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1,065 results for “Gut microbiota”
Data from: Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes
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Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients
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Kin recognition in Drosophila: Rearing environment and relatedness can modulate gut microbiota and cuticular hydrocarbon odour profiles
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Dataset: A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between Daphnia magna's gut microbiota and bacterioplankton
<p>Dataset and R codes for the publication "A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between <em>Daphnia magna</em>’s gut microbiota and bacterioplankton"</p>
Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy
<p>These files are associated with the following publication:<a href="https://doi.org/10.1210/jendso/bvaa173">https://doi.org/10.1210/jendso/bvaa173</a></p> <p>And the sequence data are available at the European Nucleotide Archive: PRJEB40801</p> <p>This link contains the metadata, sequences reads, and analysis files used in the study "Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy."</p> <p>Alpha_diversity files:<br> File: AlphaDiversity_analysis_sham_ovex<br> Description: R statistical analysis file for Faith's Phylogenetic Diversity (Faith's PD) and Observed<br> Sequence Variant (SV) alpha diversity metrics<br> File: faith_pd_sham_ovex<br> Description: QIIME2 output file for Faith's PD alpha diversity measurements for sham/ovex samples<br> File: obserevd_svs_sham_ovex<br> Description: QIIME2 output file for Observed SVs alpha diversity measurements for sham/ovex samples<br> </p> <p>Beta_diversity files:<br> File: BetaDiversity_analysis_sham_ovex<br> Description: R statistical analysis file for beta diversiy metrics<br> File: merged.sv.sham.ovex<br> Description: Combined SV table and taxa table for sham/ovex samples <br> File: sv.sham.ovex<br> Description: SV table for sham/ovex samples<br> File: table.sham.ovex.biom<br> Description: BIOM formated file for combined SV and taxa data. (For import into Phyloseq)<br> File: tax.sham.ovex<br> Description: Taxa table for sham/ovex samples<br> File: tree.nwk<br> Description: Phylogentic tree for sham/ovex data (For import into Phyloseq)<br> <br> DeSeq2 Analysis files:<br> File: merged.sv.sham.ovex.trimmed<br> Description: Combined SV table and taxa table for sham/ovex samples. SVs found in 4 samples or less removed. <br> File: sv.table.sham.ovex.trimmed <br> Description: SV table for sham/ovex samples. SVs found in 4 samples or less removed.<br> File: sham.ovex.trimmed.biom<br> Description: BIOM formated file for combined SV and taxa data. SVs found in 4 samples or less removed.(For import into Phyloseq)<br> File: tax.sham.ovex.trimmed<br> Description: Taxa table for sham/ovex samples. SVs found in 4 samples or less removed.<br> File: tree.trimmed.nwk<br> Description: Phylogentic tree for sham/ovex data. SVs found in 4 samples or less removed. (For import into Phyloseq)<br> File: Phyloseq.DeSeq2.Ovex.Sham<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time points 1-5.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week3<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 3.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week4<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 4.<br> File: Phyloseq.DeSeq2.Ovex.Sham.week5<br> Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 5.<br> <br> <br> Mapping_files including metadata (for use with sequences below):<br> File: ovex_mapping <br> Description: Mapping file - maps barcodes to samples<br> File: ovex_mapping_samples removed<br> Description: Mapping file - maps barcodes to reads. Two samples removed for low sequence count.<br> 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F<br> 2. Plate2 C02 806rcbc121 GCA ATT AGG TAC CCG GAC TAC HVG GGT WTC TAA T 26 888 (T2) Co-Sham O<br> File: ovex_mapping_sham_ovex_samples removed<br> Description: Mapping file - maps barcodes to reads. Sham/ovex samples only. One sample removed for low sequence count.<br> 1. Plate2 A08 806rcbc103 GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T 8 870 (T2) Ovex F<br> </p> <p>QIIME2 Script:</p> <p>File: QIIME2_sham_ovex<br> Description: This file includes the commands used in the QIIME2 pipeline.</p>
Data from: Mosquitoes rely on their gut microbiota for development
Field studies indicate adult mosquitoes (Culicidae) host low diversity communities of bacteria that vary greatly among individuals and species. In contrast, it remains unclear how adult mosquitoes acquire their microbiome, what influences community structure, and whether the microbiome is important for survival. Here we used pyrosequencing of 16S rRNA to characterize the bacterial communities of three mosquito species reared under identical conditions. Two of these species, Aedes aegypti and Anopheles gambiae, are anautogenous and must blood feed to produce eggs, while one, Georgecraigius atropalpus, is autogenous and produces eggs without blood feeding. Our results indicated each hosts a low diversity community comprised primarily of aerobic bacteria. However, the communities in Ae. aegypti and An. gambiae larvae were much more similar to one another than to Ge. atropalpus. Studies with Ae. aegypti indicated adults transstadially acquire many members of the larval bacterial community, whereas only four genera of bacteria in blood fed females were detected on eggs. Functional assays showed that axenic larvae of each species failed to develop beyond the first instar. Experiments with Ae. aegypti indicated several members of the microbial community and Escherichia coli successfully colonized axenic larvae and rescued development. Overall, our results provide new insights about the acquisition and structure of bacterial communities in mosquitoes. They also indicate three mosquito species spanning the breadth of the Culicidae depend on their gut microbiome for development, while suggesting the possibility the gut microbiome is an important factor in autogeny.
Data from: Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity
Individuals harbor diverse communities of symbiotic bacteria, which differ dramatically among host individuals. This heterogeneity poses an immunological challenge of distinguishing between mutualistic and pathogenic members of diverse and host-specific microbial communities. We propose that Major Histocompatibility class II (MHC) genotypes contribute to recognition and regulation of gut microbes, and thus MHC polymorphism contributes to microbial variation among hosts. Here, we confirm that, within a single wild vertebrate population of threespine stickleback, different MHC II amino acid sequence motifs are associated with among-individual variation in gut microbiota. The presence of certain MHC motifs is associated with altered relative abundance (increase or decrease) of some microbial Families. Furthermore, hosts with more diverse MHC motifs had less diverse gut microbiota. Our results show that MHC affects host regulation of gut microbiota in natural populations, consistent with limited experimental evidence that MHC controls gut microbes in laboratory mice. One implication is that MHC might influence the efficacy of therapeutic strategies to treat dysbiosis-associated disease. For example, we hypothesize that microbial transplants to treat dysbiosis might be constrained by MHC match between donor and recipient. Another implication is that macroparasite-driven selection on MHC has the potential to indirectly alter the host gut microbiota, and vice versa. Our findings therefore open up a variety of avenues for further investigation into MHC-microbiota interactions.
Data from: Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards
Adaptive radiations provide unique opportunities to test whether and how recent ecological and evolutionary diversification of host species structures the composition of entire bacterial communities. We used 16S rRNA gene sequencing of faecal samples to test for differences in the gut microbiota of six species of Puerto Rican Anolis lizards characterized by the evolution of distinct 'ecomorphs' related to differences in habitat use. We found substantial variation in the composition of the microbiota within each species and ecomorph (trunk-crown, trunk-ground, grass-bush), but no differences in bacterial alpha diversity among species or ecomorphs. Beta diversity analyses revealed subtle but significant differences in bacterial composition related to host phylogeny and species, but these differences were not consistently associated with Anolis ecomorph. Comparison of a trunk-ground species from this clade (A. cristatellus) with a distantly related member of the same ecomorph class (A. sagrei) where the two species have been introduced and are now sympatric in Florida revealed pronounced differences in the alpha diversity and beta diversity of their microbiota despite their ecological similarity. Comparisons of these populations with allopatric conspecifics also revealed geographic differences in bacterial alpha diversity and beta diversity within each species. Finally, we observed high intraindividual variation over time and strong effects of a simplified laboratory diet on the microbiota of A. sagrei. Collectively, our results indicate that bacterial communities are only weakly shaped by the diversification of their lizard hosts due to the strikingly high levels of bacterial diversity and variation observed within Anolis species.
Data from: Interpersonal variations in gut microbiota profiles supersedes the effects of differing fecal storage conditions
Due to ease of acquisition, fecal samples are often used in studies investigating gut microbiota. Improper handling of these samples can lead to bacterial growth and alter bacterial composition. While freezing samples at −80 °C is considered gold standard, this is not suitable for studies utilizing self-sampling by lay participants or field studies. Thus to effectively prevent bacterial growth, techniques that allow efficient fecal storage outside laboratory facilities are needed. Fecal samples were collected from three donors. From each donor feces, 45 samples were collected and stored either freshly frozen at −80 or −20 °C, or in three separate storage buffers at room temperature or 4 °C for 24 or 72 hours. Bacterial composition was analyzed using Illumina amplicon sequencing of the V4 region of the 16 S rRNA gene. While storage conditions did affect bacterial composition and diversity compared to storage at −80 °C, the variation between donors superseded the variations introduced by storage. Samples stored at −20 °C most closely resembled those stored at −80 °C. When investigating variations in bacterial composition between separate study populations, fecal samples can efficiently be stored in −20 °C freezers or in one of the presented storage buffers, without severe alterations in bacterial composition.
Data from: Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs
Introduction: Previous reports have shown that the gastrointestinal (GI) bacterial microbiota can have profound effects on the lungs, which has been described as the "gut-lung axis". However, whether a "lung-gut" axis exists wherein acute lung inflammation perturbs the gut and blood microbiota is unknown. Methods: Adult C57/Bl6 mice were exposed to one dose of LPS or PBS instillation (n = 3 for each group) directly into lungs. Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation. We then investigated the effects of oral neomycin and streptomycin (n = 8) on the microbiota at 4 and 24 hours post LPS instillation versus control treatment (n = 5 at baseline and 4 hours, n = 7 at 24 hours). Results: At 24 hours post LPS instillation, the total bacterial count was significantly increased in the cecum (P<0.05); whereas the total bacterial count in blood was increased at 4, 48, and 72 hours (P<0.05). Antibiotic treatment reduced the total bacteria in blood but not in the cecum. The increase in total bacteria in the blood correlated with Phyllobacteriaceae OTU 40 and was significantly reduced in the blood for both antibiotic groups (P<0.05). Conclusion: LPS instillation in lungs leads to acute changes in the bacterial microbiota in the blood and cecum, which can be modulated with antibiotics.
supplementary tables for physical activity and sedentary behavior on gut microbiota.
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Cultivar and harvest time of almonds modify the antioxidant and nutritional profile of almonds through gut microbiota modifications (Supplementary materials)
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The causal links between gut microbiota and diabetic nephropathy: A Mendelian randomization study. Supplementary material
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Dataset related to article "Identification of a gut-microbiota signature linked to epileptogenesis in a rat model of acquired epilepsy"
<p>Five excel files containing data related to the article</p>
Dataset for: Enhanced tameness by Limosilactobacillus reuteri from gut microbiota of selectively bred mice
<p>This dataset comprises a non-redundant set of 374 metagenome-assembled genomes (MAGs), generated from the shotgun metagenomic data of faecal samples from 80 mice. Among these, 27 MAGs have been identified as novel within the mice gut microbiome. Additionally, the code utilized for the generation of these MAGs has been included with the dataset for reference and reproducibility. All raw shotgun metagenomic sequencing datasets generated in this study are available in the NCBI under BioProject PRJDB15857 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJDB15857), with BioSample accession numbers from SAMD00614304 to SAMD00614383 and SRA accession numbers from DRR480456 to DRR480535. </p>
Bile Acid-Gut Microbiota Imbalance in Cholestasis and Its Long-term Effect in Mice
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Earthworms to modulate broiler gut microbiota
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Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs
<p><span><span><span><span><span><span><span><span><span><span><span>Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the re-wilded domesticated populations can re-adapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of <i>Sus scrofa </i>(wild boar, hybrid, feral and several domestic pig breeds). Porcine Single Nucleotide Polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of <i>F</i><sub>ST</sub> in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised <i>F</i><sub>ST</sub> values, re-acquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.</span></span></span></span></span></span></span></span></span></span></span></p>
Maternal sweeteners intake modulates gut microbiota and exacerbates learning and memory processes in adult male offspring
<p>Background: There is increasing evidence that gut microbiota in offspring is derived in part from maternal environment such as diet. Thus, sweeteners intake including caloric or non-caloric, during perinatal period can induce gut dysbiosis and program the offspring to develop cognitive problems later in life.<br> Objective: To determine the effect of maternal high-sweeteners intake during gestation and lactation on gut microbiota shifts in adult male offspring rats and the impact on cognitive dysfunction.</p> <p>Methods: Thirty-four male pups from dams fed standard diet (Control-C, n = 10), high-sucrose diet (HS-C, n = 11), high-honey diet (Ho-C, n = 8) and high-stevia diet (HSt-C, n = 5) were fed standard diet after weaning and body weight and food intake were recorded once a week for 26 weeks. Learning and memory tests were performed at week 23 of life using the Barnes maze. Fecal samples from the breastfeeding and adulthood periods were collected and analyzed by sequencing the 16S rRNA V3-V4 region of gut microbiota.</p> <p>Results: Maternal high-sucrose and stevia diets programmed the male offspring and changes in microbial diversity by Shannon index were observed after weaning (p < 0.01). Furthermore, maternal high-stevia diet programming lasted into adulthood. The increase of Firmicutes abundance and the decrease in phylum Bacteroidetes was significantly in HS-C and HSt-C groups. This led to an increase in the Firmicutes/Bacteroidetes index although only in HS-C group was statistically significant (p < 0.05). Of note, of the downstream gram-negative Bacteroidales and the upregulation of the gram-positive Clostridiales abundance contribute to cognitive dysfunction.</p> <p>Conclusion: These results suggest that dams fed a high-sucrose and stevia diets during gestation and lactation favor a deficient memory performance in adult male offspring rats through shifts gut microbiota diversity and relative abundance at several taxa.</p>
Influence of diet, sex and viral infections on the gut microbiota composition of Spodoptera exigua caterpillars
<p>Gut microbiota plays essential roles in very diverse processes in all organisms, including insects. Previous studies have shown that changes in gut bacterial composition of caterpillars affects to the insecticidal properties of entomopathogens, opening the possibility of improving the use of entomopathogens in pest control by manipulation of the host microbiota To do that, a better characterization of the host gut microbiota and its interaction with other microbial agents is required. Here we have analysed the gut microbiota of larvae from the major pest Spodoptera exigua under different conditions, and the results have revealed a high variability among individuals and a major influence of the environmental bacteria. These observations suggest the lack of a resident microbiota as it was already claimed for other species of caterpillars. In addition, insects naturally infected with viruses showed a different microbiota composition in comparison with virus-free insects and few taxa specifically associated to the infection have been identified.<a> </a></p>
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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)
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.