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Dataset results
319 results for “Intestinal microbiota”
Microbiota-driven epigenetic alterations in intestinal epithelial cells [ChIP-seq]
GEO Series GSE128369. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The Effects of Bacillus licheniformis-fermented Products on Chronic Feline Diarrhea and Intestinal Microbiota
GEO Series GSE203254. Bacteria. 24 samples. Type: Other.
Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice [BeadArray]
GEO Series GSE47734. Mus musculus. 6 samples. Type: Expression profiling by array.
The intestinal microbiota regulate neuronal function and fear extinction learning
GEO Series GSE135326. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Comparing the microbiota composition of stool, intestinal biopsy and saliva between patients with Adenoma and Adenocarcinoma
GEO Series GSE217490. Homo sapiens. 148 samples. Type: Other.
Microbiota-derived pentanoate promotes differentiation of regulatory T cells via enhancing iron uptake in the intestine [FeSO4_treated_Treg]
GEO Series GSE195602. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Histone butyrylation in the mouse intestine is mediated by the microbiota and associated with regulation of gene expression
GEO Series GSE216319. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors
GEO Series GSE140703. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
TGF-beta-independent function of SMAD4 preconditions naïve CD8 T-cells to prevent severe microbiota-driven chronic intestinal inflammation [RNAseq]
GEO Series GSE188933. Mus musculus. 14 samples. Type: Expression profiling by high throughput sequencing.
Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection
GEO Series GSE262811. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing.
Data from: Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli
The intestinal microbiota is vital for shaping the local intestinal environment as well as host immunity and metabolism. At the same time, epidemiological and experimental evidence suggest an important role for parasitic worm infections in maintaining the inflammatory and regulatory balance of the immune system. In line with this, the prevalence of persistent worm infections is inversely correlated with the incidence of immune-associated diseases, prompting the use of controlled parasite infections for therapeutic purposes. Despite this, the impact of parasite infection on the intestinal microbiota, as well as potential downstream effects on the immune system, remain largely unknown. We have assessed the influence of chronic infection with the large-intestinal nematode Trichuris muris, a close relative of the human pathogen Trichuris trichiura, on the composition of the murine intestinal microbiota by 16S ribosomal-RNA gene-based sequencing. Our results demonstrate that persistent T. muris infection dramatically affects the large-intestinal microbiota, most notably with a drop in the diversity of bacterial communities, as well as a marked increase in the relative abundance of the Lactobacillus genus. In parallel, chronic T. muris infection resulted in a significant shift in the balance between regulatory and inflammatory T cells in the intestinal adaptive immune system, in favour of inflammatory cells. Together, these data demonstrate that chronic parasite infection strongly influences the intestinal microbiota and the adaptive immune system. Our results illustrate the complex interactions between these factors in the intestinal tract, and contribute to furthering the understanding of this interplay, which is of crucial importance considering that 500 million people globally are suffering from these infections and their potential use for therapeutic purposes.
A catalog of genes, genomes and species of the cat (Felis catus) intestinal microbiota
<p></p><h1>Data sources</h1><br>This dataset was constructed using two different bioprojects:<br>PRJNA758898 from Ma et al. 2022. 16 samples from 16 animals.<br>PRJEB9357 from Deusch et al. 2015. 88 samples from 30 animals.<br>PRJEB4391 from Deusch et al. 2014. 36 samples from 18 animals.<br>PRJNA944553. 30 samples from 30 animals.<br>PRJNA908260 from Bai et al. 2023. 8 samples from 8 animals.<br>PRJNA923753 from Ho et al. 2023. 1 sample.<br><h1>Metagenomic assembly</h1><br>De novo metagenomic assembly was performed on samples listed above. First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (GCF_018350175.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.<br><h1>MAGs recovery</h1><br>MAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).<br><h1>Non-redundant gene catalog</h1><br>Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.<br><h1>MSPs recovery</h1><br>Samples from multiple cohorts (listed above + PRJNA906124 from Lee et al. 2022) were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,3M genes quantified in 212 samples). Then, co-abundant genes were binned in 344 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.<br><h1>MAGs and MSPs taxonomic annotation</h1><br>Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters) for PRJEB4391, PRJEB9357, PRJNA758898, PRJNA906124, PRJNA908260, PRJNA923753 and PRJNA944553 used in catalogue assembly.<p></p>
Peridontal and Intestinal Microbiota in Patients With Gingival Scarring Pemphigoid
ClinicalTrials.gov study NCT06291350. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study on the Changes and Prognosis of Intestinal Microbiota and Function in Infants With Food Allergies
ClinicalTrials.gov study NCT06854536. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Intestinal Microbiota Composition in Patients With Chronic Pancreatitis and Pancreatic Exocrine Insufficiency
ClinicalTrials.gov study NCT05132309. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Evolution of Intestinal Microbiota in Patients With Juvenile Spondylarthropathy According to Typology of Treatment
ClinicalTrials.gov study NCT04540432. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Evaluation of Intestinal Microbiota Manipulation to Treat Resistant Hypertension
ClinicalTrials.gov study NCT04398693. IPD Sharing: NO. Countries: 1. Publications: 0.
Intestinal Microbiota Transplantation for Nonalcoholic Fatty Liver Disease
ClinicalTrials.gov study NCT03648086. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Effects of Barley Green on Visceral Fat Area in the Human Body and Investigation Into the Associated Mechanism of Intestinal Microbiota
ClinicalTrials.gov study NCT06886048. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Investigation of Fecal Microbiota Transplant in Chronic Intestinal Pseudo-obstruction Patients
ClinicalTrials.gov study NCT06020365. IPD Sharing: YES. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.