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360 results for “Microbes”
Central taxa are keystone microbes during early succession
<p>Project folder for publication "Central taxa are keystone microbes during early succession" containing: 1) scripts and raw data for data processing, 2) intermediate and final files output by scripts, and 3) RMarkdown files used to perform statistical analyses and generate figures. Descriptions of files, scripts, and folders in README files.</p><p>Manuscript Abstract:</p><p>Microorganisms underpin numerous ecosystem processes and support biodiversity globally, yet we understand surprisingly little about what structures environmental microbiomes themselves. Combining culturing, sequencing, and microbial networks, we identified 'central' (highly-connected, hub taxa), 'intermediate' (moderately-connected), and 'peripheral' (weakly/un-connected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession. Our results demonstrate central early colonizers significantly (1) enhanced biodiversity, (2) increased recruitment of additional influential, hub taxa, and (3) shaped microbiome assembly trajectories. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central, hub microbes are keystones.</p><p>This research was funded by: National Science Foundation (US) (DEB-1922521, DEB-2030060), Lisa D. Anness Fellowship (US), Maytag Fellowship University of Miami (US), Department of Biology University of Miami (US).</p>
ANTIBIOTICS AND MICROB'S ENDURANCE
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Data from: The microbiota of diapause: how host-microbe associations are formed after dormancy in an aquatic crustacean
1. A critical question in symbiosis research is where and how organisms obtain beneficial microbial symbionts in different ecological contexts. Microbiota of juveniles are often derived directly from their mother or from the immediate environment. The origin of beneficial symbionts, however, is less obvious in organisms with diapause and dispersal stages, such as plants with dormant seeds and animals in ephemeral or strongly seasonal habitats. In these cases, parents and offspring are separated in time and space, which may affect opportunities for both vertical and horizontal transmission of symbionts. 2. The planktonic crustacean Daphnia produces long-lasting resting eggs to endure winter freezing and summer droughts and requires microbiota for growth and reproduction. It is unknown how hatchlings from resting stages form associations with microbial consorts after diapause. 3. Using natural samples of D. magna resting eggs after several years of storage, we show that the total bacterial community derived from both the exterior and interior of the eggs' ephippial cases is sufficiently beneficial to ensure normal Daphnia functioning in otherwise bacteria-free conditions. We do not find direct evidence that the required bacteria are of maternal origin, though sequencing reveals that the resting stage is accompanied by bacterial taxa previously found in association with adult animals. 4. These findings suggest that while Daphnia are strongly dependent on environmental bacteria for normal functioning, host-bacteria associations are somewhat general and availability of specific bacteria is not a strong constraint on host ecology. Nevertheless, animals and microbes may be ecologically linked through co-dispersal.
Supplementary material 2 from: Parisy B, Schmidt NM, Wirta H, Stewart L, Pellissier L, Holben WE, Pannoni S, Somervuo P, Jones MM, Siren J, Vesterinen E, Ovaskainen O, Roslin T (2023) Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys. Metabarcoding and Metagenomics 7: e99979. https://doi.org/10.3897/mbmg.7.99979
Key to taxa for Figure 5, figures S11A and S11B
Supplementary material 1 from: Parisy B, Schmidt NM, Wirta H, Stewart L, Pellissier L, Holben WE, Pannoni S, Somervuo P, Jones MM, Siren J, Vesterinen E, Ovaskainen O, Roslin T (2023) Ecological signals of arctic plant-microbe associations are consistent across eDNA and vegetation surveys. Metabarcoding and Metagenomics 7: e99979. https://doi.org/10.3897/mbmg.7.99979
Complementary figures and details about the article
Microbe-derived uremic solutes enhance thrombosis potential in the host
<p>Microsoft Excel file containing source data for figures included in the manuscript "Microbe-derived uremic solutes enhance thrombosis potential in the host", by Nemet et al., published in mBio.</p>
BaiJ and BaiB are key enzymes in the chenodeoxycholic acid 7a-dehydroxylation pathway in the gut microbe Clostridium scindens ATCC 35704
<p>Data set for bile acid quantification for manuscript:</p> <p>BaiJ and BaiB are key enzymes in the chenodeoxycholic acid 7a-dehydroxylation pathway in the gut microbe Clostridium scindens ATCC 35704.</p> <p>By Karin Lederballe Meibom et al.</p> <p>Gut Microbes, 2024: 16:1, 2323233</p> <p>https://doi.org/10.1080/19490976.2024.2323233</p>
Effect of Dupilumab (Anti-IL4Rα) on the Host-Microbe Interface in Atopic Dermatitis
ClinicalTrials.gov study NCT03389893. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Plasma Host-Microbe Proteomics to Predict Complications in High-risk Febrile Neutropenia
ClinicalTrials.gov study NCT07277387. IPD Sharing: YES. Countries: 1. Publications: 0.
Serial Endoscopic Surveillance & Direct Topical Antibiotics to Define the Role of Microbes in Anastomotic Healing
ClinicalTrials.gov study NCT02682485. IPD Sharing: NO. Countries: 0. Publications: 2.
The Presence of Microbes in the Sperm and Their Impact on Sperm Capacitation and IVF Treatment
ClinicalTrials.gov study NCT02585297. IPD Sharing: Not stated. Countries: 0. Publications: 9.
Data from: Co-evolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection
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Data from: Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes
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Data from: Allometry of animal-microbe interactions and global census of animal-associated microbes
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Data from: Soil microbes alter plant fitness under competition and drought
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Data from: Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes
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Data from: Genotype specificity among hosts, pathogens, and beneficial microbes influences the strength of symbiont mediated protection
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Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
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Data from: The microbiota of diapause: how host-microbe associations are formed after dormancy in an aquatic crustacean
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Data from: Microbe-mediated host defence drives the evolution of reduced pathogen virulence
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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.