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2,708 results for “microbiota”
Data of "A workflow to study the microbiota profile of piglet's umbilical cord blood: from sampling to data analysis".
<p>The present study proposes a workflow – from the sampling method to DNA extraction, bioinformatics and data analysis – that characterises the bacterial profile of umbilical cord blood samples, taking into account the contaminants found throughout the procedure of bacterial DNA extraction and amplification.</p> <p>Ps_umbilical.rds: A phyloseq object file of data containing the amplicon sequences variants (ASVs) of thirteen umbilical cord samples and two negative control samples, created by DADA2.</p> <p>R-script.doc: A word document containing the scripts used to characterize the taxonomical composition of the fifteen umbilical cord samples and two negative control samples before and after the application of Decontam R-package (Davis et al., 2018).</p> <p>metadata.docx: meta data for R-script.doc</p>
[Data S2] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data</strong> <strong>S2. GLIPH2 hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For all TCRs within each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), GLIPH2 specificity groups are generated as described in methods.</p>
[Data S1] Microbiota dictate T cell clonal selection to augment graft-vs-host disease after stem cell transplantation
<p><strong>Data S1. ALICE hits for all recipient pairs amongst B6 to B6D2F1 transplants with or without antibiotic exposure and 900cGy vs. 1300cGy TBI conditioning. </strong>For each recipient pair (12 mice total, 66 pairs for spleen; 15 pairs for SILP analysis), all ALICE hits generated as described in methods.</p>
[Github Sample Dataset] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation
<p>[Github Sample Dataset]. This is an accompanying data set for the github repository "<em>https://github.com/acyeh-lab/2023/tree/main/tcr-simulation" referred to in "</em>Non-genetic determinants of clonotypic T cell expansion following stem cell transplantation" by Yeh AC et al.</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>
Supplementary materials. Publication "Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations" by Bouilloud et al.
<p><strong>Supplementary information</strong></p> <p><strong>Supplementary Figure S1</strong>. Maps showing the sampling area (left) and localities (right) in France. Forests are indicated in green and water in blue. The four sampling localities are represented with a colored polygon. The arrow indicates the North.</p> <p> </p> <p><strong>Supplementary Figure S2</strong>. Composition of the gut bacteriota. The relative abundance of six phyla representing 99% of the total composition is represented. Individuals are grouped by sampling localities, which are ordered from North to South. (A) Bar graph shows individual variation in phyla composition (phylum=color). (B) Box and whisker plots represent median and interquartile values for each phylum. Black dots correspond to mean values, and colored dots correspond to individuals.</p> <p> </p> <p><strong>Supplementary Figure S3</strong>. Variations of alpha diversity with individual factors, for the gut bacteriota (family level), pathogenic bacteria and gastro-intestinal helminths of bank voles. Alpha diversity is estimated using the specific richness (A, B and C) and the Shannon index (D, E and F). In graphs C and F, the blue line corresponds to the linear regression line.</p> <p> </p> <p><strong>Supplementary Figure S4</strong>. Relationships between the composition of the gut bacteriota, pathogenic bacteria and gastro-intestinal helminth communities: The db-RDA triplot shows the structure of the gut bacteriota at the phylum level and the correlations with the intra-host parasite communities. The arrows correspond to the significant explanatory variables. Each point corresponds to an individual, and the colors correspond to the different sampling localities.</p> <p> </p> <p><strong>Supplementary Table S1. </strong>Variation of the Firmicutes/Bacteroidetes ratio with localities and individual factors.</p> <p> </p> <p><strong>Supplementary Table S2. </strong>Alpha diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles.</p> <p> </p> <p><strong>Supplementary Table S3. </strong>Beta diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles</p>
Lung microbiota analyses in asthma mouse model
<p class="MsoNormal"><span class="Titre2Car"><span>Background:</span></span><span> Asthma is a frequent chronic inflammatory bronchial disease affecting more than 300 million </span><span>patients worldwide, 70% of whom secondary to</span><span> allergy. The diversity of asthmatic endotypes contributes to </span><span>their</span><span> complexity. Many factors, </span><span>such </span><span>as </span><span>the </span><span>environment, allergen sensitization pathways associate with microbiota, influence asthma natural course and explain its phenotypic heterogeneity. Here</span><span>,</span><span> we compared </span><span>a </span><span>mouse model of house dust mite (HDM)-induced allergic asthma sensitized via various routes for </span><span>the </span><span>clinical features of asthma, immune responses, the lung barrier and dysbiosis.</span></p> <p class="MsoNormal"><span class="Titre2Car"><span>Method:</span></span><span> Mice were sensitized HDM by</span> <span>oral, nasal or percutaneous routes. Lung function, barrier integrity, immune response and microbiota composition were analyzed.</span></p> <p class="MsoNormal"><span>Results: </span><span>Severe </span><span>impairment of respiratory function </span><span>was</span><span> observed </span><span>in</span><span> the mice sensitized by the nasal and cutaneous paths. It was associated with epithelial dysfunction characterized by an increased permeability secondary to junction protein disruption. Conversely, </span><span>such sensitization paths induced</span><span> a </span><span>mixed</span><span> eosinophilic and neutrophilic inflammatory response with high IL-17 airways secretion. </span><span>In contrast, oral </span><span>sensitized mice showed a mild impairment of respiratory function. Epithelial dysfunction was lighter with increased mucus production but conserved epithelial junctions. Lung Th2 and eosinophilic inflammation </span><span>were observed</span><span>. Considering lung microbiota, sensitization provoked a significant loss diversity. </span><span>At</span><span> the genus level, </span><span>Cutibacterium, Acinetobacter, Streptococcus and Lactobacillus</span><span> were found to be modulated according to the sensitization pathway. An increase </span><span>in</span><span> anti-inflammatory microbiota metabolites </span><span>was</span><span> observed in the </span><span>oral group</span><span>. </span></p> <p class="MsoNormal"><span>Conclusion: Our study highlights the strong involvement of the sensitization route in allergic asthma physiopathology and the critical </span><span>phenotypic</span><span> diversity in a mouse model.</span></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>
Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"
<p>MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the OxlT-out directory. </p>
Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in mice.
<p>Raw reads for whole genome sequencing and RNAseq for Gellman et al., 2023.</p>
Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics
<p>In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.</p>
Goat milk microbiota of Dutch farms
<p>Microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels. On ten farms our results indicated that the number of microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. The milk microbiota showed a farm-specific fingerprint. Repeated sampling of a farm showed that this fingerprint changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.</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>
Microbiota of piglets with three different feed additives via maternal or neonatal administration route
<p>Feed additives aiming to improve gastrointestinal health are frequently supplied to piglets after weaning, but might be more effective when administered before weaning. In this period, feed additives can either be administered directly to neonates, or indirectly via sows feed. It is yet unknown what the effect of the administration route is on gut functionality and health. Therefore, we compared the effect of different dietary interventions on gut functionality after maternal administration (lactation feed) to the neonatal administration route (oral gavage). These feed interventions included medium chain fatty acids (MCFA), beta-glucans (BG), and galacto-oligosaccharides (GOS). We measured intestinal gene expression and microbiota composition after birth (d1) and after weaning (d31). Our results show that the type of intervention and the administration route influence gut functionality (microbiome and gene expression profiles). MCFA administration led to a more differentially orchestrated response when comparing the neonatal and maternal administration route then the other two additives, indicating the route of administration of the feed interventions is determinative for the outcome.. This implies that for each nutritional intervention in early life of a pig the optimal route of administration needs to be determined.</p>
Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom
<p>This archive contains the R code, QIIME2 script and datasets used to perform the analyses and figures in the manuscript.</p>
The gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status
<p><strong><span>Background and aim</span> </strong></p> <p><span>The association of the gut microbiota to </span><span>chronic obstructive pulmonary disease (COPD)</span><span> phenotypes is underexplored. We aimed to compare</span><span> stool samples from COPD patients and healthy controls and relate findings to common COPD phenotypes. </span></p> <p><strong><span>Methods</span></strong></p> <p><span>Single-centre case-control study with 62 current and former smoking COPD patients and 49 controls. DNA was extracted from stool samples, and the V3V4-region of the bacterial 16S-rRNA gene was sequenced. Emphysema was defined based on thoracic computed tomography (CT thorax) low attenuating areas ≥/<10% at threshold -950 and -910 Hounsfield units respectively. Microbial data were analysed with QIIME 2 and R.</span></p> <p><strong><span>Results</span></strong></p> <p><span>The genus Veillonella was decreased and a genus belonging to class Clostridia was increased in COPD compared to healthy controls. Beta diversity measure Bray Curtis differed in emphysema compared to controls, and 27 genera were differentially abundant in emphysema vs. controls. Nine of these genera belonged to the family Lachnospiraceae. Lung function, blood counts and COPD assessment test scores were correlated with the relative abundance of several genera. Some of the genera showing the strongest correlation to lung function belonged to the family Lachnospiraceae. </span></p> <p><strong><span>Conclusion</span></strong></p> <p><span>We found small but statistically significant differences in the gut microbiota of COPD versus controls. Larger differences were seen in the gut microbiota according to CT-verified emphysema status. Correlations between the gut microbiota and lung function, blood cell counts, and CAT score were found. </span></p>
Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
<p>Pigs infected with <em><span>Salmonella</span></em> may excrete large amounts of <em><span>Salmonella</span></em>, increasing the risk of spread of this pathogen in the food chain. Identifying <em><span>Salmonella</span></em> high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with <span>Salmonella</span>. Immune response was studied through total blood cell counts, production of anti-<em><span>Salmonella</span></em> antibodies and cytokines, and gene expression quantification. Total <em><span>Salmonella</span></em> shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with <em><span>Salmonella</span></em> induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to <em><span>Salmonella</span></em> modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing <em><span>Salmonella</span></em> high shedding in livestock.</p>
[Data S10] Microbiota dictate T cell clonal selection to promote graft-vs-host disease after stem cell transplantation
<p>Data S10. 10x genomics sequencing data files for Figure 5. Matrix file "sample_filtered_feature_bc_matrix.h5" and V(D)J annotations "filtered_contig_annotations.csv" are included below. Accompanying code can be found at https://github.com/acyeh-lab/2023/tree/main/scseq.</p>
Immune stimulation induced changes to the native gut microbiota of bumble bees
<p>Understanding factors influencing the maintenance and membership of beneficial host-associated microbial communities is central to understanding ecological, evolutionary, and health consequences of these communities for their hosts. Host immunity is often implicated as a potential regulator of these microbiota. However, conversely, immunity may play a disruptive role, with immune responses to infection causing collateral damage. Such effects may be more prominent from innate immune responses, with more rapid-acting and relatively non-specific components. We investigated how upregulation of antibacterial immunity in the bumble bee <em>Bombus</em> <em>impatiens</em> affects the core gut microbiota, testing the hypothesis of immunity-induced perturbation of the beneficial microbiota structure. Freshly emerged adult bees received a native microbiota inoculation before being subjected to non-pathogenic immune stimulation treatments. We quantified the microbial community using 16S rRNA amplicon sequencing and targeted qPCR. We find colonization of the core member <em>Gilliamella</em> is altered by immune stimulation treatment. Additionally, a positive association in communities between <em>Gilliamella</em> and another core bacteria, <em>Snodgrassella</em> <em>alvi</em>, is perturbed. These changes are indicative of immune-response-induced dysbiosis. As such, the potential for collateral perturbation of beneficial microbial communities upon a host's innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment.</p>
Database containing Raw Data of Growth and Survival of Pathogens and Microbiota from Fate Studies in Artisanal Fermented Foods
<p>Deliverable 5.5 is a spreadsheet containing metadata and raw data obtained from the fate studies conducted in Workpackage 5. In case of reutilisation of these data, the source should be properly cited.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.