Ontology highlight
ABSTRACT:
PROVIDER: PRJNA781221 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We collected caecal contents from 30 chickens divided into 5 groups (6 birds per group) with each group receiving different quantity of soluble inulin and insoluble cellulose. We isolated DNA, RNA, and proteins to perform metagenomics, metatranscriptomics, and metaproteomics analysis, respectively.
2025-09-17 | PXD068444 | Pride
Project description:Cruciferous vegetables and their derived compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models. In this study, broccoli-supplemented diet induced changes in the gut microbiome and its role in host and bacterial gene expression were examined in mice following consumption of the Total Western Diet (TWD), which is based on NHANES data and represents the composition of a typical American diet. C57BL/6 male mice were fed a TWD for six weeks followed by a supplementation of 0, 0.5, 1 or 2.5% broccoli powder for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S and metagenomics sequencing, and metatranscriptomics was used to assess functionality of bacterial species. Cecum tissues were also analyzed for host transcriptomics.
2025-06-30 | GSE280358 | GEO
Project description:Cruciferous vegetables and their derived compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models. In this study, broccoli-supplemented diet induced changes in the gut microbiome and its role in host and bacterial gene expression were examined in mice following consumption of the Total Western Diet (TWD), which is based on NHANES data and represents the composition of a typical American diet. C57BL/6 male mice were fed a TWD for six weeks followed by a supplementation of 0, 0.5, 1 or 2.5% broccoli powder for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S and metagenomics sequencing, and metatranscriptomics was used to assess functionality of bacterial species. Cecum tissues were also analyzed for host transcriptomics.
2025-06-30 | GSE283608 | GEO
Project description:The epithelial cell layer that lines the fish gill controls the paracellular permeation of chemicals through tight junctions. The integrity of tight junctions can be affected by inflammation, which is likely to impact the branchial bioavailability of chemicals. In this study, we experimentally induced inflammation in the rainbow trout gill cell line RTgill-W1 via exposure to bacterial lipopolysaccharides (LPS). We then co-exposed the cells to extracts of oil sands process-affected water (OSPW), which contain a complex mixture of toxicologically relevant chemicals. Cells exposed to LPS showed a significant reduction in transepithelial electrical resistance (TEER), an indicator of tight junction integrity, after 24 h of exposure. Quantitative RT-PCR analysis determined that the abundance of transcripts of genes coding for tight junction proteins (Claudin 28b and 10e) was significantly decreased in cells exposed to 20, 50, and 100 mg L-1 LPS. Chemical analysis revealed a significant increase in permeation of constituents of OSPW across the gill cell epithelial layer at all studied LPS concentrations. These in vitro findings were confirmed in vivo in rainbow trout fingerlings exposed to both LPS and 10% OSPW for 48 h, which similarly resulted in an increase in chemical uptake relative to fish exposed to OSPW alone. This research demonstrated that inflammation of gill epithelia and the resulting disruption of tight junction integrity could lead to significantly greater uptake of potentially harmful chemicals from the environment, which has important implications for risk assessment.
2022-02-28 | GSE182953 | GEO
Project description:The thermophilic Aquificales inhabit and play important biogeochemical roles in the geothermal environments globally. Although intensive studies on physiology, microbial ecology, biochemistry, metagenomics and metatranscriptomics of the Aquificales¬ species and Aquificales-containing environmental samples have been conducted, comprehensive understandings about their ecophysiology, especially in the natural niches have been limited. In the present study, an integrated suite of metagenomic, metatranscriptomic and metaproteomic analyses, for the first time, were conducted on a filamentous microbial community from the Apron and Channel Facies (ACF) of CaCO3 (travertine) deposition at Narrow Gauge, Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD006506 | Pride
Project description:The thermophilic Aquificales inhabit and play important biogeochemical roles in the geothermal environments globally. Although intensive studies on physiology, microbial ecology, biochemistry, metagenomics and metatranscriptomics of the Aquificales¬ species and Aquificales-containing environmental samples have been conducted, comprehensive understandings about their ecophysiology, especially in the natural niches have been limited. In the present study, an integrated suite of metagenomic, metatranscriptomic and metaproteomic analyses, for the first time, were conducted on a filamentous microbial community from the Apron and Channel Facies (ACF) of CaCO3 (travertine) deposition at Narrow Gauge, Mammoth Hot Springs, Yellowstone National Park.
2020-05-26 | PXD006504 | Pride
Project description:A high-density oligonucleotide microarray that targets functional genes in marine microbial community was designed as a result of a multi-institutional effort. The design is based on nucleotide sequence data obtained with metagenomics and metatranscriptomics. The chip targets ~20000 gene sequences represented by 145 gene categories relevant to microbial metabolism in the open ocean and coastal environments. The three domains of life and also viruses are represented on the chip. Using this microarray we were able to compare the functional responses of microbial communities to iron and phosphate enrichments in samples from the North Pacific Subtropical Gyre. The response was attributed to individual lineages of microorganisms including uncharacterized strains. Transcription of 68% of the gene probes was detected from a variety of microorganisms, and the patterns of gene transcription indicated a relief from iron limitation and transition into nitrogen limitation. When combined with physicochemical descriptions of each system, the use of microarrays can help to develop a comprehensive understanding of the changes in microbially-driven processes. We analyzed three samples amended with phosphate and two sample amended with iron (III) after 48h of incubation
2013-03-07 | E-GEOD-44448 | biostudies-arrayexpress