SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
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

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
Biodiversity Exploratories Rhizosphere 2015

Biodiversity Exploratories Rhizosphere 2015

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Host-associated:Birds:Digestive system:Fecal
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.

Biome: root:Environmental:Aquatic:Freshwater
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.

Biome: root:Host-associated:Human
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.

Biome: root:Engineered:Wastewater
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.

Biome: root:Engineered:Food production
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.

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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

Biome: root:Environmental:Aquatic:Marine
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).

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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".

Biome: root:Environmental:Aquatic:Marine
Contrasting summer microbiome communities of the Fram Strait


Biome: root:Environmental:Aquatic:Marine
particle-attached and free-living bacteria kongsfjorden

particle attached and free-living bacteria kongsfjorden

Biome: root:Environmental:Aquatic:Marine
Particle -attached and free-living archaea from surface waters of kongsfjorden

particle-attached and free-living archaea kongsfjorden

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
marine metagenome Targeted Locus (Loci)

Seasonal variation in bacterioplankton community composition in the Baltic Sea.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
L4 fungal time series

17 year molecular time series of fungal ITS at L4 station, WCO

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
Helgoland 2019

Environmental DNA and zooplankton samples taken at Helgoland Roads in June 2019

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_MPI

The seasonal structure of the bacterial communities of the Helgoland Roads.

Biome: root:Environmental:Aquatic:Marine
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.

Biome: root:Environmental:Aquatic:Marine
Distribution of chytrids infecting diatoms

Vertical and temporal distribution of chytrids infecting diatoms in the Gulf of Naples (Italy, Mediterranean Sea)

Biome: root:Environmental:Aquatic:Marine