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55 results for “Human gut microbiota”
Raw metabolomics data of the paper: New findings in the metabolism of the saffron apocarotenoids, crocins and crocetin, by the human gut microbiota
<p>Raw dataset of the metabolomicas data of the study : New findings in the metabolism of the saffron apocarotenoids, crocins and crocetin, by the human gut microbiota.</p> <p>The csv file contain the raw data matrix exported from MS-DIAL software after total ions aligment across all study samples.</p>
Illumina Sequencing Data for "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes"
<p>Illumina Sequencing Data for Sulaiman et al., "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes".</p>
HiFi Metagenomic Sequencing Enables Assembly of Accurate and Complete Genomes from Human Gut Microbiota.
<p>We reported 102 complete metagenome assembled genomes (cMAGs) from five human fecal HiFi sequencing samples.</p> <p>102_cMAGs_fna.tar.gz: Fasta sequence files of 102 cMAGs.</p> <p>gc_skew_figures.tar.gz: GC-skew pattern figures of 102 cMAGs. (SVG format)</p> <p>coverage_plots.tar.gz: Genome coverage plot of 102 cMAGs.</p>
Phylogenies related to: Codiversification of gut microbiota with humans
<p><span>The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, signals of codiversification were evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes, and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.</span></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>
Investigation of the Gut Microbiota in Regulating Nutrient Absorption in Humans
ClinicalTrials.gov study NCT02037295. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Phylogenies related to: Codiversification of gut microbiota with humans
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Large-scale metabolic interaction network of the mouse and human gut microbiota
<p>The role of our gut microbiota in health and disease is largely attributed to the collective metabolic activities of the inhabitant microbes. A system-level framework of the microbial community structure, mediated through metabolite transport, would provide important insights into the complex microbe-microbe and host-microbe chemical interactions. This framework, if adaptable to both mouse and human systems, would be useful for mechanistic interpretations of the vast amounts of experimental data from gut microbiomes in murine animal models, whether humanized or not. Here, we constructed a literature-curated, interspecies network of the mammalian gut microbiota for mouse and human hosts, called NJC19. This network is an extensive data resource, encompassing 838 microbial species (766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types, interacting through 8,224 small-molecule transport and macromolecule degradation events. Moreover, we compiled 912 negative associations between organisms and metabolic compounds that are not transportable or degradable by those organisms. Our network may facilitate experimental and computational endeavors for the mechanistic investigations of host-associated microbial communities.</p>
Humanization of wildlife gut microbiota in urban environments
<p>Urbanization is rapidly altering Earth's environments, demanding investigations of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans) and crested anole lizards (Anolis cristatellus) acquire gut microbiota constituents found in humans, including the gut bacterial lineages most significantly associated with urbanization in humans (e.g., Bacteroides). Comparisons of urban and rural wildlife and human populations revealed significant convergence of the gut microbiota among urban host populations. Remarkably, all microbial lineages found in humans that were overrepresented in urban wildlife relative to rural wildlife were also overrepresented in urban humans relative to rural humans. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities</p>
Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota
<div> <p><span><span>Background</span></span><span><span>: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. </span><span>This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases</span><span>, with each sample sequenced using both 16S and shotgun methods</span><span>. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models.</span></span><span> </span></p> </div> <div> <p><span><span>Results</span></span><span><span>: </span><span>As expected, the results showed that </span></span><span><span>16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The </span></span><span><span>16S </span><span>abundance data was sparser and </span><span>exhibited</span><span> lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, </span><span>partially</span><span> due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their </span><span>PCoAs</span><span>. </span><span>Regarding</span><span> the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not </span><span>demonstrate</span><span> a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques reveal</span><span>ed</span><span> taxa previously associated with CRC development, e.g., </span></span><span><span>Parvimonas</span><span> micra</span></span><span><span>.</span></span><span> </span></p> </div> <div> <p><span><span>Conclusions</span></span><span><span>: </span></span><span><span>Shotgun and 16S sequencing provide two different lenses to examine microbial communities.</span><span> While we have </span><span>demonstrated</span><span> that they can unravel common patterns (including microbial signatures), </span><span>shotgun often gives</span><span> a more detailed snapshot than 16S, both in depth and breadth. </span><span>Instead</span><span>,</span> <span>16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample.</span> <span>Therefore, w</span><span>e recommend choosing one or another sequencing technique before launching a study.</span><span> Specifically, </span><span>s</span><span>hotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is </span><span>more </span><span>suitable for tissue samples</span><span> and</span><span> studies with </span><span>targeted</span> <span>aims</span><span>.</span></span><span> </span></p> </div>
Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota
<p><span><span><span><span><span><span><span><span><span><span><span><b>Background and objectives</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen <i>Escherichia coli</i>. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methodology</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Using anaerobic gut microcosms comprising <i>E. coli</i> embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>While cross-protection gave an advantage to antibiotic-susceptible <i>E. coli</i> in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant <i>E. coli</i> in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions and implications</b></span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be key for slowing the spread of resistance. </span></span></span></span></span></span></span></span></span></span></span></p>
Low Grade Inflammation, Gut Microbiota and Barrier Function in Elderly Humans
ClinicalTrials.gov study NCT01218165. IPD Sharing: Not stated. Countries: 1. Publications: 24.
What's Hopping? Cricket Protein and Human Gut Microbiota
ClinicalTrials.gov study NCT03383341. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Human-derived Human Milk Fortifiers (H2MF), Gut Microbiota and Oxidative Stress in Premature Infants
ClinicalTrials.gov study NCT03214822. IPD Sharing: UNDECIDED. Countries: 1. Publications: 9.
Effects of Inulin and Arabinoxylan on Satiety, Energy/Food Intake and Changes in the Human Gut Microbiota
ClinicalTrials.gov study NCT02846454. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Adaptation of Human Gut Microbiota to Energetic Restriction
ClinicalTrials.gov study NCT01454232. IPD Sharing: Not stated. Countries: 1. Publications: 2.
The Role of the Gut Microbiota in the Systemic Immune Response During Human Endotoxemia
ClinicalTrials.gov study NCT02127749. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Bile Acids and Gut Microbiota as Potent Coronary Atheroma Risk Factors: a Prospective Study in Human
ClinicalTrials.gov study NCT02375893. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Interactions of Human Gut Microbiota With Intestinal Sweet Taste Receptors
ClinicalTrials.gov study NCT03032640. IPD Sharing: NO. Countries: 1. Publications: 13.
Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota
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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.