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360 results for “microbes”
Dataset: Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef
<p>This dataset contains raw data for figures 5 (genus-level microbial community compositions) and 6 (predicted metabolic functions, pathway types), R code for PERMANOVAs (Table 3), DESeq2 and random forest (rfpermute) analyses, and R code to generate figures 5, 6b, S5 & S6.</p> <p>Overview of .txt files:</p> <table> <tbody> <tr> <td> <p>Genus_16S_Counts.txt</p> </td> <td> <p>Counts data used for DESeq2 analysis (Fig. 5c).</p> </td> </tr> <tr> <td> <p>Genus_16S_relAbund.txt</p> </td> <td> <p>Relative abundance data used for Fig. 5a, b & d.</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_types_all</p> </td> <td> <p>Predicted pathway abundance data for all pathway types used for DESeq2 (Fig. 6b), PERMANOVA (Table 3) and column clustering of Fig. 6b.</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_AA_types.txt</p> </td> <td> <p>Amino acids (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_CH_types.txt</p> </td> <td> <p>Carbohydrates (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_EM _types.txt</p> </td> <td> <p>Energy metabolism (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_FAL _types.txt</p> </td> <td> <p>Fatty acids and lipids (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_SM _types.txt</p> </td> <td> <p>Secondary metabolism (Fig. 6b)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_OBiosyn _types.txt</p> </td> <td> <p>Other biosynthesis (Fig. S6)</p> </td> </tr> <tr> <td> <p>MicFunPred_MetaCyc_ODeg _types.txt</p> </td> <td> <p>Other degradation (Fig. S6)</p> </td> </tr> </tbody> </table>
Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples
<p>Welcome!</p> <p>Here you will find the codes used in the analysis we ran for our manuscript titled "Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples". We would be happy to help in way we can, so please do not hesitate to reach out if you have questions or suggestions.</p> <p>In summary, we developed this study in response to challenges encountered in our own field research. Recent advancements in culturomics and microbiology are enabling us to further explore the realm of microbiome science. We aspire for this study to serve as a foundational step toward identifying preservation methods that can help protect the microbial communities of wild animals.</p> <p>Our study aims are:</p> <ol> <li>The primary objective of this study was to evaluate the effectiveness of various preservation solutions in maintaining microbial integrity of gut samples during collection and for a short duration, simulating transportation conditions, prior to long-term storage at -80°C. We cultivated the samples in three distinct culture media to maximize the recovery of microbial diversity.</li> <li>The second objective was to compare the inventory of the preserved and cultured microbial community to that of the original uncultured samples, aiming to determine whether the preservation solutions retained unique taxa absent in the frozen original samples.</li> </ol> <p>Notes to keep in mind:</p> <ol> <li>We chose preservation solutions that have already been described for microbial culturing.</li> <li>We chose culture media that have already been described for microbial culturing, especially gut microbiome samples.</li> </ol> <p><em>As you go through the Rmd document included here, please make sure all documents have been properly downloaded. Additionally, please make sure to change the names of the alpha diversity metric files in the Rmd to that of the files here as they were modified for proper uploading methods here. </em></p>
Data for: Soil microbes alter competition between native and invasive plants
<p>Invasive plants can alter soil microbial communities and generate positive plant-soil feedbacks that facilitate their performance, but the magnitude and direction of feedbacks may change with novel conditions under climate change. We assessed how potential soil legacy effects of plant invasion and simulated drought influenced plant performance and competition in the longleaf pine ecosystem.</p> <p>We collected soil from a four-year factorial invasion (cogongrass, <i>Imperata cylindrica</i>) by drought (simulated with rainout shelters) field experiment and used it as live or sterilized soil inoculum in a greenhouse experiment that included two native foundation species, longleaf pine (<i>Pinus palustris</i>) and wiregrass (<i>Aristida stricta</i>), and cogongrass, grown individually or in competition.</p> <p>There was no evidence of biotic soil legacy effects of invasion or drought for any plant species, but microbes played a significant role in competition. When plants were grown alone, the invader had 12% greater biomass in live soil than sterile soil but both native species had 25% less biomass in live soil. When grown in competition, these effects were reversed for cogongrass (37% smaller in live soil) and pine (17% larger in live soil). In competition, the three species grown in sterile soil produced similar amounts of biomass, whereas live soil created a competitive hierarchy where pine was more competitive than wiregrass and cogongrass.</p> <p>Synthesis: These results emphasize the importance of soil biota in native plant restoration because, although the invader was highly successful when grown alone, plant-microbe interactions influenced the outcome of competition between native and invasive species by promoting native longleaf pine. There was little evidence that invasive cogongrass inhibited native plants via biotic soil legacies, instead, results suggested that plant-soil interactions can be highly resilient to global change such that the biotic legacy of invasion and drought may not promote or inhibit invasion.</p>
Salamander skin microbiome sample metadata: Variation in amphibian skin microbes
<p>These data are associated with a study that explores variation in microbial communities on western tiger salamander skin (<em>Ambystoma</em> <em>mavortium</em>) through space, time, and across life history stages. Lake water and lake substrate microbiome samples were collected to observe microbial taxa which were disproportionately abundant between salamander skin and the environment. Microbiome samples were collected at two lakes during the summer and fall of 2018, and sampling occurred at each lake every other week. During each sampling event, water quality data were collected at four or five locations within the lake and are associated with microbiome samples collected in the lake's respective regions. For each sample, bacterial and fungal communities were examined through metabarcoding of the 16S and ITS metabarcoding regions, respectively, using Illumina next-generation sequencing. The dataset includes negative control samples to aid in detecting contamination, and the dataset includes mock community samples to aid in validating our bioinformatics methods. Each sample received spike-ins of cross-contamination oligos and synthetic genes to observe cross-contamination during library preparation and to allow for the estimation of absolute microbial abundances, respectively. This dataset includes spatiotemporal, ontogenetic, morphometric, and water quality metadata for microbiome samples along with essential information for processing the DNA sequence data.</p>
Isotopic evidence for increased carbon and nitrogen exchanges between peatland plants and their symbiotic microbes with rising atmospheric CO2 concentrations since 15000 cal. yr BP
<p>Whether nitrogen (N) availability will limit plant growth and removal of atmospheric CO<sub>2</sub> this century is controversial. Studies have suggested that N could progressively limit plant growth, as trees and soils accumulate N in slowly cycling biomass pools in response to increases in carbon sequestration. However, a question remains over the longer-term (decadal to century) feedbacks between climate, CO<sub>2</sub> and plant N uptake. The symbiosis between plants and microbes can help plants with mycorrhizal N uptake or biological N2 fixation – the pathway through which N can be rapidly brought into ecosystems and thereby partially or completely alleviate N limitation on plant productivity. Here we present results for plant N isotope composition (δ<sup>15</sup>N) in a peat core that dates to 15000 cal. yr BP to ascertain ecosystem-level N cycling responses to rising atmospheric CO<sub>2</sub> concentrations in the past. We found that an increase in atmospheric CO<sub>2</sub> concentration happened with a decrease in δ<sup>15</sup>N values of both <em>Sphagnum</em> moss and Ericaceae over this time period when constrained for climatic factors. A modern experiment demonstrated that δ<sup>15</sup>N of <em>Sphagnum</em> mosses decreased with increasing N2 fixation rates. These findings suggested that N2 fixation in <em>Sphagnum</em> moss by symbiosis with cyanobacteria and N uptake in Ericaceae by symbiosis with mycorrhizal fungi both likely increased with rising atmospheric CO<sub>2</sub> concentrations, highlighting a longer-term feedback mechanism whereby N constraints on terrestrial carbon storage can be overcome. </p>
Dataset: The dispersal of microbes among and within flowers by butterflies
<p>This data set was collected to examine the ability of Lepidoptera to transport microbes among flowers, while foraging. The first set, "experiment 1", records bacteria and yeasts carried by two species of generalist-nectar-feeding butterflies, <em>Speyeria mormonia </em>and <em>Glaucopsyche lygdamus</em>. We captured wild butterflies in the central Colorado Rockies. We recorded butterfly species, sex, wing wear (which measures age, from 1 = youngest to 5 = oldest), date caught, date tested, and the number of colonies on a YM plate that was streaked by the proboscis, or by a wash from the thorax or by allowing the butterfly to walk across the plate.</p> <p>The second data set, "experiment 2", records the number of colonies of a test bacteria, <em>Rhodococcus fascians</em>, on stigma, anthers and nectaries of <em>Pyrrocoma</em> <em>crocea</em>. Data were collected using flowerheads and adult <em>Speyeria mormonia </em>collected in the field. A butterfly was allowed to feed on a floret; the floret was immediately dissected, and the stigma, anthers and nectaries streaked on a YM plate. A floret on a second flowerhead was then innoculated with the bacteria. The butterfly was allowed to feed on the innoculated floret, and the floret was immediately dissected and parts streaked as for the training floret. The butterfly then fed on a floret in the first flowerhead, and that floret was immediately dissected and parts streaked as for other florets. Data include the identity, sex and wing wear of the butterfly, the date captured, the date the experiment was run, the number of colonies of <em>R. fascians</em> from stigma, anthers and nectaries of all three floret types.</p>
Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response
<p>We examined the role of the plant vs the environment in selecting for beneficial microbes to plants in their home moisture environment, in either wet vs dry conditions. To this end, we first conditioned soil microbial communities, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After 3 plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants, using the soil from the prior 3 generations as an inoculum. From plants inoculated with these ‘evolved’ soils, we measured plant biomass and height. We also measured soil nitrogen of the inoculum, and measured inoculum respiration across a water content gradient. <br> </p>
Prochlorococcus marinus digital microbe
<p>This is the digital microbe describing the model organism Prochlorococcus marinus MIT 9301. The data includes:</p> <p>- (P_MARINUS_MIT9301-contigs.db) the complete genome sequence of P. marinus MIT 9301, along with NCBI PGAP gene annotations and automatically-generated annotations from NCBI COGs, KEGG KOfam/BRITE, Pfams, and anvi'o single-copy core gene sets.</p> <p>- (P_marinus_reproducible_workflow.md) a reproducible workflow describing how the database was generated.</p>
Gut microbe compositions in High Fat diet
<p>This study aimed to explore the relationship between the gut microbiome and liver function, with the objective of identifying a specific bacterial species that may exhibit beneficial effects in improving the symptoms of NAFLD. We conducted a comparative analysis of the gut microbiome composition between mice fed a normal chow (NC) diet and mice fed a high-fat (HF) diet in order to identify specific gut microbes. The consumption of a high-fat diet led to a decrease in the prevalence of Kineothrix bacteria. To assess the effects of Kineothrix on liver health, we conducted a comparative analysis of the gut microbiome composition between mice fed a diet high in fat and fructose (HFHF), with and without the administration of Kineothrix.</p>
Data from: Soil microbes mediate the effects of resource variability on plant invasion
<p>A fundamental question in ecology is which species will prevail over others amid changes in both environmental mean conditions and their variability. Although the widely accepted fluctuating resource hypothesis predicts that increases in mean resource availability and variability therein will promote non-native plant invasion, it remains unclear to what extent these effects might be mediated by soil microbes. We grew eight invasive non-native plant species as target plants in pot-mesocosms planted with five different synthetic native communities as competitors and assigned them to eight combinations of two nutrient-fluctuation (constant vs pulsed), two nutrient-availability (low vs high) and two soil-microbe (living vs sterilized) treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of non-native plants under overall low nutrient availability, whereas the nutrient fluctuation had minimal effect under high nutrient availability. In contrast, when plants grew in living soil, nutrient fluctuation promoted the dominance of non-native plants under high nutrient availability rather than under low nutrient availability. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the relative abundance of the most dominant pathogenic fungal family or genus under high nutrient availability, while decreasing it under low nutrient availability. Our findings are the first to indicate that besides its direct effect, environmental variability could also indirectly affect plant invasion via changes in soil microbial communities.</p>
Designing a Synthetic Microbial Community through Genome Metabolic Modeling to enhance Plant-Microbe Interaction
<p>Supplementary data 1 - <strong>Reconstructed genome-scale metabolic networks from MAGs and Hosts</strong></p> <p>Supplementary data 2 - P<strong>lant growth-promoting traits among members of the minimal community</strong></p> <p> </p> <p>Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynCom, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and a careful selection of compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed an <em>in-silico</em> approach using genome metabolic modeling to design a synthetic microbial community aimed at improving the yield of important crop plants. We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, EPS production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our selection process for the SymCom, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. Our study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.</p>
Heatwave grazing kelp microbes sequences
<p class="MsoNormal"><span>The range-expansion of tropical herbivores due to ocean warming can profoundly alter temperate reef communities by overgrazing the seaweed forests that underpin them. Such ecological interactions may be mediated by changes to seaweed-associated microbiota in response to warming, but empirical evidence demonstrating this is rare. We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp <em>Ecklonia radiata</em>'s microbiotain sustained warming and MHW treatments were enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid <em>Sargassum linearifolium</em>'s microbiota was unaffected by temperature<em>.</em> Consumption by the tropical sea-urchin <em>Tripneustes gratilla </em>was greater on <em>Ecklonia</em> where the microbiota had been altered by higher temperatures, while <em>Sargassum</em>'s consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. Effects of warming and MHWs on seaweed holobionts (host plus its microbiota) are likely species-specific. The effect of increased temperature on <em>Ecklonia</em>'s microbiota and subsequent increased consumption suggest that changes to kelp microbiota may underpin kelp-herbivore interactions, providing novel insights into potential mechanisms driving change in species' interactions in warming oceans.</span></p>
Gut Microbe Composition, Exercise, and Breast Breast Cancer Survivors
ClinicalTrials.gov study NCT04088708. IPD Sharing: YES. Countries: 1. Publications: 1.
Dispersal of nectar microbes in California flowering communities
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Temperature perturbation of cellular host-microbe interactions explains continent-wide endosymbiont prevalence
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Data from: The effect of root-associated microbes on plant growth and chemical defence traits across two contrasted elevations,
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Dataset: The dispersal of microbes among and within flowers by butterflies
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Nutrient availability and invader density regulate the diversity–invasibility relationship mediated by soil microbes
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Data for: Soil microbes alter competition between native and invasive plants
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Data from: Insect-microbe-fungus interplay in citrus agro-ecosystems: Cuticular symbionts mediate <em>Diaphorina citri</em> resistance to <em>Beauveria bassiana</em>
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ScienceDex guides
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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.