestinal tract. The results showed the gene expression profiles were significantly different under these two different conditions. The change of the gene expression profile may be helpful to comprehend the role of delivery vehicles in enhancing the survival of probiotics. Twelve samples of bacterial cells in the absence and presence of fermented milk were collected at 3 h in simulated gastric juice, 4 h and 8 h in intestinal juice, 2 biological replicates were obtained in each time point. The average of the normalized expression values of the 2 biological replicates for each probe was regarded as the expression value of a predicted gene. To identify the expression pattern of each gene across different treatments, n-fold change ratios were calculated for every gene in pure L. casei Zhang versus L. casei Zhang in fermented milk.
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Project description:The microbial community and enzymes in fermented rice using defined microbial starter, containing Rhizopus oryzae, Saccharomycopsis fibuligera, Saccharomyces cerevisiae and Pediococcus pentosaceus, play an important role in quality of the fermented rice product and its biological activities including melanogenesis inhibitory activity. The microbial metaproteome revealed large-scale proteins expressed by the microbial community to better understand the role of microbiota in the fermented rice.
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Project description:Fermented dairy milks have been associated with many health benefits including the regulation of metabolic dysfunction. Different circulating clinical biomarkers have been used to explore the effect of fermented milks on metabolic health but the development of whole blood transcriptomics has recently been proposed as a source of novel biomarkers for this health outcome. In a randomised, cross-over study, we evaluate the changes in the whole blood transcriptome after the intake of a probiotic yoghurt compared to a milk acidified with gluconic acid in seven healthy young men. The effects of the dairy foods on whole blood gene expression were assessed at three time points during a 6 h postprandial test (800g single dose) and in the fasting state after a daily intake of the products over two-weeks (400g/d). RNA was extracted from Paxgene ® whole blood samples and sequenced on the Illumina HiSeq platform.
2018-02-28 | GSE98645 | GEO
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon. Three different soil types from the Canadian high Arctic were sampled at two depths within the active layer of soil and at two sampling dates (winter and summer conditions), for a total of 20 samples.
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