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11 results for “gut bacterial microbiome”
Degenerative Cervical Myelopathy (DCM) induces sex-specific dysbiosis in the mouse gut bacterial microbiome, altering abundance and function
<p><strong>Background:</strong> Degenerative cervical myelopathy (DCM) represents the commonest cause of spinal cord impairment induced by non-traumatic events in the elderly population. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, as well as gastrointestinal dysfunction. The gut microbiota has been increasingly recognized as an environmental factor that can modulate both the central nervous system and immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or in the microbiota producing factors have been linked in the progression and development of several different pathologies such as traumatic spinal cord injury (SCI). Little is known about the molecular mechanisms that trigger DCM manifestation, and the potential role of the gut microbiota.</p> <p><strong>Results: </strong>Herein DCM was induced in female and male C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition, also known as dysbiosis, was assessed by 16S rRNA sequencing from fecal samples at 3 different time points (6, 9 and 12 weeks after DCM induction). Several bacterial members were identified based on BLAST against the largest collection of metagenome-derived genomes from the mouse gut up to date. In both, female and males DCM caused gut dysbiosis compared with the sham group. However, dysbiosis was more pronounced in males than females, where several bacterial members of the families <em>Lachnospiraceae</em> and <em>Muribaculaceae</em> were significantly altered in the DCM group. These changes were also associated with altered immune cell composition in gut-associated lymphoid tissue, blood, and microbe-derived metabolic changes in propionate, butyrate, and lactate-producing bacterial members.</p> <p><strong>Conclusions: </strong>Our results demonstrate for the first time that DCM causes dynamic changes over time in the gut microbiota. Furthermore, we identify specie-specific abundance changes during DCM progression. DCM strongly reduces the abundance of butyrate-producing bacteria, and lactate-producing bacteria in much less extent. Sequence-based pangenomics cores were not resolved between the latter bacteria, but the gap-filling reactions and metabolic modelling successfully identified pyruvate-to-butanoate and pyruvate-to-propionate genes such as Buk and ACH1, respectively. These results aid to better understand markers and the molecular mechanisms that over time trigger DCM manifestation in females and males.</p>
Enterosignatures define common bacterial guilds in the human gut microbiome (data)
<p>Additional data related to the manuscript <em>Enterosignatures define common bacterial guilds in the human gut microbiome.</em></p> <p>The deposit contains the following files:</p> <ul> <li>GMR_dataset.zip - data and results related to enterosignature computation in the GMR dataset: raw data, enterosignature composition, metabolic potentials of the associated metagenomic species</li> </ul> <p><strong>GMR_dataset</strong><br> ├── NMF_results <em># results of NMF decomposition, from k = 2 signatures to 10, 5 being the optimal number</em><br> │ ├── 10_H.tsv<br> │ ├── ....<br> │ ├── 9_W.tsv<br> │ └── README.txt<br> ├── age_metadata.tsv <em># age of individuals in the GMR dataset</em><br> ├── drama_MGS_gtdbtk_taxonomy.tsv <em># taxonomy of the MGS </em><br> ├── drama_genus_level_abundance.tsv <em># genus-level abundance table used for NMF</em><br> └── metabo_data <em># Metabolic potential of the MGS associated to the enterosignatures</em><br> ├── cazymes_by_genome.tsv <em># cazymes</em><br> ├── gene_numbers.tsv <em># number of genes</em><br> ├── kegg_metabolic_processes_by_genome.tsv <em># Kegg annotations</em><br> ├── level1_onto_metabolites.tsv <em># Metacyc classes of metabolites, highest level</em><br> ├── level2_onto_metabolites.tsv <em># Metacyc classes of metabolites, second level</em><br> ├── metabolic_producers_full_community.tsv <em># predicted producers of metabolites, all genomes considered</em><br> ├── metabolic_producers_withinES.tsv <em># predicted producers of metabolites, within an ES</em><br> └── westerndiet.sbml <em># nutrients considered for metabolic modelling</em></p> <ul> <li>BMIS_dataset.zip - data and results related to enterosignature computation in the BMIS dataset</li> </ul> <p><strong>BMIS_dataset</strong><br> ├── bmis_es_composition.tsv <em># ES assignments of BMIS samples (ES computed on the GMR dataset)</em><br> ├── bmis_es_et_assignments.tsv<em> # ES and enterotype assignments of BMIS samples</em><br> └── bmis_genus-level_abundance.tsv <em># genus-level abundance matrix used for ES abundance computation</em></p> <ul> <li>NonWestern_dataset.zip - data and results related to enterosignature computation in the non-western dataset</li> </ul> <p><strong>NonWestern_dataset</strong><br> ├── nonwestern_es_composition.tsv <em># ES assignments of Non-western samples (ES computed on the GMR dataset)</em><br> └── nonwestern_genus_abundance_normalised.tsv <em># genus-level abundance matrix used for ES abundance computation</em></p> <p>The data is also available in the following repository:<em> </em><a href="https://gitlab.inria.fr/cfrioux/enterosignature-paper/">https://gitlab.inria.fr/cfrioux/enterosignature-paper/</a>.</p> <p>See also <a href="https://enterosignatures.quadram.ac.uk/">https://enterosignatures.quadram.ac.uk/</a>.</p>
The significance of genetic distance and nest occupation on the worker-worker similarity of gut bacterial microbiome and cuticular hydrocarbon profile in a sweat bee
Open the record for dataset details and reuse information.
PIBAC: Extensive cultivation of the pig gut microbiome identifies novel bacterial diversity and functions and enables tailored functional studies
<p>In-depth cultivation of the pig gut microbiome towards novel bacterial diversity and tailored functional studies:</p> <ul> <li>780 MAGs from all-in-one assembly of 295 pig gut metagenomic samples (Xiao, 2016)</li> <li>38 isolates representing novel species (single draft genomes)</li> <li>representing in total 617 species (hqMAGs-dereplicated_genomes, comp>90%, con<5%</li> </ul> <p>More information you can find here:</p> <p>https://github.com/tillrobin/PIBAC</p> <p>https://www.dsmz.de/pibac</p> <p> </p> <p>External study providing data:</p> <p>Xiao, Liang, et al. "A reference gene catalogue of the pig gut microbiome." Nature microbiology 1.12 (2016): 16161. <a href="https://doi.org/10.1038/nmicrobiol.2016.161">https://doi.org/10.1038/nmicrobiol.2016.161</a> </p>
Dynamics of bacterial recombination in the human gut microbiome — figure data
<p>Data associated with Figures 1-6, S1-41 in the manuscript "Dynamics of bacterial recombination in the human gut microbiome" (DOI: <a href="https://doi.org/10.1101/2022.08.24.505183">10.1101/2022.08.24.505183)</a></p>
Effects of Lactobacillus Pentosus KCA1 on the Gut and Vaginal Microbiome of Women With Bacterial Vaginosis
ClinicalTrials.gov study NCT04329338. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect of Probiotic on Gut Microbiome and Bacterial Translocation in Healthy Asian Volunteers
ClinicalTrials.gov study NCT05083572. IPD Sharing: NO. Countries: 1. Publications: 2.
The bacterial microbiome modulates the initiation of brain metastasis by impacting the gut-to-brain axis.
GEO Series GSE286123. Mus musculus. 37 samples. Type: Other.
Botanical Blend on the Gut Microbiome and Gut-Skin-Axis in Small Intestinal Bacterial Overgrowth (SIBO)
ClinicalTrials.gov study NCT04867512. IPD Sharing: NO. Countries: 1. Publications: 0.
Serial Gut Microbiome and Bacterial Gene Markers Changes After Endoscopic Resection of Colorectal Advanced Neoplasia
ClinicalTrials.gov study NCT05381792. IPD Sharing: NO. Countries: 1. Publications: 0.
Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip
GEO Series GSE65790. Homo sapiens. 6 samples. Type: Expression profiling by array.
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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)
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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.