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2,708 results for “Microbiota”
Data from: A zebrafish model to elucidate the impact of host genes on the microbiota
<p>Every host species and organism provide a unique environmental niche contributing to the overall diversity of microbial ecosystems from the intestine of an animal to the oceans and forests of our planet. The study of host-microbiota interactions has long focused on the well-established effects the microbiota has on its host. In contrast, little focus has been allocated to the role of the host in these intricate interactions. However, understanding the role of the host may well be an essential key to understanding the complexity of the relationship between the host and its microbiota. In this study, we present a model in which the effects of host genes on the microbiota can be elucidated and how such genetic effects may shape host-associated microbiota. We demonstrate a hologenomic approach implementing the CRISPR/Cas system in the zebrafish model to combine the effects of a host gene with 16S metabarcoding and metabolomics data. We show that knocking out the gene coding for the rate-limiting enzyme in melanogenesis, tyrosinase <em>(tyr</em>), correlates with changes in the intestinal microbiota of zebrafish and differences in the abundance of specific metabolites illustrating the value of our model for studying the impact of host genes on the composition and function of the intestinal microbiota.</p>
Something in the water: Aquatic microbial communities influence the larval amphibian gut microbiota, neurodevelopment, and behavior
<p>Microorganisms colonize the gastrointestinal tract of animals and establish symbiotic host-associated microbial communities that influence vertebrate physiology. More specifically, these gut microbial communities influence neurodevelopment through the microbiota-gut-brain (MGB) axis. We tested the hypothesis that larval amphibian neurodevelopment is affected by the aquatic microbial community present in their housing water. Newly hatched Northern Leopard Frog (<em>Lithobates pipiens</em>) tadpoles were raised in pond water that was unmanipulated (natural) or autoclaved. Tadpoles raised in autoclaved pond water had a gut microbiota with reduced bacterial diversity and altered community composition, had decreased behavioral responses to sensory stimuli, were larger in overall body mass, had relatively heavier brains, and had altered brain shape when compared with tadpoles raised in natural pond water. Further, the diversity and composition of the gut microbiota was associated with tadpole behavioral responses and brain measurements. Our results suggest that aquatic microbial communities shape tadpole behavior and brain development, providing strong support for the occurrence of the MGB axis in amphibians. Lastly, the dramatic role played by aquatic microbial communities on vertebrate neurodevelopment and behavior should be considered in future wildlife conservation efforts.</p>
Data from: Gut microbiota composition and functionality are associated with REM sleep duration and continuous glucose levels
<p><span><strong>Context</strong>:</span><span> Sleep disruption is associated with poorer glucose metabolic control and altered gut microbiota in animal models.</span></p> <p><span><strong>Objective</strong>:</span><span> We aimed to evaluate the possible links among REM sleep duration, continuous glucose levels, and gut microbiota composition.</span></p> <p><strong><span>Design</span></strong><span>: This is an observational, prospective, real-life, cross-sectional case-control study. </span></p> <p><span><strong>Setting</strong>: </span><span>Tertiary Hospital recruiting healthy volunteers.</span></p> <p><span><strong>Patients or Other Participants</strong>:</span><span> One-hundred and eighteen (60 with obesity), middle-aged (39.1-54.8) subjects.</span></p> <p><span><strong>Intervention(s)</strong>:</span><span> Glucose variability and REM sleep duration were assessed by 10-day continuous glucose monitoring (CGM) (Dexcom G6®) and wrist-actigraphy (Fitbit Charge 3®), respectively</span></p> <p><span><strong>Main Outcome Measure(s)</strong>:</span><span>. Glucose variability was evaluated through standard deviation (SD), coefficient of variation (CV), and interquartile range (IQR). The percentage of time in range (% TIR), 126-139 mg/dL (TIR2), and 140-199 mg/dL (TIR3) were calculated. Shotgun metagenomics sequencing was applied to study gut microbiota taxonomy and functionality. </span></p> <p><span><strong>Results</strong>:</span><span> Increased glycemic variability (SD, CV, and IQR) was observed among subjects with obesity in parallel to increased % TIR2 and % TIR3. REM sleep duration was independently associated with the % TIR3 (β=-0.339; p<0.001) and glucose variability (SD, β=-0.350; p<0.001). Microbial taxa from Christensenellaceae family (Firmicutes phylum) were positively associated with REM sleep and negatively with glucose continuous monitoring levels, while bacteria from Enterobacteriacea family and bacterial functions involved in iron metabolism showed opposite associations. </span></p> <p><span><strong>Conclusions</strong>:</span><span> Decreased REM sleep duration was independently associated with a worse glucose profile. The associations of species from Christensenellaceae and Enterobacteriaceae families with REM sleep duration and continuous glucose values suggest an integrated picture of metabolic health.</span></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>
Data from: Association between gut health and gut microbiota in a polluted environment
<p>Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, aid in digestion of otherwise indigestible foodstuffs, and even changing host behaviour. Stress, such as environmental pollution, parasites, predators, and intraspecies competition, can alter the composition of the gut microbiome, which in turn can change host-microbiome interactions in ways that are detrimental to the host such as causing metabolic dysfunction and inflammation. While host-microbiome interactions have been extensively studied in humans and captive animals, studies into wild animal microbiomes have been scarce. We assessed the effects of disturbed environment on gut health of bank voles exposed to radionuclides in natural habitat using a combined approach of transcriptomics, microbial community analysis by 16S amplicon sequencing, histological staining analyses of colon tissue, and quantification of gut microbiota -produced short-chain fatty acids in faecal matter and blood that act as mediators of host-microbiome interactions. We found signs of weakened mucus layer and related changes in <em>Clca1</em> and <em>Agr2</em> gene expression and microbiome composition in animals exposed to radionuclides. These results imply that disturbed environment can have widely reaching effects through gut health.</p>
Data from: Vertically inherited microbiota and environment modifying behaviors conceal genetic variation in dung beetle life history
<p>Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feedback on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating i) physical environmental modifications, and ii) the vertical inheritance of microbes, we assess how environment modifying behavior and microbiome transmission shape heritable variation. We found that depriving larvae from symbionts and environment modifying behaviors increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that alter the degree to which they can be manipulated. Furthermore, we found heritable variation for the response to the elimination of environmental modifications, indicating that genotypes differ in their dependence on the ability to manipulate their environment. Our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.</p>
With or without you: Gut microbiota does not predict aggregation behavior in European earwig females
<p>The reasons why some individuals are solitary and others gregarious are the subject of ongoing debate as we seek to understand the emergence of sociality. Recent studies suggest that the expression of aggregation behaviors may be linked to the gut microbiota of the host. Here, we tested this hypothesis in females of the European earwig. This insect is ideal for addressing this question, as adults both naturally vary in the degree to which they live in groups and show inter-individual variation in their gut microbial communities. We video-tracked 320 field-sampled females to quantify their natural variation in aggregation and then tested whether the most and least gregarious females had different gut microbiota. We also compared the general activity, boldness, body size, and body condition of these females and examined the association between each of these traits and the gut microbiota. Contrary to our predictions, we found no difference in the gut microbiota between the most and least gregarious females. There was also no difference in activity, boldness, and body condition between these two types of females. Independent of aggregation, gut microbiota was overall associated with female body condition, but not with any of our other measurements. Overall, these results demonstrate that a host's gut microbiota is not necessarily a major driver or a consequence of aggregation behavior in species with inter-individual variation in group living and call for future studies to investigate the determinants and role of gut microbiota in earwigs.</p>
Data from: Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite
<p>Data from the manuscript: </p> <p><strong>Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite</strong></p> <p><em>Summary - </em><em>Revealed once accepted</em></p> <p>The data in this repository covers the following datasets:</p> <ul> <li>4-way screening of BW, pyrE and the triple mutant (TM) -> <em>4_way.csv </em>files</li> <li>RNA-seq raw and normalised counts (from salmon), with their metadata -> files starting with <em>RNAseq</em></li> <li>Proteomics data from Perseus</li> <li>Biolog metabolites for PM plates PM-PM11 to PM14 with a curated classification of their targets, molecule types and processes -><em> biolog_metabolites_cancer.xlsx</em></li> <li>Drug (Biolog and DrugBank) fingerprints -> <em>Drug_FP.xlsx</em></li> </ul>
Supplemental Data for "Embryonic Exposure to Tryptophan Yields Bullying Victimization via Reprogramming the Microbiota-Gut-Brain Axis in a Chicken Model"
<p>This is data set associated with an article "Embryonic Exposure to Tryptophan Yields Bullying Victimization via Reprogramming the Microbiota-Gut-Brain Axis in a Chicken Model" by Xiaohong Huang, Jiaying Hu, Haining Peng, and Heng-wei Cheng, including Supplemental Table S1, S2, S3, S4, S5, S6.</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>
The lower airways microbiota and antimicrobial peptides indicate dysbiosis in sarcoidosis
<p><span><strong>Rationale</strong>: </span><span>The role of the pulmonary microbiome in sarcoidosis is unknown.</span><br><br><span><strong>Objectives</strong>: </span><span>The objectives of the current study was to: 1) </span><span>Examine whether the pulmonary fungal and bacterial microbiota differed in patients with sarcoidosis compared with controls. 2) Examine whether there was an association between the microbiota and levels of the antimicrobial peptides (AMPs) in protected bronchoalveolar lavage (PBAL), indicating an interaction with the innate immune response.</span><br><br><span><strong>Methods</strong>: </span><span>35 sarcoidosis patients and 35 healthy controls underwent bronchoscopy and were sampled with oral wash (OW), protected BAL (PBAL) and left protected sterile brushes (LPSB). The fungal ITS1 region and the V3V4 region of the bacterial 16SrDNA gene were sequenced. Bioinformatic analyses were performed with QIIME 2. The AMPs secretory leucocyte protease inhibitor (SLPI) and human beta defensins 1 and 2 (hBD-1 & hBD-2), were measured in PBAL by enzyme linked immunosorbent assay (ELISA).</span><br><br><span><strong>Measurements and Main Results</strong>: </span><em><span>Aspergillus</span></em><span> dominated the PBAL samples in sarcoidosis. Differences in bacterial taxonomy were minor. There was no significant difference in fungal alpha diversity between sarcoidosis and controls, but the bacterial alpha diversity in sarcoidosis was significantly lower in OW (p=0.047) and PBAL (p=0.03) compared with controls. The beta diversity for sarcoidosis compared with controls differed for both fungi and bacteria. AMP levels were significantly lower in sarcoidosis compared to controls (SLPI & hBD-1: p<0.01). No significant correlations were found between </span><span>a</span><span>-diversity and AMPs.</span><br><br><span><strong>Conclusions</strong>: </span><span>The pulmonary fungal and bacterial microbiota in sarcoidosis differed from controls, with lower antimicrobial peptides levels in sarcoidosis.</span></p>
Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay
<p>Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and <sup><span>15</span></sup><span>N</span> isotopic signature, <span>hydrolytic and lignin-modifying enzyme activities. Each </span>specimen <span>was </span>incubated with bromodeoxyuridine (BrdU) to label <span>metabolically active fungal and bacterial community members, which were assessed using an amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerisation, and N<sub>2</sub> fixation. The latter were governed by the genus <em>Sphingomonas</em>, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic </span><span><em>Allorhizobium</em>-<em>Neorhizobium</em>-<em>Pararhizobium</em>-<em>Rhizobium</em></span><span> group were significantly correlated with mass loss, N content and <sup>15</sup>N isotopic signature. In contrast, presence of obligate predator <em>Bdellovibrio</em> spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonising bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.</span></p>
structure of microbiota in gut of fish 1992-2021
<p>You don’t need to provide an elaborate abstract for the moment. However, keep in mind that, together with the title, the abstract is one of the fields that a potential user will check in order to decide whether the dataset is useful for him/her or not. Have a look at the checklist in this page to get a feeling of what a good abstract should include.</p>
Composition and functional potential of the mammary microbiota prior to and following breast tumor diagnosis
<p>These data were generated to analyze the human breast tissue microbiome composition and functional potential. We analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H) with those of tissues donated prior to (pre-diagnostic, PD, ) and after (adjacent normal, AN, and tumor, T) breast cancer diagnosis to determine the role of the breast tissue microbiome in breast cancer. DNA was isolated from 165 tissue samples, 9 negative controls, and 1 positive control and submitted for Illumina Miseq paired-end sequencing of the V3 - V4 region of the 16S gene. 16S amplicons were pre-processed into amplicon sequence variants (ASVs) using DADA2. To infer bacterial function in breast cancer, we predicted the functional bacteriome from these ASVs using PICRUSt2 and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. </p>
Sexual dimorphism of the gut microbiota in the Chinese alligator and its convergence in the wild environment
<p>The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analysed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA sequencing to analyse the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sex-biased differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus <em>Cetobacterium</em> were highly abundant in adult alligators, similar to that in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment. It also provides insights into host-microbiota interactions in the wild.</p>
Data for: Soil microbiota explain differences in herbivore resistance between native and invasive populations of a perennial herb
<p><span>Soil microbiota can either slow down or facilitate plant invasions through their effects on plant performance. Associations with soil microbiota can also modify other plant traits such as herbivore resistance, which can indirectly affect the outcome of plant introductions. </span></p> <p><span>We studied the effects of soil microbiota on the perennial herbaceous legume <em>Lupinus polyphyllus</em> that hosts nitrogen-fixing mutualistic bacteria. We compared the plant performance, herbivore resistance, and volatile organic compounds (VOCs) of plants from native (North American) and invasive (Finnish) populations of the species that were inoculated with intact or autoclaved soil from an invasive population. </span></p> <p><span>We found that plants of both origins greatly benefited from the intact soil inoculum with respect to all performance measures considered, suggesting that beneficial nitrogen-fixing rhizobia in the soil play a major role in shaping plant phenotypes. For three traits, effects of the intact soil inoculum were stronger in plants of native origin than in plants of invasive origin (number of leaves, herbivore resistance, and total biomass). With the intact soil inoculum, plants of invasive origin were more resistant to snails than plants of native origin. Strikingly, differences in resistance to snails between plants of different origins disappeared entirely when soil microbes were reduced. Soil inoculum treatment altered the composition of the leaf VOC bouquet similarly regardless of plant origin. </span></p> <p><span>Synthesis: These results demonstrate the ability of <em>L. polyphyllus</em> to associate with and benefit from putatively novel soil microbiota including rhizobia, which has likely contributed to its invasion success. Furthermore, it appears that the invasive populations have adapted to be less reliant on their symbionts, which further facilitates species spread. To our knowledge, this is the first study to demonstrate that differences in herbivore resistance between native and invasive plant populations of the same species can depend entirely on soil microbiota.</span></p>
Proccessed Data for the Pipelines of the Project "Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome"
<p><strong>Proccessed and Input Data for the Pipelines of the Project "Multiomics and quantitative modelling disentangle diet, host, and microbiota contributions to the host metabolome"</strong></p> <p>-----------------------------------------------------------------------------------------------------</p> <p>Contents:</p> <p>-----------------------------------------------------------------------------------------------------</p> <p>Folder /ProcessedData/metabolomics/ contains processed metabolomics data from the project:</p> <p>/metabolomics/metabolites_allions_combined_norm_intensity.csv - file containing normalized intensities of ions detected across tissues with six measurement methods.<br> /metabolomics/metabolites_allions_combined_formulas_with_metabolite_filters_spatial100clusters_with_mean.csv - file containing metabolite attribution to spatial clusters and mean intensity values across tissues and conditions.</p> <p>Other files are described in README_ProcessedData.md.</p> <p>-----------------------------------------------------------------------------------------------------</p> <p>Folder /ProcessedData/sequencing/ contains raw and normalized counts of metagenomics and metatransriptomics data mapped to bacterial genomes.</p> <p>Folder /ProccessedData/util/ contains files used for data preprocessing and attribution to chemical classes and pathways.</p> <p>Folder /ProcessedData/example_output/ contains example output of the pipelines:</p> <p>/output/model_results_SMOOTH_raw_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (intestinal flux and metabolic flux values) for the forward problem for metabolomics measurements in the GIT.<br> /output/model_results_SMOOTH_normbyabsmax_reciprocal_problem_allions.csv - file containing estimated model parameters for the reverse problem (metabolite intensities) for the parameters estimated with the forward problem.<br> /output/model_results_SMOOTH_normbyabsmax_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (intestinal flux and metabolic flux values) for the forward problem for metabolomics measurements in the GIT, normalized by absolute maximum value.<br> /output/model_results_SMOOTH_normbyabsmax_ONLYMETCOEF_2LIcoefHost1LIcoefbact_allions.csv - file containing estimated model parameters (only metabolic flux values) for the forward problem for metabolomics measurements in the GIT, normalized by absolute maximum value.<br> /output/table_hierarchical_clustering_groups.csv - file containing attribution of the annotated metabolites to groups according to hierarchical clustering of the normalized model parameters.<br> /output/cgo_clustergrams_of_model_coefficients.mat - matlab object containing clustergram of the normalized model parameters and manually derived sub-clustergrams corresponding to different largest parameter values.</p> <p>Description of other files is provided in the file README_ProcessedData.md.</p> <p>-----------------------------------------------------------------------------------------------------</p> <p>Folder /InputData/ contains HMDB and KEGG tables used for metabolite annotations and chemical group analysis.</p> <p>Folder InputData_KEGGreaction_path contains matlab files with metabolite-metabolite paths calculated from KEGG reaction-pair information (Each matrix contains a subset of paths). These files are used by the script workflow_extract_keggECpathes_for_SPpairs_final.m.</p> <p>Folder InputData_metabolomics_data contains raw metabolomics data from six methods (three LC columns: C08, C18 and HILIC, and positive and negative acquisition modes) and file tissue_weights.txt with tissue weight information used for normalization.</p> <p>Folder InputData_sequencing_data contains folders ballgown_DNA and ballgown_RNA with results of metagenomic and metatranscriptomic data analysis (raw counts, GetMM normalized counts, EdgeR and DeSeq2 analysis). </p> <p>Description of folders is provided in the file readme_InputData.md.</p> <p>-----------------------------------------------------------------------------------------------------</p>
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
<p><span>Intestinal microbes</span><span> regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal</span><span>, </span><span>and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha diversity of bacteria in </span><span>the ileum, colon, and </span><span>feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.</span></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>
Functional and metabolic alteration of gut microbiota in children with new-onset type 1 diabetes
<p>Worldwide T1D incidence has been steadily increasing annually over the past 30 years. The etiology of T1D is multifactorial, consisting of genetic susceptibility and environmental factors, including gut microbiota alterations. The comprehensive profiling of functional and metabolic dysbiosis of gut microbiota in T1D is lacking. To decipher the T1D-associated functional features of gut dysbiosis, we performed integrative metagenomic and metabolomic analyses in pediatric patients with new-onset T1D.</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.