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360 results for “Microbes”
Expanded catalog of metagenome-assembled genomes reveals resistome characteristics athletic performance- associated microbes in horse
<p><strong>Background</strong><br> As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.<br> <strong>Results</strong><br> Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing wide use of antibiotic in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in elite racehorses than that in normal horses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fiber fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.<br> <strong>Conclusions</strong><br> Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalog for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.</p>
Data from: Root inoculation with beneficial soil microbes enhances indirect plant defenses induced by insect feeding and egg deposition
<p>Plants can respond to insect egg deposition by emitting oviposition-induced plant volatiles (OIPVs) recruiting parasitoids. The recruitment of carnivore insects in response to egg deposition is considered an indirect defense strategy that is widespread in the plant kingdom. In recent years, there has been increasing evidence showing that microbial colonization can influence the strength of plant responses to insect herbivory, yet no information is available on how beneficial microbes modulate indirect defenses induced by insect egg deposition. In this work, we evaluated the effects of inoculation with the beneficial soil fungus <em>Trichoderma harzianum</em> strain T22 on a tritrophic system consisting of tomato, the southern green stink bug <em>Nezara viridula</em> and its associated egg parasitoid <em>Trissolcus basalis</em>. We used Y-tube olfactometer assays to evaluate the behavioral responses of the parasitoids to OIPVs emitted by plants colonized with beneficial soil microbes. We also used gas chromatography coupled with mass spectrometry (GC-MS) to investigate how root inoculation with <em>T. harzianum</em> T22 affects the chemical composition of induced plant volatiles. 3. In olfactometer assays, we found that root inoculation with <em>T.</em> <em>harzianum</em> T22 enhanced the attraction of the egg parasitoid towards tomato plants induced by <em>N. viridula</em> feeding and oviposition activities. In particular, the egg parasitoid preferred OIPVs emitted by tomato plants previously inoculated with <em>T. harzianum</em> T22 over OIPVs emitted by non-inoculated plants. Furthermore, chemical analysis showed that root inoculation with <em>T. harzianum</em> T22 resulted in changes in the composition of OIPVs, which was consistent with the behavioral observations. Among the compounds that strongly contribute to the chemical differences between OIPVs from non-inoculated and inoculated plants, chemical analysis identified green leaf volatiles ((Z)-3-hepten-1-ol, (E,E)-2,4-hexadienal), along with terpenoids (terpinen 4-ol, α-tujene and δ-elemene). 4. Taken together our results indicate that beneficial soil microbes enhance indirect plant defenses induced by feeding and oviposition, broadening our understanding of plant responses to insect eggs. Our results underscore the importance of taking into account the role of microorganisms to fully comprehend the intricate interactions among plants, herbivore eggs and their associated egg parasitoids.</p>
Data for: Iron limitation differentially affects viral replication in key marine microbes
<p>Data for a draft manuscript entitled: Iron limitation differentially affects viral replication in key marine microbes</p>
Continental scale α- and β-diversity patterns of terrestrial eukaryotic microbes: effect of climate and microhabitat on testate amoeba assemblages in Eurasian peatlands
Open the record for dataset details and reuse information.
Structural and functional dynamics of soil microbes following bark beetle infestation
<p>Provided are the bacterial and fungal phyloseq objects for Structural and functional dynamics of soil microbes following spruce beetle infestation". Authored by: Gordon Custer, Dr. Linda van Diepen, and Dr. William Stump. All of the University of Wyoming</p>
Dataset related to "Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution"
<p>Three .zip files contain the PDB files, mature protein sequences (without predicted signal peptides), and corresponding JSON files from AlphaFold2 containing pLDDT scores.</p> <p>Two .output files contain the all-vs-all sequence and structural similarity scores.</p>
Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth
<p>Project folder for publication "Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth" containing: 1) scripts 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><span>As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they <span> </span>are integral to ecosystem health and functioning. Despite microbiomes’ importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration – fungal microbiomes’ importance in “reconstructive” restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature – tree islands – in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared to their natural <span> </span>counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on <span> </span>constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.</span></p>
In situ sampling uncovers seasonal variability in community structure and metabolism of active deep-sea microbes
<p>Non-rRNA metatranscriptome and MAG datasets of research "In situ sampling uncovers seasonal variability in community structure and metabolism of active deep-sea microbes"</p>
Data from: Using a 'time machine' to test for local adaptation of aquatic microbes to temporal and spatial environmental variation
Local adaptation occurs when different environments are dominated by different specialist genotypes, each of which is relatively fit in its local conditions and relatively unfit under other conditions. Analogously, ecological species sorting occurs when different environments are dominated by different competing species, each of which is relatively fit in its local conditions. The simplest theory predicts that spatial, but not temporal, environmental variation selects for local adaptation (or generates species sorting), but this prediction is difficult to test. Although organisms can be reciprocally transplanted among sites, doing so among times seems implausible. Here we describe a reciprocal transplant experiment testing for local adaptation or species sorting of lake bacteria in response to both temporal and spatial variation in water chemistry. The experiment used a −80 °C freezer as a 'time machine'. Bacterial isolates and water samples were frozen for later use, allowing transplantation of older isolates 'forward in time' and newer isolates 'backward in time'. Surprisingly, local maladaptation predominated over local adaptation in both space and time. Such local maladaptation may indicate that adaptation, or the analogous species sorting process, fails to keep pace with temporal fluctuations in water chemistry. This hypothesis could be tested with more finely-resolved temporal data.
Data from: Changes in plant, soil and microbes in a typical steppe from simulated grazing: explaining potential change in soil carbon
Grazing can directly or indirectly influence carbon (C) inputs, turnover, and retention in grassland soil. However, relative to the plant response to grazing, belowground biota and process responses are more complex and often do not correlate with the aboveground responses. Ungulate grazing involves three mechanisms - defoliation (removal of plant shoot tissue), dung and urine return, and trampling. An evaluation of the relative roles of these mechanisms and their combinations in grazing can explain the causes of changes in grassland, thereby explaining the soil carbon sequestration in a steppe ecosystem. In this study, we examined the changes in plants attributes, soil abiotic characteristics, and the soil microbial community in response to mowing (M), dung and urine addition (DU), simulated trampling (T), and their combinations by conducting a 3-year experiment in a steppe ecosystem in Inner Mongolia, China. Most of the variation in the grazing effects on grassland was explained by defoliation through decreased plant production and soil respiration and altered vegetation composition. Dung and urine return was second to defoliation in explaining grazing effects on grassland, and lead to increasing plant C inputs to the soil, while simultaneously potential loss of soil C due to the increase of the abundance of bacteria and soil respiration, eventually accelerated soil C cycling. An interaction between defoliation and trampling on microbial growth was observed in our study: trampling increased the abundance of total bacteria, fungi, and AMF only in the no-mowing plots. Trampling led to plant allocation to the belowground tissues and increased the abundance of fungi and AMF, which is critical for soil carbon sequestration, and trampling with defoliation further decreased the abundance of soil microbes, which may decelerate soil C cycling and increase its retention time. These results indicate that defoliation and dung and urine return play major roles in explaining grazing effects on grassland systems, including plant, soil, and microbe parameters examined, but the trampling effects and the interaction between defoliation and trampling are the two key factors that contribute to explaining the overall effects of grazing on soil carbon sequestration in a typical steppe ecosystem in Inner Mongolia.
Effect of emodin on lung inflammation and intestinal microbes in Chronic Obstructive Pulmonary Disease
<p><strong>Effect of emodin on lung inflammation and intestinal microbes in Chronic Obstructive Pulmonary Disease</strong></p>
Experimental evidence root-associated microbes mediate seagrass response to environmental stress
<ol> <li>Below-ground microbiota play an important role in mediating environmental conditions with important consequences for plant performance. Microorganisms involved in plant-soil interactions may be associated with roots or bulk-soil; however, the relative influence of these below-ground microbial assemblages on plant performance is poorly known, particularly for marine plants. </li> <li>We separately manipulated the root and sediment microbial assemblages of the seagrass <em>Zostera muelleri</em> in a fully factorial experiment to determine how these assemblages determined plant response (e.g., growth) to nutrient enrichment, a major stressor in marine systems. </li> <li>Under ambient nutrient conditions, seagrass growth was maintained regardless of root microbial assemblage disruption. Under high nutrient stress, however, seagrasses with disrupted root microbiota had reduced growth, whereas growth was maintained in seagrasses with an intact root microbiota. Disruption of bulk-sediment microbiota did not affect seagrass growth. Nutrient elevation was correlated to enhanced abundances of several putatively beneficial microbial taxa (e.g. sulfide-oxidizing Beggiatoaceae and denitrifying <em>Geofilum rubicundum</em>) associated with roots. </li> <li> <em>Synthesis</em>: Our results suggest that under ambient nutrient conditions, microorganisms play a reduced role in influencing plant performance, but under more stressful conditions positive plant-root microorganism interactions strengthened. These results are among the first to experimentally determine that interactions between marine plants and the root-associated microbiota are key drivers of seagrass performance under human-induced environmental changes. This suggests that as in terrestrial systems, marine plant resilience depends on the stress-mitigating functions of their root-associated microbiota and disturbance to those plant-microbiota interactions can be deleterious for plant performance. Improving our understanding of these plant-microorganism interactions may be critical for understanding the functioning and resilience of threatened marine plants and developing more effective restoration strategies for them.</li> </ol>
Project SHARE (motherS Have All the Right microbEs)
ClinicalTrials.gov study NCT03239197. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Transplantation of Microbes for Treatment of Metabolic Syndrome & NAFLD
ClinicalTrials.gov study NCT02496390. IPD Sharing: NO. Countries: 1. Publications: 7.
Molecular Analysis of Intracanal Microbes After Chemomechanical Procedure and Root Canal Medication: A Randomized Controlled Trial
ClinicalTrials.gov study NCT06291623. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Pan-TB Regimen Targeting Host and Microbe
ClinicalTrials.gov study NCT05686356. IPD Sharing: YES. Countries: 3. Publications: 0.
The Impact of Maternal Microbes on Infant Health Programming
ClinicalTrials.gov study NCT03552939. IPD Sharing: Not stated. Countries: 1. Publications: 10.
DIetary plAnt Extracts, Colonic MicrObes, and Apoe geNetics Interactions stuDy
ClinicalTrials.gov study NCT05905822. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Effect of a Propolis Tablet on the Saliva and the Amount of Adolescent Dental Plaque Microbes
ClinicalTrials.gov study NCT03394729. IPD Sharing: NO. Countries: 1. Publications: 1.
Missing Microbes in Infants Born by Cesarean Section
ClinicalTrials.gov study NCT04134819. IPD Sharing: NO. Countries: 1. Publications: 1.
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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.