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319 results for “Intestinal microbiota”
raw data of Gut microbiota remodeling and intestinal adaptation to lipid malabsorption after enteroendocrine cell loss in adult mice
<p>Microbiome dataset for "Gut microbiota remodeling and intestinal adaptation to lipid malabsorption after enteroendocrine cell loss in adult mice" publication</p> <p>https://doi.org/10.1016/j.jcmgh.2023.02.013</p> <p> </p>
The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Tarsiger rufilatus)
<p>Migratory birds experience changes in their environment and diet during seasonal migrations, thus requiring interactions between diet and gut microbes. Understanding the co-evolution of the host and gut microbiota is critical for elucidating the rapid adaptations of avian gut microbiota. However, dynamics of gut microbial adaptations concerning elevational migratory behavior, which is prevalent but understudied in montane birds remain poorly understood. We focused on the Himalayan bluetail (<em>Tarsiger rufilatus</em>) in the montane forests of Mt. Gongga to understand the diet-gut microbial adaptations of elevational migratory birds. Our findings indicate that elevational migratory movements can rapidly alter gut microbial composition and function within a month. There was a significant interaction between an animal-based diet and gut microbiota across migration stages, underscoring the importance of diet in shaping microbial communities. Furthermore, the gut microbial composition of <em>T. rufilatus</em> may be potentially altered by high-altitude acclimatization. An increase in fatty acid and amino acid metabolism was observed in response to low temperatures and limited resources, resulting in enhanced energy extraction and nutrient utilization. Moreover, microbial communities in distinct gut segments varied in relative abundance and responses to environmental changes. While the bird jejunum exhibited greater susceptibility to food and environmental fluctuations, there was no significant difference in metabolic capacity among gut segments. This study provides initial evidence of rapid diet-gut microbial changes in distinct gut segments of elevational migratory birds and highlights the importance of seasonal sample collection. Our findings provide a deeper understanding of the unique high-altitude adaptation patterns of the gut microbiota for montane elevational migratory birds.</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>
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
<p>This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <em>et al., <a href="https://www.biorxiv.org/content/10.1101/2023.03.01.530589v1">bioRxiv</a>, </em>2023.</p> <p>Article Summary</p> <p>Characterizing trajectories of the composition and function of hominid gut microbiota across diverse environments and host species can help reveal specific properties of the human microbiota, with possible implications for host evolution and health. Using shotgun metagenomic sequencing, we investigated taxonomic and functional diversity in the gut microbiota of wild-living great apes, including two gorilla subspecies (<em>Gorilla gorilla gorilla, Gorilla beringei beringei</em>), three chimpanzee subspecies (<em>Pan troglodytes verus, P.t. troglodytes, P.t. schweinfurthii</em>), and bonobos (<em>Pan paniscus</em>), together with human samples from Africa and Europe. We identified microbial taxonomic and functional adaptations convergent with host phylogeny at both the community and microbial genomic levels. We could show that repeated horizontal gene transfer and gene loss are processes involved in these adaptations. We hypothesize, that these adaptation processes and changes in the microbiome predispose the host to chronic inflammatory disorders, such as type 2 diabetes via altered histidine metabolism and inflammatory bowel disease indicated by adaptation of microbes to aerobic conditions. Additionally, we find multiple lines of evidence suggesting a widespread loss of microbial diversity and evolutionary conserved clades in the human microbiota, especially in the European population. Lastly, we observed patterns consistent with codivergence of hosts and microbes, particularly for the bacterial family <em>Dialisteraceae</em>, though we find that overall, co-phylogeny patterns are frequently disrupted in humans.</p>
The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Tarsiger rufilatus)
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Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection
<p>Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as well as exposure to a natural environment, increased microbiota diversity and altered community composition. Community composition in mice exposed to high temperatures and humidity diverged as much from the microbiota of mice housed outdoors as from the microbiota of control mice. Additionally, infection with the nematode <i>Trichuris muris</i> modulated how the microbiota responded to environmental transitions: The dynamics of several families were buffered by the nematodes, while invasion rates of two taxa acquired outdoors were magnified. These findings suggest that gut bacterial communities respond dynamically and simultaneously to changes within the host's body (e.g., the presence of nematodes) and to changes in the wider environment of the host.</p>
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>
Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
<p>The intestinal microbiota, an invisible organ supporting a host's survival, has essential roles in metabolism, immunity, growth, and development. Since intestinal microbiota influences a host's biology, application of such data to wildlife conservation has gained interest. There are standard protocols for studying the human intestinal microbiota, but no equivalent for wildlife. A major challenge is sampling the intestinal microbiota in an effective, unbiased way. Fecal samples are a popular proxy for intestinal microbiota because collection is non-invasive, convenient, and allows for longitudinal sampling. Yet, it is unclear whether the fecal microbiota is representative of the intestinal microbiota. In amphibians, research on sampling methodology is limited. In this study, we characterize and compare microbiota (small intestine, large intestine, feces) of two Hong Kong stream-dwelling frog species: Lesser Spiny Frog (<em>Quasipaa exilispinosa</em>), and Hong Kong Cascade Frog (<em>Amolops hongkongensis</em>). We found that both species have similar dominant phyla and families, but diverge in terms of the dominant genera. Next, we assess the performance of fecal microbiota in representing the intestinal microbiota in these two species. We found that (1) microbiota of small and large intestine differs significantly, (2) feces are not an appropriate proxy of both intestinal sections, and (3) a set of microbial taxa significantly differs between sample types. Our cautions equating fecal and intestinal microbiota. Sampling feces can avoid sacrifice of an animal, but researchers should avoid over-extrapolation and interpret results carefully.</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>
Effects of Atractylodes Macrocephala Rhizoma polysaccharide on intestinal microbiota composition in rats with mammary gland hyperplasia
<p class="MsoNormal"><strong><span>Background</span></strong><span>: In recent years, Mammary gland hyperplasia (MGH) </span><span>has been</span><span> considered to be one of the diseases caused by endocrine disorders. It has been shown that diseases caused by endocrine disorders can be treated by regulating intestinal microbial. As a commonly used medicine in clinical practice, <em>Atractylodes </em></span><em><span>M</span></em><em><span>acrocephala Rhizoma</span></em><span> has good functions in regulating intestinal homeostasis. Therefore, this paper studied the effect of <em>Atractylodes </em></span><em><span>M</span></em><em><span>acrocephala Rhizoma</span></em><span> polysaccharide (AMP), on the intestinal flora of MGH rats, providing a new idea for polysaccharide treatment of MGH.</span></p> <p class="MsoNormal"><strong><span>Materials and methods</span></strong><span>: </span><span>Eighteen</span><span> female SD rats were selected and randomly divided into three groups, blank control group (Con), model control group (Mod) and AMP group, six rats in each group. MGH rat models were established by estradiol-progesterone combination and treated with AMP gastric infusion. The levels of E<sub>2</sub>, P and PRL in the serum of rats were measured, the intestinal contents were collected, and 16s rRNA high-throughput sequencing technology was used to analyze the changes of intestinal flora in the MGH rats.</span></p> <p class="MsoNormal"><strong><span>Results</span></strong><span>: AMP has good therapeutic effects on MGH rats, decreasing estradiol (E<sub>2</sub>) and prolactin (PRL) levels and increasing progesterone (P) levels, at the same time, it can regulate the abundance and diversity of intestinal flora of MGH rats, improve the disorder of intestinal flora caused by MGH </span><span>and </span><span>change the community structure, increase the abundance of beneficial flora and decrease the abundance of pathogenic flora.</span></p> <p class="MsoNormal"><strong><span>Conclusion</span></strong><span>: AMP can improve the intestinal microbiological environment of MGH rats, maintain the microecological balance of intestinal microbial</span><span>, and improve MGH symptoms</span><span>.</span></p>
Small intestinal microbiota data of pigs receiving control or pharmaceutical levels of ZincOxide
<p>To improve our understanding of host and intestinal microbiome interaction, this research investigated the effects of a high level zinc oxide in the diet as model intervention on the intestinal microbiome and small intestinal functionality in clinically healthy post-weaning piglets.</p> <p>In study 1 piglets received either a high concentration of zinc as zinc oxide (Zn, 2690 mg/kg) or a low Zn concentration (100 mg/kg) in the diet during the post weaning period (d 14-23). We investigated the effects on the piglet’s small intestinal microbiome and functionality of intestinal tissue. In study 2 we investigated the impact of timing of the dietary zinc intervention, i.e. between d 0-14 and/or d 14-23 post weaning, and the consecutive effects on the piglet’s intestinal functionality. We acquired data on the microbiota composition in small intestinal digesta and gene expression profiles of both jejunum and ileum tissue.</p> <p>Overall, we observed differences in the small intestinal functionality during the post weaning period between piglets receiving a diet with a low or high concentration ZnO content.</p>
Antimicrobial peptides modulate lung injury by altering the intestinal microbiota
<p>This repository contains the OTU tables for "Antimicrobial peptides modulate pulmonary inflammation by altering the intestinal microbiota" by Abdelgawad and Nicola et al., an analysis of the role of antimicrobial peptide in the gut-lung axis during hyperoxia-induced lung injury. This work was supported by the National Heart, Lung, and Blood Institute of the U.S. National Institutes of Health, K NIH: K08 HL151907 (KW), K08 HL141652 (CL), K08 DK120871 (AO); the Kaul Pediatric Research Institute at Children’s of Alabama (KW), and the Microbiome Center at UAB (KW). The funding agencies had no role in the design, conduct, and analysis of the study or in the decision to submit the manuscript for publication. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. All data in this repository is the intellectual property of the authors and may be utilized for academic publication only with prior written permission.</p>
Pilot Feasibility Study of Fecal Microbiota Transplant for the Treatment of Small Intestinal Bacterial Overgrowth
ClinicalTrials.gov study NCT05967871. IPD Sharing: YES. Countries: 1. Publications: 25.
Role of Oral and Intestinal Microbiota in Rheumatoid Arthritis (RA)
ClinicalTrials.gov study NCT01198509. IPD Sharing: Not stated. Countries: 1. Publications: 8.
Defining the Intestinal Microbiota in Premature Neonates
ClinicalTrials.gov study NCT01102738. IPD Sharing: NO. Countries: 1. Publications: 2.
Intestinal Permeability and Intestinal Microbiota in Irritable Bowel Syndrome
ClinicalTrials.gov study NCT05379036. IPD Sharing: NO. Countries: 1. Publications: 1.
Impact of Dietary Fiber as Prebiotics on Intestinal Microbiota in Obese Thai Children
ClinicalTrials.gov study NCT03968003. IPD Sharing: YES. Countries: 1. Publications: 7.
Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection
Open the record for dataset details and reuse information.
The trisaccharide melezitose impacts honey bees and their intestinal microbiota
Open the record for dataset details and reuse information.
Data from: Are fecal samples an appropriate proxy for amphibian intestinal microbiota?
Open the record for dataset details and reuse information.
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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.