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915 results for “metagenomics”
Whole metagenome profiles of particulates collected from the International Space Station.
The microbial composition of the International Space Station (ISS) environment is of critical interest due to potential impact of its constituents on human health and operational mission success. This study examined the whole metagenome of ISS microbes at both a species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Samples were collected from ISS and cleanroom environments and treated to examine DNA from total versus viable populations. Microbial genes relevant to human health such as antimicrobial resistance and virulence genes were quantified.
SpaceX Inspiration4 Stool Metagenome Profiling
The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included stool collected in OMNIgene•GUT tubes (DNA Genotek, OMR-200). Samples were collected pre-flight (L-92, L-44) and post-flight (R+45, R+82). This study hosts stool data. Additional skin, oral and nasal metagenome data is deposited in OSD-572. Dragon capsule data metagenome is deposited in OSD-573. Skin biopsy-site metagenome data is deposited in OSD-574.
SpaceX Inspiration4 Dragon Capsule Metagenomic and Metatranscriptomic Microbial Swabs
The SpaceX Inspiration4 mission was a 3-day mission with four private astronauts to low Earth orbit that occurred in September 2021. The crew collected biospecimen samples before, during, and after flight. One of these biospecimen collections included microbial swabs collected from nine surfaces in the Dragon capsule (execute button, G-meter button, control touch screen - left, control touch screen - right, side hatch mobility aid, lid of waste locker, seat 2, commode panel, viewing dome) and one open air control. Swabs were collected twice during flight (flight day 2 (FD2), and flight day 3 (FD3)) and twice pre-flight in the crew training capsule in Hawthorne, CA (L-92, L-44). Swabs were stored in 400uL of Zymo Research DNA/RNA Shield at 4C until nucleic acid extraction. DNA and RNA were extracted from the same swab to generate metagenomic and metatranscriptomic profiles.
Metagenomic analysis of feces from mice flown on the RR-9 mission
The objective of the Rodent Research-9 (RR-9) mission was to use mice to understand the molecular basis of phenomena that affect astronauts during long-duration spaceflight, particularly visual impairment and joint tissue degradation. To this end, a flight group (FLT) of 10-week-old male C57BL/6J mice was launched from Kennedy Space Center (KSC) on 8/14/2017 and housed in Rodent Habitats on the ISS for 33 days before being returned alive to Earth. After splashdown in the Pacific Ocean, the animals were transported to Loma Linda University (LLU) for testing, euthanasia and dissection on 9/18/2018. A Basal Control (BSL) was housed in standard cages at Kennedy Space Center (KSC) and euthanized one day after launch of the FLT animals (8/15/2017). Ground Control (GC) and Vivarium Control (VIV) studies were planned to commence at KSC approximately one-week after the conclusion of the flight experiments. However, all the GC and VIV mouse studies at KSC had to be cancelled due to Hurricane Irma and potential adverse effects on the animal housing facility. The GC and VIV studies were therefore rescheduled and begun in May, 2018. The GC was euthanized and dissected 6/18/2018 - 6/20/2018, while the VIV was euthanized and dissected 6/22/2018 - 6/23/2018. Because this resulted in a different cohort of mice being used for the GC and VIV controls as compared to the flight (FLT) and basal (BSL) groups, two cohort controls were included in the study. The first, Cohort Control 1 (CC_C1), was from the same cohort as the FLT and BSL animals, and was sacrificed and dissected 4 days after the FLT group (9/22/2017). The second, Cohort Control 2 (CC_C2), was from the same cohort as the GC and VIV animals, and was sacrificed and dissected 2-8 days after the GC and VIV groups, (6/24/2018 - 6/26/2018). The CC_C1 and CC_C2 groups were housed in standard cages and fed standard chow in contrast to all other groups which received Rodent Foodbars. To clarify the connections between treatment groups and animal cohorts, the following group abbreviations are used in the sample metadata: Flight (FLT_C1); Basal (BSL_C1); Ground Control (GC_C2); Vivarium Control (VIV_C2), Cohort Control 1 (CC_C1); Cohort Control 2 (CC_C2). Fecal pellets were isolated directly from mice during dissection and preserved by flash freezing in liquid nitrogen before stored at -80 C. DNA was then extracted, shotgun metagenomic libraries generated, and libraries sequenced (target 10 M clusters at PE 250 bp). Metagenomic data was generated from the following groups: Basal Control (n=5), Ground Control (n=5), Vivarium Control (n=5), Cohort Control 1 (n=5), Cohort Control 2 (n=5), Flight (n=5).
Metagenomics assessment of WKY and SHR rodents
GEO Series GSE186517. Rattus norvegicus. 33 samples. Type: Other.
Shotgun metagenomic profiling of human fecal microbiota before and after aerobic exercise intervention
GEO Series GSE314617. feces metagenome. 66 samples. Type: Other.
To explore the change of the gut microbiota in yki3SA tumor-bearing flies by metagenomics sequencing.
GEO Series GSE204975. insect gut metagenome. 6 samples. Type: Expression profiling by high throughput sequencing.
Metagenomic sequencing of adult zebrafish feces after SMZ exposure (Exposure of Danio rerio to environmental sulfamethoxazole may contribute to neurobehavioral abnormalities via gut microbiome disturb
GEO Series GSE255986. feces metagenome. 6 samples. Type: Other.
Metagenomic analysis revealed higher microbial and functional gene diversities in deep landfill
GEO Series GSE68712. Bacteria. 15 samples. Type: Other.
Metagenomic analysis revealed the microbial-mediated soil organic carbon loss under the degeneration succession in alpine meadow
GEO Series GSE93158. uncultured soil microorganism. 20 samples. Type: Other.
Soil metagenome from avocado orchards in Channybearup, Western Australia in 2024
GEO Series GSE298403. soil metagenome. 122 samples. Type: Other.
Distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae
GEO Series GSE274269. Homo sapiens. 174 samples. Type: Expression profiling by high throughput sequencing.
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment
GEO Series GSE68603. Mus musculus. 9 samples. Type: Expression profiling by array.
Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis
<p>Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and <em>in situ</em> microcosms (BACTRAP®s) amended with hydrocarbons (<sup>13</sup>C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and “<em>shotgun</em>” Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, <em>in situ</em> BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus <em>Pelotomaculum</em>), coupled to nitrate, iron and/or sulfate reduction.</p>
Metadata: Samples collected for metagenomic analyses from Andhra Pradesh (AP), Goa (GA) and Deciduous forest Kinwat, Maharashtra (Forest)
<p><strong>Table 1.</strong> Samples collected for metagenomic analyses from Andhra Pradesh (AP), Goa (GA), and Deciduous forest Kinwat, Maharashtra (Forest)</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.