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315 results for “human intestine”
Human intestinal Bacteria Collection (HiBC): Isolates and genomes metadata
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the taxonomy of the isolates, as well as metadata regarding their cultivation and isolation. We also provide metadata regarding the sequencing, genome assembly process and the biological sequences.</p> <p><strong>UPDATE v7</strong>: INSDC accession for <em>Segatella sinensis</em> CLA-AA-H117 was a missing value and is now the correct value of GCA_040324585.2.</p> <p><strong>UPDATE v6: </strong>The growth atmosphere is now indicated by anaerobic or aerobic instead of "Anaerobe/Aerobe" that was a misleading term. The risk group of these two isolates went from 1 to 2:</p> <ul> <li>CLA-AA-H205: <em>Anaerostipes caccae </em></li> <li>CLA-AA-H83: <em>Bacteroides fragilis</em></li> </ul> <p>The risk group of the following isolates has been updated (usually from unknown to 1, or from 2 to 1):</p> <ul> <li>CLA-SR-H026: <em>Aedoeadaptatus acetigenes</em></li> <li>CLA-KB-H139:<em> Bacteroides xylanisolvens</em></li> <li>CLA-SR-H015: <em>Bacteroides xylanisolvens</em></li> <li>CLA-AA-H187: <em>Blautia fusiformis</em></li> <li>CLA-AA-H274: <em>Brotaphodocola catenula</em></li> <li>CLA-AA-H286: <em>Butyricimonas faecihominis</em></li> <li>CLA-AA-H278:<em> Clostridium fessum</em></li> <li>CLA-AA-H147: <em>Dorea ammoniilytica</em></li> <li>CLA-SR-H027: D<em>orea formicigenerans</em></li> <li>CLA-KB-H89: <em>Dorea longicatena</em></li> <li>CLA-KB-H94: <em>Dorea longicatena</em></li> <li>CLA-SR-H022: <em>Enterococcus lactis</em></li> <li>CLA-AA-H250: <em>Hominenteromicrobium mulieris</em></li> <li>CLA-AA-H232: H<em>ominilimicola fabiformis</em></li> <li>CLA-AA-H246: <em>Hominisplanchenecus faecis</em></li> <li>CLA-AA-H276:<em> Hominiventricola filiformis</em></li> <li>CLA-AA-H213:<em> Oliverpabstia intestinalis</em></li> <li>CLA-AA-H241: <em>Oliverpabstia intestinalis</em></li> <li>CLA-AA-H58: <em>Pilosibacter fragilis</em></li> <li>CLA-KB-H110: <em>Ruthenibacterium lactatiformans</em></li> <li>CLA-AA-H174: <em>Segatella sinensis</em></li> <li>CLA-AA-H2: <em>Veillonella parvula</em></li> <li>CLA-AA-H273: <em>Waltera acetigignens</em></li> </ul> <p>Typos in media list have been fixed. </p> <p><strong>UPDATE v5</strong>: The accessions number for the genomes on INSDC databases are added under the column Accession. Plus two typos in the risk group column have been corrected as follow:</p> <ul> <li>CLA-AA-H173: from Risk Group 4 (!) to 2 like the other strain of <em>Sutterella wadsworthensis</em></li> <li>CLA-AA-H198: from Risk Group 4 (!) to 1 like the other <em>Bifidobacterium </em>species.</li> </ul> <p><strong>UPDATE v4</strong>: Only the taxonomy of a couple of isolates has been changed, as follow:</p> <ul> <li>CLA-ER-H4: <em>Collinsella sp900547855</em> instead of <em>Collinsella sp900544645</em></li> <li>CLA-AA-H142: <em>Pilosibacter fragilis</em> (<em>f__Clostridiaceae</em>) instead of <em>Sakamotonia hominis gen. nov.</em> (<em>f__Lachnospiraceae</em>)</li> <li>CLA-AA-H58: <em>Pilosibacter fragilis </em>(<em>f__Clostridiaceae</em>) instead of <em>Sakamotonia hominis gen. nov. </em>(<em>f__Lachnospiraceae</em>)</li> <li>CLA-AA-H89B: <em>Lachnospira intestinalis sp. nov.</em> instead of <em>Lachnospira hominis sp. nov.</em></li> <li>CLA-JM-H10: <em>Lachnospira hominis sp. nov.</em> instead of <em>Lachnospira intestinalis sp. nov.</em></li> <li>CLA-JM-H7B: <em>Faecalibacterium taiwanense</em> instead of <em>Faecalibacterium faecis sp. nov.</em></li> <li>CLA-JM-H45: <em>Merdimmobilis hominis</em> instead of <em>Hominicola intestinalis gen. nov.</em></li> </ul> <p><strong>UPDATE v3</strong>: The genome of one of our isolate had been unfortunately swapped. This mistake has been now corrected on Zenodo and Coscine. The genome of <em>Segatella sinensis</em> CLA-AA-H117 should be considered correct with 103 contigs and 3 671 232 nt. Please note that the genome available at the NCBI is the correct one (GCA_040324585.2). Two typos regarding taxonomy have been corrected as well: <em>Maccoya intestinihominis</em> has been corrected to <em>Maccoyia intestinihominis</em> and <em>Faecousia faecis</em> to <em>Faecousia intestinalis</em>.</p>
Human intestinal Bacteria Collection (HiBC): 16S rRNA gene sequences
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the sequences of the 16S rRNA gene sequences of the isolates in the FASTA nucleotide format. Sequences ending in Sanger were obtained using the Sanger dideoxy sequencing technology. Sequences ending in Genome were obtained from the genome sequence using barrnap.</p>
Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine
<p>Supplementary Table Captions:</p> <p>Supplementary Table S9. Evaluation and parameter determination of host and microbiome RNA read classification using simulation datasets</p> <p>Supplementary Table S10. 40 pathways significantly upregulated in the cecum as compared to the transverse colon</p> <p>Supplementary Table S11. Host-microbiome gene co-expression network edges</p> <p>Supplementary Table S12. Host-host gene co-expression network edges</p> <p>Supplementary Table S13. Microbiome-microbiome gene co-expression network edges</p> <p>Supplementary Table S14. List of genes included in each gene module identified from the gene co-expression network</p> <p>Supplementary Table S15. Results of enrichment analysis for each gene module identified from the gene co-expression network</p> <p>Supplementary Table S16. The top 32 bacterial species in terms of expression abundance based on metatranscriptome profiles</p> <p>Supplementary Table S17. Number of microbiome RNA reads annotated by the KEGG database</p> <p>Supplementary Table S18. Results of enrichment analysis of gene modules for each parameter</p> <p>Supplementary Table S19. Evaluation of modules in each parameter of Newman algorithm</p> <p>Supplementary Table S20. Evaluation of modules in each parameter of Louvain algorithm</p> <p>Supplementary Table S21. Evaluation of modules in each parameter of Leiden algorithm</p> <p>Supplementary Table S22. Evaluation of modules in each parameter of WGCNA</p>
The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"
<p>The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.</p> <p> </p> <p><strong>Table S1.</strong> Upregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S2.</strong> Downregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S3. </strong>The enriched GO terms in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S4. </strong>The enriched KEGG pathways in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Figure S1. </strong>The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes. </p>
Human intestinal Bacteria Collection (HiBC): Genome sequences
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the genome sequences of the isolates in the FASTA nucleotide format. Plasmids sequences when present are located at the very end of the file.</p> <p><strong>UPDATE v3</strong>: The genome of one of our isolate had been unfortunately swapped. This mistake has been now corrected on Zenodo and Coscine. The genome of <em>Segatella sinensis</em> CLA-AA-H117 should be considered correct with 103 contigs and 3 671 232 nt. Please note that the genome available at the NCBI is the correct one (GCA_040324585.2). Two typos regarding taxonomy have been corrected as well: <em>Maccoya intestinihominis</em> has been corrected to <em>Maccoyia intestinihominis</em> and <em>Faecousia faecis</em> to <em>Faecousia intestinalis</em>.</p>
The impact of cefuroxime prophylaxis on human intestinal microbiota in surgical oncological patients - Dataset (FASTQ FILES)
<p>Dataset containing FASTQ files of the sequenced samples, generated by the Illumina MiSeq platform. </p> <p><span>This data is freely available under a CC-BY license; if you use it in your work, please cite our paper, "The impact of cefuroxime prophylaxis on human intestinal microbiota in surgical oncological patients" (DOI 10.3389/frmbi.2022.1092771).</span></p>
Processed single cell data from CODEX multiplexed imaging of the human intestine
<p>We performed CODEX (co-detection by indexing) multiplexed imaging on 64 sections of the human intestine (~16 mm2) from 8 donors (B004, B005, B006, B008, B009, B010, B011, and B012) using a panel of 57 oligonucleotide-barcoded antibodies. Subsequently, images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), single cell segmentation, and column marker z-normalization by tissue. The outputs of this process were data frames of 2.6 million cells with 57 antibody fluorescence values quantified from each marker. Each cell has its cell type, cellular neighborhood, community of neighborhooods, and tissue unit defined with x, y coordinates representing pixel location in the original image. This is from a total of 25 cell types, 20 multicellular neighborhoods, 10 communities of neighborhoods, and 3 tissue segments that could be used to understand the cellular interactions, composition, and structure of the human intestine from the duodenum to the sigmoid colon and understand differences between different areas of the intestine. This data could be used as a healthy baseline to compare other single-cell datasets of the human intestine, particularly multiplexed imaging ones. </p> <p>The overall structure of the datasets is individual cells segmented out in each row. Columns MUC2 through CD161 are the markers used for clustering the cell types. These are the columns that are the values of the antibody staining the target protein within the tissue quantified at the single-cell level. This value is the per cell/area averaged fluorescent intensity that has subsequently been z normalized along each column as described above. OLFM4 through MUC6 were captured in the quantification but not used within the clustering of cell types. Other columns are explained in the table in the Usage Notes section below.</p> <p>Along with this main data table, there is also a donor metadata table that links the donor ids to clinical metadata such as: age, sex, race, BMI, history of diabetes, history of cancer, history of hypertension, and history of gastorintestinal disease.</p> <p>The raw imaging data can be found at (<a href="https://portal.hubmapconsortium.org/">https://portal.hubmapconsortium.org/</a>). We have created a landing page with links to all the raw dataset IDs and the HuBMAP ID for this Collection is HBM692.JRZB.356 and the DOI is:10.35079/HBM692.JRZB.356. This can be used to also pair it with the matched snRNAseq and snATACseq for each section of tissue.</p>
scRNA data from: Organization of the human Intestine at single cell resolution
<p>The human adult intestinal system is a complex organ that is approximately 9 meters long and performs a variety of complex functions including digestion, nutrient absorption, and immune surveillance. We performed snRNA-seq on 8 regions of of the human intestine (duodenum, proximal-jejunum, mid-jejunum, ileum, ascending colon, transverse colon, descending colon, and sigmoid colon) from 9 donors (B001, B004, B005, B006, B008, B009, B010, B011, and B012). In the corresponding paper, we find cell compositions differ dramatically across regions of the intestine and demonstrate the complexity of epithelial subtypes. We map gene regulatory differences in these cells suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation, and organization in the human intestine, and serve as an important reference map for understanding human biology and disease.</p>
scATAC data from: Organization of the human intestine at single cell resolution
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Human intestine processed CODEX multiplexed images for donors B004-6, B008 (Part 1/2)
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scRNA data from: Organization of the human Intestine at single cell resolution
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Human intestine processed CODEX multiplexed images for donors B009-B012 (Part 2/2)
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Processed single cell data from CODEX multiplexed imaging of the human intestine
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Link to dataset related to article "Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth "
<p>This record contains raw data related to article “ Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth"</p> <p>The microbiota has been shown to promote intestinal tumourigenesis, but a possible anti-tumourigenic effect has also been postulated. Here, we demonstrate that changes in the microbiota and mucus composition are concomitant with tumourigenesis. We identified two anti-tumourigenic strains of the microbiota-Faecalibaculum rodentium and its human homologue, Holdemanella biformis-that are strongly under-represented during tumourigenesis. Reconstitution of Apc<sup>Min/+</sup> or azoxymethane- and dextran sulfate sodium-treated mice with an isolate of F. rodentium (F. PB1) or its metabolic products reduced tumour growth. Both F. PB1 and H. biformis produced short-chain fatty acids that contributed to control protein acetylation and tumour cell proliferation by inhibiting calcineurin and NFATc3 activation in mouse and human settings. We have thus identified endogenous anti-tumourigenic bacterial strains with strong diagnostic, therapeutic and translational potential.</p>
Human intestinal Bacteria Collection (HiBC): Plasmids sequences
<p>The <a href="https://hibc.rwth-aachen.de/" target="_blank" rel="noopener">Human intestinal Bacteria Collection (HiBC)</a> is a collection of bacterial strains, isolated from the human gut for which 16S rRNA gene sequences, genome sequences and culture conditions are made available to the research community. In addition to previously described bacteria, we include strains that represent novel species which have been taxonomically described and validly named, or will be in the future. This collection will be updated regularly.</p> <p>This dataset includes the plasmids sequences of some of the isolates in the FASTA nucleotide format.</p>
Intra-cellular polarization of RNAs and proteins in the human intestinal epithelium
<p>We preformed laser capture microdissection on human and mouse epithelial apical and basal compartments from the villus bottom and top followed by RNAseq. Human samples also undergone proteomics mass-spectrometry.</p>
Dataset supporting "From mouth to gut: microfluidic in vitro simulation of human gastro-intestinal digestion and intestinal permeability"
<p>Manuscript abstract:</p> <p>Reproducible <em>in vitro</em> studies of bioaccessibility, intestinal absorption and bioavailability are key to the successful development of novel foods and drugs aiming for oral administration. There is currently a lack of methods that offer the finesse required to study these parameters for valuable molecules in small volumes - as is the case of nanomaterials under research. Here, we describe a modular microfluidic-based platform for total simulation of the human gastro-intestinal tract. Digestion-chips and cell-based gut-chips were fabricated from PDMS by soft lithography. On-chip digestion was validated using a fluorescently-labelled casein derivative, which followed typical Michaelis-Menten kinetics and showed temporal resolution and good agreement with well-established bench-top protocols. Irreversible inhibition of serine proteases using Pefabloc® SC and a 1:6 dilution was sufficient to mitigate the cytotoxicity of simulated digestion fluids. Caco-2/HT29-MTX co-cultures were grown on-chip under continuous flow for 7 days to obtain a differentiated cell monolayer forming a 3D villi-like epithelium with clear tight junction formation, and with an apparent permeability (P<sub>app</sub>) of Lucifer Yellow closely approximating values reported <em>ex vivo</em> (3.7x10<sup>-6</sup> ± 1.4x10<sup>-6</sup> vs 4.0x10<sup>-6</sup> ± 2.2x10<sup>-6</sup>). Digesta from the Digestion-chips were flowed through the Gut-Chip demonstrating the capacity to study sample digestion and intestinal permeability in a single microfluidic platform holding great promise for its use in pharmacokinetics studies.</p>
Dataset supporting the paper "Effect of prebiotic fermentation products from primary human gut microbiota on an in vitro intestinal model"
<p>Short chain fatty acids (SCFA) originate from the bacterial fermentation of dietary fibre in the gastrointestinal tract. They are hypothesised to play a key role in microbiota–gut–brain crosstalk and the effect of individual SCFAs or mixtures thereof has been broadly studied. However, studies using fermentation products to evaluate the effect of microbiota-targeted interventions, such as prebiotics, probiotics, or diet, are sparse, particularly in humans. In addition, the complexity of these physiological processes translates as a challenge for their simulation<em> in vitro</em>. In this work, fermentation products of prebiotic-enriched media by bacteria present in primary human faecal samples were tested using an epithelium model based on a Caco-2/HT29-MTX co-culture. The prebiotics raftilose and fructo-oligosaccharides (FOS) were tested and the experimental conditions (contact time and minimal dilution) optimised to avoid cytotoxicity. None of the conditions tested compromised the intestinal epithelium integrity as verified by the TEER and the expression of the tight junction-specific protein – occludin. In addition, none of the fermentation products caused an inflammatory response as determinedby the expression of inflammatory genes by qRT-PCR. The products of fermentation of media enriched with FOS showed a moderate protective effect against the formation of reactive oxygen species. This work provides an important basis for the development of <em>in vitro</em> models using a simple approach to evaluate host-gut microbiota interactions, using co-cultures of intestinal cell lines and products of <em>in vitro</em> fermentations by primary human gut microbiota. </p>
Sitagliptin Regulation of Intestinal and Hepatic Lipoprotein Particle and Hepatic Glucose Production in Humans
ClinicalTrials.gov study NCT01600703. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Human Pilot Study - HA35 (Hyaluronan Molecular Weight 35) Dietary Supplement for Promoting Intestinal Health
ClinicalTrials.gov study NCT02867605. IPD Sharing: Not stated. Countries: 1. Publications: 2.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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International Brain Laboratory public data
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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.