SantiagoSanchezF/BiomedBERT_mgnify_studies
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MGYS00006748 | Soils' metagenomes (countryside of Sao Paulo - Brazil) | We collected eight soil samples from different locations in the countryside of Sao Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing and analyzed the soil metagenomes based on shotgun sequencing to identify antibiotic resistance genes. | root:Environmental:Terrestrial:Soil |
MGYS00006747 | 16S microbiome sequences from 101 fecal samples from zoo mammals | In this study, we examine the taxonomic composition and metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using 16S amplicon sequencing and an untargeted metabolomics platform to analyze 101 fecal samples from a range of mammalian species. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species were related to the host-microbe interface, including modified and degraded host and dietary compounds. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically-distant microbiomes are more functionally diverse than redundant. | root:Host-associated:Mammals:Digestive system:Fecal |
MGYS00006746 | General soil fungi from 150 German grassland and 150 German forest plots from 2011, 2014 and 2017 (Illumina MiSeq) | The German Biodiversity Exploratories aim to regularly monitor general fungi in German soils. The project considers 150 grassland and 150 forest plots in total, which are distributed along a north-south transect across Germany. The three sites, each consisting of 50 grassland and 50 forest plots, are Schorfheide-Chorin in Northern Germany, Hainich-Duen in Central Germany and Swabian Alb in the South of the country. Grasslands and forests are characterized by different land-use intensities and management regimes, respectively. The arbuscular mycorrhiza fungi were assessed using Illumina MiSeq sequencing of the internal transcripted spacer2 (ITS2) region after a joint soil sampling carried out in May 2011, 2014 and 2017, each time on all 300 plots. | root:Environmental:Terrestrial:Soil |
MGYS00006745 | Arbuscular mycorrhizal fungi from 150 German grassland and 150 German forest plots from 2011, 2014 and 2017 (Illumina MiSeq) | The German Biodiversity Exploratories aim to regularly monitor arbuscular mycorrhizal in German soils. The project considers 150 grassland and 150 forest plots in total, which are distributed along a north-south transect across Germany. The three sites, each consisting of 50 grassland and 50 forest plots, are Schorfheide-Chorin in Northern Germany, Hainich-Duen in Central Germany and Swabian Alb in the South of the country. Grasslands and forests are characterized by different land-use intensities and management regimes, respectively.The arbuscular mycorrhiza fungi were assessed using Illumina MiSeq sequencing of the small subunit (SSU) gene after a joint soil sampling carried out in May 2011, 2014 and 2017, each time on all 300 plots. | root:Environmental:Terrestrial:Soil |
MGYS00005502 | Bacterial diversity and community composition in grassland and forest soils of the German Biodiversity Exploratories | Bacterial diversity and community composition should be assessed for grassland and forest soils in the three German Biodiversity Exploratories (Schorfheide-Chorin, Hainich-Dün, Schwäbische Alb). Grassland soil samples were derived from meadows, pastures or mown pastures that were either fertilized or non-fertilized. Forest soil samples were derived from age class forest, selection forest or natural forest and dominated by either beech, oak, pine or spruce trees.The study focused on the effect of land use, management, fertilization and tree species as well as edaphic parameters onto the bacterial community and diversity to identify drivers of diversity and community composition. | root:Environmental:Terrestrial:Soil |
MGYS00006741 | Analysis of Candidatus Udaeobacter representatives in forest and grassland soils | The aim of the project was to investigate Candidatus Udaeobacter phylotypes in forest and grassland soils derived from the German Biodiversity Exploratories | root:Environmental:Terrestrial:Soil |
MGYS00006743 | Soil fungi from forest and grassland ecosystems across Germany (raw sequence reads 2011) | The provided sequences were produced in the frame of the core project "Soil Fungi" of the German Biodiversity Exploratories. In May 2011, soil was taken on 300 study plots across three regions in Germany (south - Schwäbische Alb, central - Hainich-Dün, north - Schorfheide-Chorin). After extracting the DNA with the MoBio PowerSoil extraction kit, the fungal ITS (primers: ITS1f and ITS4) was targeted and amplified. The provided sequences are produced with the Roche 454 pyrosequencer. | root:Environmental:Terrestrial:Soil |
MGYS00006744 | Changes in acidobacterial community composition from German grassland soils with land use intensity | In the frame of the German Biodiversity Exploratories (http://www.biodiversity-exploratories.de), the sampling plots were located in three regions in Germany: Schorfheide-Chorin in Brandenburg, national park Hainich-Dün Thuringia, and biosphere reserve Schwäbische Alb in Baden-Wuerttemberg. In every region, 50 grassland sites with different land use intensities were investigated, resulting in a total of 150 plots analysed in this study. The coordinated soil sampling campaign took place in May 2011. The acidobacterial community composition in soil samples was analyzed by high-throughput Illumina sequencing targeting the V3 region of the 16S rRNA. | root:Environmental:Terrestrial:Soil |
MGYS00006740 | Biodiversity Exploratories Rhizosphere 2015 | Biodiversity Exploratories Rhizosphere 2015 | root:Environmental:Terrestrial:Soil |
MGYS00000692 | 16S rRNA gene and transcript based analysis of different methods to extract DNA and RNA from soil | Central objective of this study is to compare different nucleic acid extraction methods with respect to abundance and diversity of 16S rRNA genes and transcripts. Grassland soil derived from the German Biodiversity Exploratories Schwäbische Alb, Schorfheide Chorin and Hainich-Dün. | root:Environmental:Terrestrial:Soil |
MGYS00006742 | Microbial genomic DNA was extracted from the root, rhizosphere and bulk soil compartments from grassland phytometer plant species and was then used as templates for bacterial 16S and/or fungal ITS rDNA paired-end amplicon sequencing using Illumina MiSeq | Investigation of the root and rhizosphere microbial community composition of forb and grass phytometer plants out planted in sites of different land-use intensity in the German Biodiversity Exploratories (Hainich-Dün) by means of 16S and ITS rDNA paired-end amplicon sequencing using Illumina MiSeq. The study focused on the effect of plant functional group (grasses vs. forbs) and land-use as well as edaphic parameters onto the bacterial and fungal community and diversity. | root:Environmental:Terrestrial:Soil |
MGYS00006736 | Shotgun metagenomics of faecal samples collected from Brent geese | A set of 29 faecal samples were collected from light-bellied brent geese (Branta bernicla) in Iceland in May 2023 and were stored dry frozen at -70 degrees Celsius. The DNA was extracted using Qiagen DNEasy PowerSoil Pro kits and shotgun metagenomic data produced using Illumina Novaseq 250bp chemistry. | root:Host-associated:Birds:Digestive system:Fecal |
MGYS00001228 | 16S rRNA amplicon sequences for dugout DNA samples | Three methods to profile microbial community are compared. This sample is 16S rRNA amplicon sequencing of a single DNA sample. | root:Environmental:Aquatic:Freshwater |
MGYS00001980 | EMG produced TPA metagenomics assembly of the Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase (human metagenome) data set | The human metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set,(PRJNA48479). This project includes samples from the following biomes : Fecal,Oral,Attached Keratinized gingiva,buccal mucosa,hard palate,Palatine tonsils,Saliva,Subgingival plaque,Supragingival plaque,Throat,Introitus,Midpoint vagina,posterior fornix,anterior nares,retroauricular crease. | root:Host-associated:Human |
MGYS00006570 | EMG produced TPA metagenomics assembly of PRJNA230567 data set (Systems Biology of Lipid Accumulating Organisms). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA230567, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Engineered:Wastewater. | root:Engineered:Wastewater |
MGYS00006725 | DNA meta-barcoding strategies for species identification in food of animal origin | Two projects: 1. species identification/quantification for processed fish food; 2. species identification/quantification for pure, processed and mock meat products. | root:Engineered:Food production |
MGYS00006724 | Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2018-2019) | This dataset contains 16S rRNA amplicon sequences, derived from autonomous sampling between August 2018 to August 2019 in the West Spitsbergen Current (mooring F4-S-3). The data is part of the LTER "FRAM" (Fram Strait, Arctic Ocean) of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research. | root:Environmental:Aquatic:Marine |
MGYS00006722 | Annual Dynamics of Microeukaryotic Communities in the West Spitsbergen Current (2018-2019) | 18S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-3). | root:Environmental:Aquatic:Marine |
MGYS00006723 | Annual Dynamics of Microeukaryotic Communities in the West Spitsbergen Current (2019-2020) | 18S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-4). | root:Environmental:Aquatic:Marine |
MGYS00006721 | Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2019-2020) | 16S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-4). | root:Environmental:Aquatic:Marine |
MGYS00006720 | Annual Dynamics of Bacterial & Archaeal Communities in the West Spitsbergen Current (2018-2019) | 16S rRNA amplicon sequences derived from autonomous sampling in the West Spitsbergen Current (mooring F4-S-3). | root:Environmental:Aquatic:Marine |
MGYS00006719 | Annual Dynamics of Bacterial & Archaeal Communities in the East Greenland Current (2018-2019) | 16S rRNA amplicon sequences derived from autonomous sampling in the East Greenland Current (mooring EGC-5). | root:Environmental:Aquatic:Marine |
MGYS00006717 | Annual Dynamics of Microeukaryotic Communities in Fram Strait (2016-2017) | 18S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-1, HG-IV-S-1, Fevi-34, EGC-3 | root:Environmental:Aquatic:Marine |
MGYS00006718 | Annual Dynamics of Bacterial & Archaeal Communities in the East Greenland Current (2019-2020) | 16S rRNA amplicon sequences derived from autonomous sampling in the East Greenland Current (mooring EGC-6). | root:Environmental:Aquatic:Marine |
MGYS00006714 | Regional and vertical patterns in microbial communities across Fram Strait (2015-2019) | This study portrays bacterial and archaeal community composition over five summers in the Arctic Fram Strait (80°N). The dataset includes 16S rRNA gene amplicons derived from annual samplings along a longitudinal transect (6°W–12°E) from the surface to the lower photic zone, covering Arctic- / Atlantic-influenced waters in western / eastern Fram Strait. | root:Environmental:Aquatic:Marine |
MGYS00006716 | Annual Dynamics of Microeukaryotic Communities in Fram Strait (2017-2018) | 18S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-2, HG-IV-S-2, Fevi-36, EGC-4. | root:Environmental:Aquatic:Marine |
MGYS00006715 | Pelagic free-living and particle-associated microbial communities across Fram Strait | Water samples were collected in Fram Strait during the Polarstern cruise PS99.2 (June 24th – July 16th 2016) from Greenland shelf to west coast of Spitsbergen. For assessing bacterial and archaeal community composition 4-8 L of water were filtered with peristaltic pump through successive membrane filters of 5 μm and 0.22 μm. The extracted genomic DNA was isolated and the hypervariable V4-V5 (515F - 926R) region of the 16S rRNA was amplified and sequenced using Illumina MiSeq platform in a 2 × 300 bp paired-end run. | root:Environmental:Aquatic:Marine |
MGYS00006712 | Annual Dynamics of Bacterial & Archaeal Communities in Fram Strait (2016-2017) | 16S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-1, HG-IV-S-1, Fevi-34, EGC-3. | root:Environmental:Aquatic:Marine |
MGYS00006713 | Annual Dynamics of Bacterial & Archaeal Communities in Fram Strait (2017-2018) | 16S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-2, HG-IV-S-2, Fevi-36, EGC-4. | root:Environmental:Aquatic:Marine |
MGYS00006709 | Kongsfjorden_July_2016 | In an Arctic glacial fjord, the phytoplankton bloom is controlled by light transparency together with nutrient supply and Atlantic inflow. To explore the issues of climate change and glacial melting in an Arctic fjord, the biological and physiochemical environments of Kongsfjorden, a glacial fjord in Svalbard, have been investigated. The hydrography of Kongsfjorden is controlled by the water mass balance of Atlantic inflow, Arctic waters, and glacial melt through the cross-shelf exchange, and its dominant water masses are determined according to the temperature-salinity diagram. | root:Environmental:Aquatic:Marine |
MGYS00006711 | Phytoplankton-derived biopolymers and seasonal bacterial diversity in Fram Strait | Here, we investigated seasonal bacterial community composition in context of the bioavailable fraction of dissolved organic carbon (DOC) in the eastern Fram Strait. The dataset is affiliated with the project "Plankton Ecology and Biogeochemistry in a Changing Arctic Ocean" (PEBCAO) and the LTER "FRAM". | root:Environmental:Aquatic:Marine |
MGYS00006710 | Contrasting summer microbiome communities of the Fram Strait | null | root:Environmental:Aquatic:Marine |
MGYS00004542 | particle-attached and free-living bacteria kongsfjorden | particle attached and free-living bacteria kongsfjorden | root:Environmental:Aquatic:Marine |
MGYS00006708 | Particle -attached and free-living archaea from surface waters of kongsfjorden | particle-attached and free-living archaea kongsfjorden | root:Environmental:Aquatic:Marine |
MGYS00006707 | 16S rDNA amplicon sequencing of NEREA size-fractionated samples | Analysis of the V4-V5 region of 16S rDNA through amplicon sequencing. Samples were collected monthly across different sampling sites in the Gulf of Naples (Italy). Seawater was collected at different depths and subjected to size fractionation filtering. The DNA was extracted and amplified by PCR. | root:Environmental:Aquatic:Marine |
MGYS00006706 | 18S rDNA amplicon sequencing of NEREA size-fractionated samples | Analysis of the V9 region of 18S rDNA through amplicon sequencing. Samples were collected monthly across different sampling sites in the Gulf of Naples (Italy). Seawater was collected at different depths and subjected to size fractionation filtering. The DNA was extracted and amplified by PCR. | root:Environmental:Aquatic:Marine |
MGYS00006705 | Seasonality of rare and abundant bacterial taxa in Radiales E2 Gijon/Xixon time-series station | In this 3-years time-series study in coastal waters of the Bay of Biscay we have identified the largest number of bacterial taxa with significant seasonality to date (83 taxa). Among these seasonal taxa, 24 cycled between rare and abundant, but most of them were always-rare (59 taxa), with maximum abundances predominately found in winter. We demonstrate that recurrent seasonal patterns in marine bacterioplankton are largely driven by lineages that never account >1% of total community abundance. Such dynamics characterized by seasonal growth and loss opens new perspectives in the ecology of rare marine bacteria, hitherto characterized by dormancy and episodic boom and bust, as envisioned by the seed-bank hypothesis. The effect of abiotic factors and phytoplankton composition on the dynamics of abundant and rare taxa have been also explored in this study, including taxa in the attached fraction (> 3 microns) in a selection of samples over the 3 years. | root:Environmental:Aquatic:Marine |
MGYS00006702 | LMO 16S 2012-13 (3 um) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2012-13 collected directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006704 | LMO 2015, 2016, 2019 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00002774 | marine metagenome Targeted Locus (Loci) | Seasonal variation in bacterioplankton community composition in the Baltic Sea. | root:Environmental:Aquatic:Marine |
MGYS00006703 | LMO 2012 (3-0.2) resequencing | Resequencing of bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2012 using a single filter setup: 0.2 um after prefiltering with a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006700 | LMO 2011-16 (0.2, 3-0.2, 3) resequencing | Resequencing of bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-16 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006701 | LMO 16S 2013 (3 um) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 collected on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006699 | LMO 2018 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2018 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00002766 | Baltic Sea high-frequency temporal study 2012 at the Linnaeus Microbial Observatory Targeted Locus (Loci) | The goal of our high temporal resolution study is to elucidate intra- and interannual detailed differences in bacterial community composition between different filter size fraction, i.e. particle attached vs. free living marine bacterioplankton. | root:Environmental:Aquatic:Marine |
MGYS00006697 | LMO 16S 2014, 2015 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2014-15 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006696 | LMO 16S 2011, 2012, 2013 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-13 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006698 | LMO 2017 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2017 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006695 | LMO 2011, 2012, 2013 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2011-13 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006694 | LMO 2015, 2016 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2015-16 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006693 | LMO 2016, 2017 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2016-17 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00006690 | L4 fungal time series | 17 year molecular time series of fungal ITS at L4 station, WCO | root:Environmental:Aquatic:Marine |
MGYS00006691 | Baltic Sea 16S gene amplicons from Linnaeus Microbial Observatory sampled regularly since 2011 | This study includes surveys of microbial communities at Linnaeus Microbial Observatory (LMO) since 2011. Samples have been collected at LMO at different time intervals, 16S amplicons have been sequenced from different filter fractions and also in different sequencing projects. | root:Environmental:Aquatic:Marine |
MGYS00006692 | LMO 2013 (0.2, 3-0.2, 3) | Bacterial (and some archaeal) V3V4 sequences collected at the Linnaeus Microbial Observatory (LMO) in the Baltic Sea 2013 using three different filter setups: directly on 0.2 um, on 0.2 um after prefiltering with a 3 um filter and directly on a 3 um filter. | root:Environmental:Aquatic:Marine |
MGYS00002841 | Transplant and re-transplant microcosms of Baltic Proper and Bothnian Sea bacterioplankton Targeted Locus (Loci) | The aim of this study was to investigate the effects of increased precipitation, meaning increased loads of terrigenous carbon and lowered salinity by transferring marine bacterioplankton between humic rich and low saline Bothnian Sea water and transparent higher saline Baltic proper water and vice versa. | root:Environmental:Aquatic:Marine |
MGYS00006686 | Helgoland 2019 | Environmental DNA and zooplankton samples taken at Helgoland Roads in June 2019 | root:Environmental:Aquatic:Marine |
MGYS00003999 | 16s data marine community of L4 station | We collected monthly water samples at the L4 station of the Western Channel Observatory. The prokaryote community composition was determined by sequencing of the 16s rRNA gene using the illumina platform. | root:Environmental:Aquatic:Marine |
MGYS00006688 | Eukaryotic microbial community at the LTER site Helgoland Roads | Water samples were collected from the long-term ecological research (LTER) site at Helgoland and the eukaryotic microbial community was assessed. 18S V4 region was amplified using the primer set 528iF /964iR and amplicon sequencing was performed on an Illumina MiSeqTM sequencer in a 2 × 300 bp paired-end run. | root:Environmental:Aquatic:Marine |
MGYS00006689 | Marine metagenome ICM_MPI | The seasonal structure of the bacterial communities of the Helgoland Roads. | root:Environmental:Aquatic:Marine |
MGYS00006687 | 18S community profiles at the the end of a spring bloom at LTER Helgoland Roads | This data set includes eukaryotic microbial community profiles from samples collected in May 2016, via the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. | root:Environmental:Aquatic:Marine |
MGYS00006684 | Distribution of chytrids infecting diatoms | Vertical and temporal distribution of chytrids infecting diatoms in the Gulf of Naples (Italy, Mediterranean Sea) | root:Environmental:Aquatic:Marine |
MGYS00006685 | Metabarcoding Eukaryotic plankton time series samples from long-term ecological research site MareChiara (LTER-MC) | Metabarcoding analysis of a 48 sample time series from Jan 2011 to Dec 2013 targeting 18S V4 rRNA of Eukaryotic plankton from the Long-Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples, Mediterranean Sea. For DNA extraction, about 3 liters of surface sea-water sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were stored at −80°C. Nextera dual index approach and 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform. | root:Environmental:Aquatic:Marine |
MGYS00006683 | Temporal diversity and community structure of the planktonic protist assemblage at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples(Mediterranean Sea) assessed using V4 Illumina sequencing. | We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using V4 Illumina sequencing. Samples for metabarcoding analyses were collected from surface waters at the LTER-MC station on eight dates from February to December 2011. The dates were selected based on light microscopy phytoplankton data, which were used as proxies for the seasonal phase and trophic status of the system. For DNA extraction, about 3 litres of surface sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were immediately frozen with liquid nitrogen and stored at −80◦C. Nextera dual index approach and to 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform. | root:Environmental:Aquatic:Marine |
MGYS00006680 | SOLA sampling point Raw sequence reads | Raw environmental eukaryotic samples from the SOLA (Service d'Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2015 to 2017. | root:Environmental:Aquatic:Marine |
MGYS00004525 | SOLA Raw sequence reads | Raw environmental eukaryotic samples from the SOLA (Service d''Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2007 to 2015, that is investigating the seasonal reoccurrence of rhythmic species. | root:Environmental:Aquatic:Marine |
MGYS00006682 | Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes | The deep-sea provides global vital functions such as sequestration of carbon from the atmosphere. The increased anthropogenic pressures and interest in expanding deep-sea fisheries makes this pristine ecosystem particularly vulnerable, whose conservation largely depends on rapid knowledge acquisition. In view of the limitations of traditional methods to explore the biodiversity of this vast ecosystem, the analysis of traces of macroorganismal DNA released into the water column arises as a cost-effective, non-invasive alternative. Yet, the success of this approach requires understanding of the stratification of DNA traces in the ocean. This study provides evidence that fish DNA traces can be used to establish depth-specific fish diversity and abundance throughout the water column, opening a promising avenue for gathering knowledge about the deep-sea ecosystem. | root:Environmental:Aquatic:Marine |
MGYS00006681 | Marine fish eDNA metabarcoding | null | root:Environmental:Aquatic:Marine |
MGYS00006679 | Time series of Synechococcus diversity at the SOMLIT-ASTAN station | The genetic diversity of Synechococcus population in the English Channel off Roscoff was assessed every two weeks by sequencing the high resolution petB gene marker at the long-term coastal observatory SOMLIT-ASTAN station from July 1st 2009 to December 19th 2011. | root:Environmental:Aquatic:Marine |
MGYS00006678 | Dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea | Here we report a comprehensive dataset covering spatiotemporal variations in prokaryotic and eukaryotic microbial communities and physicochemical parameters in the Baltic Sea. Within 13-months (Jan 2019-Feb 2020), we took 346 water samples during monthly cruises at 19 stations along the salinity gradient. We performed 16S and 18S DNA metabarcoding and microscopy based counting, and saw that both salinity and season are strongly reflected in the dataset.
It provides unique opportunities for both technical and ecological analyses, and is valuable for both environmental monitoring and as a biodiversity reference for future studies, in the context of eutrophication and the prospect of climate change. | root:Environmental:Aquatic:Marine |
MGYS00006676 | Blanes Bay Microbial Observatory (BBMO) time-series 18S rRNA gene pico- and nano-plankton (10 years monthly samples) | This study includes 18S rRNA-gene sequences (V4 region) of pico- and nanoplankton from Blanes Bay Microbial Observatory (BBMO) monthly sampled during 10 years. It contains 120 pico-samples and 120 nano-samples. | root:Environmental:Aquatic:Marine:Coastal |
MGYS00006675 | 16S rRNA gene amplicon time-series in Blanes Bay Microbial Observatory (BBMO) | This study includes 16S rRNA-gene sequences (V3-V4 region) of bacterioplankton monthly sampled from the Blanes Bay Microbial Observatory (BBMO). It contains 11 years of samples from the 0.22-3 μm size fraction and 10 years from the 3-20 μm size fraction. | root:Environmental:Aquatic:Marine:Coastal |
MGYS00006677 | Bacterial diversity of marine planktonic size-fractionated samples | 16S rRNA sequencing of a 2-years temporal serie in Blanes Bay Microbial Observatory. | root:Environmental:Aquatic:Marine:Coastal |
MGYS00000335 | Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis | Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases with controversial reports about the vaginal microbiota diversity. We determined the vaginal microbial community in patients with VVC, bacterial vaginiasis (BV), and mixed infection of VVC and BV using the Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed an increased order from normal control, VVC only, mixed infection of BV and VVC, to BV. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV. Detailed comparison showed that while the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern with relatively higher abundance of Lactobacillus than the BV group but higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. The VVC-only group, however, could not be described by any single profile. They spanned from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC showed inconsistent changes of vaginal microbiota, with four BV/VVC samples recovered to a higher Lactobacillus level while many VVC-only patients did not. These results will be useful for future study about the role of vaginal microbiota in VVC and related infectious diseases. | root:Host-associated:Human:Reproductive system:Vagina |
MGYS00001412 | 16S metabarcoding of bacteria associated with cultured strains of the brown alga Ectocarpus sp. | We examined the bacterial flora associated with 20 cultured strains of Ectocarpus sp. from different locations, and recorded both the bacterial diversity associated directly to the alga and that found in the culture medium. Experiments were carried out to amplify an approximately 400 bp fragment of the bacterial 16S comprising the V3 and V4 regions and sequenced on the Illumina MiSeq platform using V2 reagents ( 2x250 bp reads). | root:Host-associated:Algae:Brown Algae |
MGYS00005333 | EMG produced TPA metagenomics assembly of the Gut microbial dysbiosis in young adults with obesity (Gut microbial dysbiosis in young adults with obesity) data set. | The Gut microbial dysbiosis in young adults with obesity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12123. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal. | root:Host-associated:Human:Digestive system:Large intestine:Fecal |
MGYS00001538 | Oil spill dispersant strategies and bioremediation efficientcy | After accidental oil spills to seawater from production or transport facilities the oil will be spread on the water surface and in the water column, and a number of weathering processes will appear. Typical operational methods to remove the oil from the sea surface include physical limitation of the surface spreading with booms and collection of the oil by skimmers. An alternative method to remove surfaced oil is to use chemical dispersants. These chemicals create a more hydrophilic oil surface, resulting in the generation of small droplets by wave actions, which are spread into the water column. The generation of small droplet dispersions may increase the natural biodegradation of the oil in the seawater column. Recently, dispersant methods have also been used for sub-surface oil spills (blow-outs). The Norwegian Research Council and several oil companies have funded this research project in order to improve our knowledge and understanding about the effects of dispersant strategies on oil biodegradation and the microbial communities and processes involved. The data from this project will contribute to the optimization of dispersant strategies. The project will include experimental studies simulating both surface and subsurface oil discharges. The focus will be molecular microbiology analyses and bioinformatics, including phylogenetic characterization of microbial communities (characterization of 16S rRNA genes) and investigations of biochemical pathways associated with degradation of alkanes and aromatic oil compounds. Metagenomic and metatranscriptomic studies may be expected to be part of this work. Finally, generated experimental data should be incorporated into OSCAR model, a industry standard model for predicting the fate of the oil in the marine water column after an accidental oil spill. | root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated |
MGYS00004561 | nifH gene in KH-11-10 and KH-13-7 cruises | This study aims to describe diazotroph community structure in the euphotic zone in the western and eastern subtropical South Pacific | root:Environmental:Aquatic:Marine |
MGYS00002949 | Baltic Sea | This is a 16S rRNA pyrosequencing study of ferruginous surface sediment samples collected from the Skagerrak (North Sea) and Bothnian Bay (Baltic Sea area). | root:Environmental:Aquatic:Marine:Sediment |
MGYS00000793 | Temperate forest soil Metagenome | The overall aims of this study were (1) to explore soil bacterial communities in four typical temperate forest types from Changbai Mountain (Broad-leaved Korean pine mixed forest, Secondary poplar-birch forest, Spruce-fir forest, and Larch forest) with newly developed bar-coded 454 pyrosequencing method; (2) to elucidate the biotic and abiotic factors controlling the abundance, diversity and composition of soil bacterial communities; (3) to test if the differentiation of soil bacterial communities in these temperate forests support the copiotroph/oligotroph functional classification model and the non-random co-occurrence patterns. This study will provide the first glimpse at the potential role of above-ground vegetation in allowing niche differentiation of soil bacterial communities in natural temperate forests situated in Changbai Mountain, and tries to reveal the intrinsic mechanism of such differentiation. | root:Environmental:Terrestrial:Soil:Forest soil |
MGYS00003084 | Marine metagenome ICM_AWP | Variation of Microplanktonic Communities Composition with Depth in an area under a Meddy Influence. | root:Environmental:Aquatic:Marine |
MGYS00003008 | Marine subseafloor sediment Targeted Locus (Loci) | We propose to apply 454-based tag pyrosequencing to investigate how microbial communities change with depth, lithology, and porewater geochemistry in the sediment that underlies one of the highest productivity regions in the world ocean. To accomplish this goal, we propose to analyze extracted DNA from 16 samples taken in high resolution in conjunction with detailed porewater geochemistry. This dataset will provide an unprecedented insight into the microbial ecology of a highly productive open ocean site (35 cm/k.y) to a sediment depth of 750 m and an age of 2.1 Ma. We anticipate that through this use of next-generation sequencing technology in combination with biogeochemical and cell count data sets collected during IODP expedition 323, we will obtain significant insight into this previously uncharted ecosystem. | root:Environmental:Aquatic:Marine:Sediment |
MGYS00002670 | Macroalgal Morphology affects composition and settlement of microbial communities | Macroalgae (seaweeds) have an intimate relationship with their microbial symbionts. Microbial communities associated with macroalgal surfaces (epibiota) are generally host-specific and, historically, there has been great interest in the role of biological compounds and chemical warfare in microbial community assembly on seaweeds. However, the interaction between seaweeds and their environment may also influence community assembly of their microbiota. In this experiment, I ask whether the interaction between water flow and seaweed morphology affects the settlement and structure of microbial biofilms. I test whether three common algal morphologies select for differential biofilm communities using artificial macro algae units (AM units) made out of latex. I find that morphology does affect initial microbial settlement and community structure, but that eventual dominance of substrate specialists (in our case, a latex degrader) swamps the influence of morphology in long-term biofilms. | root:Environmental:Aquatic:Marine |
MGYS00001223 | Interferon-lambda and interleukin-22 cooperate for the induction of interferon-stimulated genes and control of rotavirus infection | The epithelium is the major entry point for many viruses but the processes protecting barrier surfaces against viral infections are incompletely understood. We identify interleukin (IL)-22 produced by group 3 innate lymphoid cells (ILC3s) as an amplifier of interferon (IFN)-lambda signaling, a synergism required to curtail replication of rotavirus, the leading cause of childhood gastroenteritis. Cooperation between IL-22 and IFN-lambda receptors, both of which are preferentially expressed by intestinal epithelial cells, was required for optimal STAT1 transcription factor activation and expression of interferon-stimulated genes. This data suggests that epithelial cells are protected against virus replication by co-opting two evolutionarily related cytokine networks. These data may inform the design of novel immunotherapies of virus infections that are sensitive to IFNs. | root:Host-associated:Mammals:Digestive system:Large intestine |
MGYS00003985 | Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Caribbean Sea near Curacao (including saline pond samples in Curacao) 2015 | The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the Caribbean Sea near Curacao (and saline ponds in Curacao as well) in April 2015 to examine phytoplankton community diversity. | root:Environmental:Aquatic:Marine |
MGYS00001789 | Amplicon sequencing of Tara Oceans RNA samples corresponding to size fractions for protists. | Analysis of RNA tags in Tara Oceans Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The RNA was extracted, cDNA prepared then amplified by PCR. | root:Environmental:Aquatic:Marine |
MGYS00004246 | Successional trajectories of coastal bacterioplankton communities in response to co-exposure of cadmium and phenanthrene | Coexistence of multiple contaminants in coastal aquatic ecosystems can lead to complicated circumstances in ecotoxicological assessment for biological communities due to potential interaction between contaminants. We chose cadmium (Cd) and phenanthrene (PHE) as representatives of heavy metals and polycyclic aromatic hydrocarbons, respectively. Contamination process was mimicked using coastal water microcosms contaminated by Cd (1 mg/L), PHE (1 mg/L), and their mixture over two weeks. | root:Environmental:Aquatic:Marine:Coastal |
MGYS00002449 | Nuunat- ORMS formation during oil biodegradation at low temperature | Biodegradation study of chemically dispersed oil and ORMS formation in cold local (5C) Norwegian seawater over 64 days incubation period containing natural microbial community and selected diatom population of Fragilariopsis cylindrus. | root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated |
MGYS00005230 | Flores_fecal_EBI | Fecal samples from Flores_SMP for EBI submission | root:Host-associated:Human:Digestive system:Large intestine:Fecal |
MGYS00002121 | PETROMAKS E#9 | Biodegradation study was conducted with two different oils (naphthenic and asphaltenic) at two different temperatures (5C and 13C). The aim of the study was to evaluate differences in biodegradation and microbial community dynamics between two oils at different temperatures. | root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated |
MGYS00004077 | Planktonic bacterial communities in the arctic Canada Basin and
Kongsfjorden | Planktonic bacteria play key role in biogeochemical cycles and energy
flow in marine ecosystems. However, our knowledge of the extent and character of
bacterial diversity in polar marine environments is still limited. Here we present
the use of high throughput DNA pyrosequencing and statistical inference to assess
the diversity of planktonic bacteria in the arctic Canada Basin, and Kongsfjorden in
Spitsbergen. The V3 region of the 16S rRNA gene was amplified from seawater samples
collected from the upper water column. The number of bacterial 16S rRNA sequences
obtained from each sites varied from 7433 to 9218. In the Canada Basin, the most
abundant bacterial groups in two sites of water at 10m depth were the Proteobacteria
(mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria.
Different bacterial communities were observed in the deeper water (80 or 100m depth)
at the two sites. The Proteobacteria and Bacteroidetes also formed the dominant
bacterial groups in surface water of Kongsfjorden. However, Gammaproteobacteria
accounted for more than 90% of the Proteobacteria. | root:Environmental:Aquatic:Marine |
MGYS00004040 | marine sediment metagenome Targeted Locus (Loci) | Site U1387 offers a chance to study the response of microbial assemblage to specific seafloor events such as contourite depositions, changes in bottom current energy, shifts in organic matter deposition rates, and geochemical changes that are representative of seafloor processes during rapid climate change. | root:Environmental:Aquatic:Marine:Sediment |
MGYS00004148 | Microbial community structures of chimney in DODO and Solitaire hydrothermal fields | Difference of microbial diversity by the 16S rRNA gene in chimney structures between two hydrothermal fields on central Indian Ridge. | root:Environmental:Aquatic:Marine:Hydrothermal vents |
MGYS00006674 | WGS of bacterial strains from food industry | In this study, strains were isolated from different points of the food industry and characterized by classical microbiological methods. DNA was then extracted and sequenced by shotgun technology to assess metabolic potential. | root:Engineered:Food production |
MGYS00006670 | EMG produced TPA metagenomics assembly of PRJEB31095 data set (The intestinal microbiome from two ecotypes of Atlantic cod and three additional Gadidae species.). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB31095, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine. | root:Host-associated:Fish:Digestive system:Intestine |
MGYS00006672 | EMG produced TPA metagenomics assembly of PRJNA482836 data set (Gut microbiome from Piaractus mesopotamicus Metagenome). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA482836, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system. | root:Host-associated:Fish:Digestive system |
MGYS00006673 | EMG produced TPA metagenomics assembly of PRJEB42464 data set (Gut Microbiomes of European Farm Rainbow Trout). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42464, and was assembled with megahit v1.2.9, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system. | root:Host-associated:Fish:Digestive system |
MGYS00006671 | EMG produced TPA metagenomics assembly of PRJEB19833 data set (Mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diet). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19833, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system. | root:Host-associated:Fish:Digestive system |
MGYS00006668 | EMG produced TPA metagenomics assembly of PRJNA663846 data set (Metagenomic analysis of stomach contents of Acanthopagrus latus). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA663846, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system. | root:Host-associated:Fish:Digestive system |
MGYS00006666 | EMG produced TPA metagenomics assembly of PRJEB29346 data set (Metagenomic shotgun sequencing of the Atlantic cod intestinal microbiome). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB29346, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine. | root:Host-associated:Fish:Digestive system:Intestine |
MGYS00006669 | EMG produced TPA metagenomics assembly of PRJEB19785 data set (Metagenomics of the mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diets). | The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19785, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system. | root:Host-associated:Fish:Digestive system |
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