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Dataset results
29 results for “Microbial Pathogens”
In vitro antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance
<p>Supplemental material to the publication "<i>In vitro</i> antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance"</p>
Distribution System Environmental and Sequencing Datasets for Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System
<p>The dataset of environmental parameters and sequence fastqs used to create figures and do analysis in the paper <strong>Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking Water Associated Pathogens in a Full-Scale Drinking Water Distribution System </strong>submitted to Environmental Science & Technology</p>
Pan-European database for pathogenic microbial taxa in birds and bats
<p><span>The spatially extensive multidimensional database of the prevalence of pathogenic microbial taxa for humans and wildlife in birds and bats was compiled by systematically reviewing publications for 121 pathogenic taxa. It covered pathogenic taxa mostly at the genus level (species level for most of the viruses), including sampling from ~450,000 host individuals of 376 bird species and 39 bat species. </span></p> <p><span>Data S1</span><span>. </span><span>Taxonomic details of the covered bird and bat species and pathogen prevalence of the most studied pathogenic microbial taxa in these host species. </span></p> <p><span>Data S2</span><span>. </span><span>Taxonomic details and sample sizes of the covered pathogenic microbial taxa.</span></p> <p><span>Data S3</span><span>. </span><span>Pan-European database for pathogenic microbial taxa from systematic review.</span></p> <p><span>Data S4</span><span>.</span><span> Input data for modelling. The filtered dataset follows the protocol </span><span>illu</span><span>strated in "Database quality control" of Methods in the corresponding article.</span></p> <p><span>Because the database includes endangered species that were listed by the IUCN as anything from Threatened or more severe, the geographical coordinates in the datasets were required by the platform to be masked as numbers with a scale of 1. The finer resolution coordinates (with a scale of 4) can be requested by contacting the corresponding author: Yanjie Xu (<a href="mailto:yanjie.xu5@gmail.com">yanjie.xu5@gmail.com</a> or <a href="mailto:yanjie.xu@helsinki.fi">yanjie.xu@helsinki.fi</a>).</span></p> <p><span>The comprehensive methods about the data collection and database quality control are illustrated in the corresponding article.</span></p> <p><span>Xu, Y., Poosakkannu, A., Suominen, K.M., Laine V.N., Lilley T.M., Pulliainen A.T. & Lehikoinen, A. (2023). Continental-scale climatic gradients of pathogenic microbial taxa in birds and bats. Ecography. https://doi.org/10.1111/ecog.06783</span></p>
Data from: Host species, pathogens, and disease associated with divergent nasal microbial communities in tortoises
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Raw data and code for: Arbuscular mycorrhizal fungus alters the phyllosphere microbial community of alfalfa and modifies plant defenses against dual pea aphid and pathogen attack
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Pan-European database for pathogenic microbial taxa in birds and bats
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Streptomyces pathogen suppressive activity in plant communities varying in diversity:Plant host and plant diversity effects on rhizosphere microbial community composition, diversity, structure, and function.
Effects of plant host and plant community diversity on soil rhizosphere microbial community composition, diversity, structure, and function were explored in long-term experimental plots. Soil samples were collected from the rhizosphere of one of 4 target plants species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, or Lupinus perennis) growing in 1, 4, 8, 16, or 32-species plots. Pathogen-suppressive activities of soil streptomycetes were determined for every sample. In addition, soil metagenomic analyses were performed targeting bacterial or streptomycete communities. Soil edaphic characteristics were determined for every sample. Analyses consider both the effects of plant host and plant community diversity on microbial community structure and function, and the relationships of diverse taxa with plant host, plant community diversity, and soil edaphic characteristics.
Data from: Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)
Bacterial gut symbiont communities are critical for the health of many insect species. However, little is known about how microbial communities vary among host species or how they respond to anthropogenic disturbances. Bacterial communities that differ in richness or composition may vary in their ability to provide nutrients or defenses. We used deep sequencing to investigate gut microbiota of three species in the genus Bombus (bumble bees). Bombus are among the most economically and ecologically important non-managed pollinators. Some species have experienced dramatic declines, probably due to pathogens and land-use change. We examined variation within and across bee species and between semi-natural and conventional agricultural habitats. We categorized as 'core bacteria' any operational taxonomic units (OTUs) with closest hits to sequences previously found exclusively or primarily in the guts of honey bees and bumble bees (genera Apis and Bombus). Microbial community composition differed among bee species. Richness, defined as number of bacterial OTUs, was highest for B. bimaculatus and B. impatiens. For B. bimaculatus, this was due to high richness of non-core bacteria. We found little effect of habitat on microbial communities. Richness of non-core bacteria was negatively associated with bacterial abundance in individual bees, possibly due to deeper sampling of non-core bacteria in bees with low populations of core bacteria. Infection by the gut parasite Crithidia was negatively associated with abundance of the core bacterium Gilliamella and positively associated with richness of non-core bacteria. Our results indicate that Bombus species have distinctive gut communities, and community-level variation is associated with pathogen infection.
FIGURE 8 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 8. Phylogenetic analysis was performed using the MEGA (version 5.0) program based on the four different amino acid sequences from various insects. The phylogenetic tree was constructed using the neighbor-joining algorithm method and bootstrap values (1000 repetitions) of the branches are indicated. The HSP90s from other organisms are: Antheraea pernyi (APX61061.1), Helicoverpa armigera (ATB54999.1), Spodoptera litura (ADK55517.2), Mythimna separata (ATN45250.1), Danaus plexippus plexippus (OWR53421.1), Bombyx mori (NP_001036876.1), Apis mellifera (NP_001153536.1), Plutella xylostella (NP_001296043.1), Drosophila melanogaster (NP_523899.1), Nilaparvata lugens (XP_022202749.1), Bicyclus anynana (XP_023945769.1);The PGRPs from other organisms are: Antheraea pernyi (AME17978.1), Samia ricini (BAF03522.1), Trichoplusia ni (XP_026737257.1), Helicoverpa armigera (AHK59818.1), Antheraea mylitta (ABG72709.1), Manduca sexta (AAO21509.1), Spodoptera litura (XP_022825445.1), Bombyx mori (NP_001036836.1);The Ras homolog genes from other organisms are: Spodoptera litura (XP_022819713.1), Vanessa tameamea (XP_026494920.1), Zootermopsis nevadensis (XP_021927562.1), Drosophila miranda (XP_017145574.1), Drosophila persimilis (XP_002015385.2), Nasonia vitripennis (XP_008209835.1); The MyD88s from other organisms are: Diaphorina citri (NP_001316117.1),Tribolium castaneum (XP_008190563.1), Drosophila melanogaster (NP_610479.1), Nasonia vitripennis (XP_008206894.1), Ceratitis capitata (XP_020716287.1), Bactrocera dorsalis (XP_011205590.1), Bombus terrestris (XP_003394201.1), Bombyx mori (XP_004921572.1), Antheraea pernyi (AHH80650.1).
FIGURE 7 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 7. RT-qPCR analysis of 11 immune-related DEGs in ML vs. PBS group. The y-axis shows relative expression levels (Blue colour represents the PBS control group and yellow colour represents the M. luteus treatment group, * p <0.05, **p <0.01).
FIGURE 6 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 6. RT-qPCR analysis of 19 immune-related DEGs in Bb vs. PBS group. The y-axis shows relative expression levels (Blue colour represents the PBS control group and red colour represents the B. bassiana treatment group, * p <0.05, **p <0.01).
FIGURE 4 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 4. GO classification of annotated differentially expressed genes in Bb vs. PBS group. The DEGs were categorized into 41 functional groups and were summarized in three main categories: biological process, cellular component and molecular function. The X-axis represents the number of genes noted on the GO item, and the Y-axis represents the GO functional classification.
FIGURE 5 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 5. GO classification of annotated differentially expressed genes in ML vs. PBS group. The DEGs were categorized into 41 functional groups and were summarized in three main categories: biological process, cellular component and molecular function. The X-axis represents the number of genes noted on the GO item, and the Y-axis represents the GO functional classification.
FIGURE 3 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 3. KEGG classification map of differentially expressed genes in ML vs. PBS group. The X axis was the number of genes annotated into a certain KEGG Pathway category, and the Y axis was the KEGG Pathway category. Different colors present different metabolic functions.
FIGURE 2 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 2. KEGG classification map of differentially expressed genes in Bb vs. PBS group. The X axis was the number of genes annotated into a certain KEGG Pathway category, and the Y axis was the KEGG Pathway category. Different colors present different metabolic functions.
Data from: Variation in gut microbial communities and its association with pathogen infection in wild bumble bees (Bombus)
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Data from: Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici
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FIGURE 9 in The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)
FIGURE 9. Larva and adult of Actias selene.
Data from: Microbial ‘gardening’ by a seaweed holobiont: surface metabolites attract protective and deter pathogenic epibacterial settlement
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International Space Station - Microbial Observatory of Pathogenic Virus Bacteria and Fungi project
This study investigated the interplay between the microbial community of the International Space Station and its crew. Environmental samples were collected from 8 habitable locations around the ISS. The microbial composition was measured using shotgun metagenomic sequencing and procesed using the Livermore Metagenomics Analysis Toolkit.
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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.