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2,708 results for “microbiota”
16S rRNA Sequencing Data of Fecal Microbiota in an Italian Cohort of Patients with CDKL5 Deficiency Disorder
<h3>Summary of the study </h3> <p>CDKL5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by global developmental delay, early-onset seizures, intellectual disability, visual and motor impairments, distinct from Rett Syndrome (RTT) due to the absence of a clear regression period. Gastrointestinal (GI) disturbances and signs of subclinical immune dysregulation are common in CDD patients, yet the underlying causes are unknown. Recent studies hint at a possible link between neurological disorders and gut microbiota, an unexplored area in CDD. In this groundbreaking study, we examined fecal microbiota in CDD patients and their healthy relatives, revealing differences in bacterial diversity and composition. We further investigated microbiota changes based on various factors, including the severity of GI issues, seizure frequency, sleep disorders, food intake type, neuro-behavioral features (assessed through the RTT Behaviour Questionnaire – RSBQ), and ambulation capacity. </p> <p>Our findings suggest a potential connection between CDD, microbiota, and symptom severity. This study represents the first exploration of the gut-microbiota-brain axis in CDD patients, contributing to the growing body of research on the role of gut microbiota in neurodevelopmental disorders. It opens doors to potential interventions targeting intestinal microbes to enhance the well-being of individuals with CDD.</p> <h3>Mehods</h3> <p>The Dataset represent the raw data (.fastq) obtained from the sequencing of the fecal samples from 17 Italian Patients with CDD, and 17 Healthy Relatives (i.e. siblings or mother), collected at a single time-point.</p> <p>Samples from Patients affected by CDD are called CDD, samples from Healthy Relatives are called HC-CDD (i.e. healthy controls of patients affected by CDD). For details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted from fecal samples using the QIAmp Powerfexal DNA Kit (Qiagen, Germany) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Germany).</p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). </p>
Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue - IMC+RNAScope images
<p><span>Intestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides.<span> </span>We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.</span></p>
Microbiota study Juvenile Idiopathic Arthritis AG Chang
<p>We have investigated a juvenile idiopathic arthritis (JIA) cohort and paediatric healthy controls (pHC) by our multi-parameter microbiota flow cytometry approach to characterise the microbiota on single-cell level for attributes of the disease. The microbiota is isolated from stool samples and stained according to the published protocol for (a) host immunoglobulins IgA1, IgA2, IgM, IgG and (b) agglutinin binding to mannose, galactose or N-Acetyl-glucosamine surface sugar moieties. For all samples we also determined the microbiome composition by 16S rRNA (V3-V4) sequencing on the illumina MiSeq platform. We provide the raw .fcs and FASTQ files of 54 JIA patients and 38 paediatric controls. For comparison towards disease progression, we additionally analysed 16 rheumatoid arthritis (RA) patients and 18 adult healthy donors (aHC).</p> <p>All .fcs files were generated on <span>BD Influx®.</span></p> <p> </p> <p>The metadata is collected in the provided meta_JIA.csv.</p> <p><span>The staining parameters are summarized in provided panel.csv. </span></p>
The gut microbiota affects the social network of honey bees
<p>This dataset contains input files needed to reproduce the automated behavioral tracking data analyses of the research article "The gut microbiota affects the social network of honey bees”. Codes using these data and additional datasets are available at: https://github.com/JoanitoLiberti/The-gut-microbiota-affects-the-social-network-of-honey-bees/</p> <p> </p>
Limited effect of thermal pruning on wild blueberry crop and its root-associated microbiota - Agricultural dataset
<p>These datasets contain all the agricultural data (soil chemistry, blueberry performance, weeds and diseases...) used in our study.</p>
Analysis Data, "Drivers and Determinants of Strain Dynamics Following Fecal Microbiota Transplantation"
<p>This package contains datasets in `Rdata` format that underlie the analyses presented in the study, "Drivers and Determinants of Strain Dynamics Following Fecal Microbiota Transplantation" by Schmidt, Li et al.<br> </p> <p>Corresponding code, referring to these datasets, is available via `github`:</p> <p>https://github.com/grp-bork/fmt_metastudy</p> <p> </p> <p>The study is available as a preprint:</p> <p>https://www.biorxiv.org/content/10.1101/2021.09.30.462010v1</p> <p> </p> <p>The present package contains processed/derived data. Metagenome-Assembled Genomes generated for the same study are available via `Zenodo` under:</p> <p>https://zenodo.org/record/5534163#.YpoRFy8RrzA<br> doi: 10.5281/zenodo.5534163</p>
MOLECULAR MIMICRY BETWEEN TUMOR ASSOCIATED ANTIGENS AND MICROBIOTA-DERIVED EPITOPES.
<p><strong>Background: </strong>The gut microbiota profile is unique for each individual and are composed by different bacteria species according to individual birth-to-infant transitions. In the last years, the local and systemic effects of microbiota on cancer onset, progression and response to treatments, such as immunotherapies, have been extensively described. Here we offer a new perspective, proposing a role for the microbiota based on the molecular mimicry of tumor-associated antigens by microbiome-associated antigens.</p> <p><strong>Methods:</strong> In the present study we looked for homology between published TAAs and non-self microbiota-derived epitopes. Blast search for sequence homology was combined with extensive bioinformatics analyses.</p> <p><strong>Results:</strong> Several evidences for homology between TAAs and microbiota-derived antigens have been found. Strikingly, three cases of 100% homology between the paired sequences has been identified. The predicted average affinity to HLA molecules of microbiota-derived antigens is very high (<100nM). The structural conformation of the microbiota-derived epitopes is, in general, highly similar to the corresponding TAA. In some cases, it is identical and contact areas with both HLA and TCR chains are indistinguishable. Moreover, the spatial conformation of TCR-facing residues can be identical in paired TAA and microbiota-derived epitopes, with exactly the same values of planar as well as dihedral angles.</p> <p><strong>Conclusions:</strong> The data reported in the present study show for the first time the high homology in the linear sequence as well as in structure and conformation between TAAs and peptides derived from microbiota species of the Firmicutes and the Bacteroidetes phyla, which together account for 90% of gut microbiota. Cross-reacting CD8<sup>+</sup> T cell responses are very likely induced. Therefore, the anti-microbiota T cell memory may turn out to be an anti-cancer T cell memory, able to control the growth of cancer developed during the lifetime if the expressed TAA is similar to the microbiota epitope. This may ultimately represent a relevant selective advantage for cancer patients and may lead to a novel preventive anti-cancer vaccine strategy.</p>
STORMS checklist: Dysbiosis of the enteric microbiota due to Crohn's disease treatment associated with MAIT cell activation
<p>STORMS checklist initiative to standardize reporting of human microbiome research, regarding submission to peer-reviewed journal.</p>
Complex plant quality - microbiota - population interactions modulate the response of a specialist herbivore to the defense of its host plant.
<p>1. Many specialist herbivores have evolved strategies to cope with plant defenses, with gut microbiota potentially participating to such adaptations.</p> <p>2. In this study we assessed whether the history of plant use (population origin) and microbiota may interact with plant defense adaptation.</p> <p>3. We tested whether microbiota enhance the performance of <em>Melitaea cinxia </em>larvae on their host plant, <em>Plantago lanceolata</em> and increase their ability to cope the defensive compounds, iridoid glycosides (IGs).</p> <p>3. The gut microbiota was significantly affected by both larval population origin and host plant IG level. Contrary to our prediction, impoverishing the microbiota with antibiotic treatment did not reduce larval performance.</p> <p>5. As expected for this specialized insect herbivore, sequestration of one of IGs was higher in larvae fed with plants producing higher concentration of IGs. These larvae also showed metabolic signature of intoxication (<em>i.e. </em>decrease in Lysine levels). However, intoxication on highly defended plants was only observed when larvae with history of poorly defended plants were simultaneously treated with antibiotics.</p> <p>6. Our results suggest that both adaptation and microbiota contribute to the metabolic response of herbivores to plant defense though complex interactions.</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>
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>
Genome of the isolates: Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities
<p>The draft genome of the isolates in Mouse Intestinal Bacteria Collection (miBC)</p> <p> </p> <p>Microbiome research is hampered by the fact that many bacteria are still unknown and by the lack of publicly available isolates. Fundamental and clinical research is in need of comprehensive and well-curated repositories of cultured bacteria from the intestine of mammalian hosts. Due to host-specific features of the gut microbiota, it is sound to establish collections of isolates from single host species. Hence, this project established a collection of bacterial strains isolated from the intestine of mice.</p> <p>The original version of the collection published in 2016 (Lagkouvardos, et. al. 2016.<em> Nat. Microbiol.</em>). was doubled by the addition of 112 strains, representing a total of 141 species across 6 phyla and 35 families for the entire collection. As we aimed to create a well-curated resource, all bacterial species within miBC have been taxonomically described and are publicly available.</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>
Figure 6 in Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota
Figure 6. Neighbor-Joining consensus tree (A) and Haplotype network analysis (B) of the Spiroplasma in G. tachinoides in Burkina Faso and Ghana. (A) Neighbor-Joining consensus tree was built after alignment of all the concatenated sequences. The method used to calculate the distance was Tamura-Nei. (B) Haplotype network generated based on the ML tree which was generated based on Spiroplasma sequences. The black lineaments on the lines represent mutation events between the haplotypes. The different colors represent the locations. The reference sequence of Spiroplasma in G. fuscipes fuscipes species (KX159391) was used as the outgroup for construction of both phylogenetic tree and haplotype network.
Figure 2 in Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota
Figure 2. Prevalence of Spiroplasma according to location. Bars marked with the same lower-case letter do not differ significantly at the 0.05 level.
Figure 5 in Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota
Figure 5. Normalized density of Spiroplasma (A), Trypanosoma (B), and Wigglesworthia (C) according to Spiroplasma-Trypanosoma co-infection in wild G. tachinoides. Bars marked with the same lower-case letter do not differ significantly at the 0.05 level.
Figure 3 in Prevalence of Spiroplasma and interaction with wild Glossina tachinoides microbiota
Figure 3. Prevalence of Spiroplasma and Trypanosoma (single and multiple) infections per country, location, and sex. Prevalence data were square root transformed and averaged based on location-sex and the matrix display was conducted in PRIMER version 7 + software. Tree on the left of the matrix is the similarity dendrogram based on the similarity index of the square root of the prevalence values. The color index is the square root of the prevalence values ranged 0–9 which is the square root of 0–81% prevalence.
Figure 2 in Occurrence of ticks and tick-borne mixed parasitic microbiota in cross-bred cattle in District Lahore, Pakistan
Figure 2. RLB specific primer PCR detection of DNA in cross-bred Cattle (Friesian x Sahiwal). L1 100bp ladder. L2 & L3 negative control, L4 PCR positive control. L6, L8, L9, L11, L12, L13, L15, L16, L17, L18, L19 positive for protozoan specific to primers.
Illumina Sequencing Data for "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes"
<p>Illumina Sequencing Data for Sulaiman et al., "Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes".</p>
Data and code: Gut microbiota structure differs between honey bees in winter and summer
<p>This dataset contains data and code underlying the qPCR, amplicon sequencing, and statistical analysis of the research article "Gut microbiota structure differs between honey bees in winter and summer”. Short read datasets are available under NCBI Bioproject accession PRJNA578869.</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.