SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJEB22062 data set (As part of the EFFORT project, we sampled feces from pig and poultry livestock in nine European countries (BE, BG, DK, FR, ES, GE, NL, PL, SP). More than 9000 animals were sampled, across 181 pig and 178 poultry herds to generate herd-level composite fecal samples. Using shotgun metagenomics, we have quantified and characterized the antimicrobial resistance gene pools (resistomes) in Europes two most intensively raised livestock species.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB22062, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system.

Biome: root:Host-associated:Birds:Digestive system
EMG produced TPA metagenomics assembly of PRJNA193217 data set (Chicken cecal contents Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA193217, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
EMG produced TPA metagenomics assembly of PRJNA291299 data set (Caecal microbiome metagenome of laying hens).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA291299, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Caecal microbiome metagenome of laying hens

To evaluate the effects of feeding prebiotic, probiotic and synbiotic on the functional potential of caecal microbiome

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Gene expression anlayses of saliva-derived in vitro biofilms during carbohydrate fermentation and pH stress

Dental caries, one of the most globally widespread infectious diseases is intimately linked to pH dynamics. In supragingival plaque, after the addition of a carbohydrate source, bacteria rapidly decrease the pH which then subsequently recovers. In this project we studied gene transcription in naturally diverse saliva-derived in vitro grown biofilms as they were amended with sugar (corresponding to a dietary intake of carbohydrates). We applied an in vitro biofilm model system that was previously determined to be functionally and taxonomically robust and representative of health-associated dental plaque. The major goal was to characterize critical gene expression mechanisms supporting the understudied pH-recovery stage associated with health. This study provides a solid baseline for defining healthy and disease-like states and highlights the power of moving beyond single and dual species applications to capture key players and their orchestrated metabolic activities within a human oral microbiome model.

Biome: root:Host-associated:Arthropoda:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA427880 data set (Baikal Rift Zone hot springs metagenome sequencing).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA427880, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Baikal Rift Zone hot springs metagenome sequencing

The study aims to discover novel extremophilic taxa and extremozymes that could be used in biotechnological applications

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Kermadec arc raw sequence reads

16S amplicon libraries and metagenomes from the Microbial Diversity in the Kermadec Arc project, looking at microbial diversity in subaerial hot springs and enrichments from deep-sea hydrothermal vents along the Kermadec volcanic arc. Related sequences can also be found in BioProject PRJNA412936 , which archives data from hot springs on Raoul Island/Rangitahua.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA563459 data set (Kermadec arc raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA563459, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Iron reduction in an alkali-chloride hot spring community

The study examines the potential contribution of hyperthermophilic iron-reducing organisms to maintaining reduced iron minerals in near-boiling hot spring clay sediment.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA432589 data set (Iron reduction in an alkali-chloride hot spring community).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA432589, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA339844 data set (subsurface metagenome Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA339844, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Deep subsurface.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
subsurface metagenome Metagenome

The shale gas basins in the Ohio-Pennsylvania-New York region contain the largest natural gasreserves in the U.S. In 2012, over 7,000 Marcellus shale gas wells were active in Pennsylvania, and Ohio isexpecting a similar level of development in its deeper, Utica-Point Pleasant shale over the next 5 years.These shale have insufficient permeability to produce natural gas at economical rates, thus their developmentrequires horizontal drilling coupled to hydraulic fracturing, or fracking. The hydraulic fracturing processinvolves wellbore detonation and high-pressure injection of large volumes (up to 20 million L) of freshwaterand sand mixed with chemical additives to propagate fissures in the shale matrix, maximizing the surfacearea for natural gas release to the wellbore. As a result of fracturing, larger flow paths and newly exposedshale surfaces offer greater biogeochemical gradients for microbial colonization with greater opportunitiesfor nutrient and genetic exchange. We know little about the indigenous microbial membership of Marcellusshale, but given current physicochemical conditions of this formation (depths > 1000m, pressures > than 50MPa, temperatures > 60oC, 20% salt content, and pore sizes < 1 m) we anticipate that organisms enrichedduring energy development will encode adaptations to these physical and geochemical conditions. Ourmotivation is to understand the biotic and engineered factors responsible for alter

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA311332 data set (Bacteria isolated from carboxylate platform fermentations inoculated with microbial communities from extreme environments.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA311332, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Bacteria isolated from carboxylate platform fermentations inoculated with microbial communities from extreme environments.

In an effort to identify microbial communities with superior performances in the carboxylate platform for biofuel and high value chemical production, we screened 501 microbial communities from 77 sites across the continental U.S., Hawaii and Puerto Rico as inocula. From the best performing communities, we collected >1800 individual isolates by culturing with a variety of media and oxygen conditions. We generated draft genome sequence for 64 of the isolates, selected based on phylogenetic, ecological, and phenotypic variation. These sequences will be used to advance a system to study 1) the role of diversity in functional types within carboxylate platform fermentation communities, 2) the genetic basis for superior performance in these fermentations and 3) the basis of adaptation to extreme conditions.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA431961 data set (Geothermal fumarole subsurface microbial communities from Mt. Erebus, Antarctica).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA431961, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Geothermal fumarole subsurface microbial communities from Mt. Erebus, Antarctica

Using metagenomic sequencing and binning techniques, we identified and enumerated members of the subsurface-associated microbial community in the high-elevation fumarolic sediments of Tramway Ridge

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA528468 data set (CH09 Metavirome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA528468, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
CH09 Metavirome

Generation of a metavirome from the CH09 hotspring in Yellowstone National Park for the identification of a virus infecting a Nanoarchaea.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Coral microbial communities from various places in Mexico - Orbicella C B metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
coral metagenome Genome sequencing

The goal of this project is to produce microbial metagenomes from corals to better understand how coral-associated microbes interact with their host.

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Broiler Caecal Metagenome

Broiler caecal samples were analysed using metagenomics

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Coral microbial communities from various places in Mexico - Orbicella T R B metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Coral microbial communities from various places in Mexico - Orbicella T R C metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Coral microbial communities from various places in Mexico - Orbicella T R A metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Coral microbial communities from various places in Mexico - Orbicella C C metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
Coral microbial communities from various places in Mexico - Orbicella C A metatranscriptome metatranscriptome

Metatranscriptomic analysis of microbial communities associated with coral hosts

Biome: root:Host-associated:Invertebrates:Cnidaria:Coral
EMG produced TPA metagenomics assembly of PRJEB19090 data set (Potential and active functions in the gut microbiota of a healthy human cohort).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19090, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJNA472060 data set (Reclaimed water Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA472060.  This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.

Biome: root:Engineered:Wastewater:Water and sludge
EMG produced TPA metagenomics assembly of PRJNA542280 data set (Oral Microbiome in Fanconi Anemia).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA542280, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Human:Digestive system:Oral
Oral Microbiome in Fanconi Anemia

Characterization of the oral microbiota in patients with Fanconi anemia and healthy controls.

Biome: root:Host-associated:Human:Digestive system:Oral
EMG produced TPA metagenomics assembly of PRJNA78025 data set (Human Oral Subgingival Plaque Microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA78025, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
Human Oral Subgingival Plaque Microbiome

The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth, harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within the mouth gives rise to periodontitis, an inflammatory disease known to also constitute a risk factor for cardiovascular disease.  While much is known about individual species associated with pathogenesis, the system-level mechanisms underlying the transition from health to disease are still poorly understood. Our pilot study demonstrates the power of high-throughput sequencing as a tool for understanding the role of the oral microbiome in periodontal disease.   After the removal of supragingival plaque with sterile gauze, individual subgingival plaque samples were taken from the meio-buccal aspect of four molar teeth in four quadrants per subject using sterile periodontal curettes. Bacterial DNA extraction was performed using commercially available DNA purification kit. For 16S rRNA sequencing, DNA samples were amplified using specific primers and sequenced by 454 machines. Metagenomic shotgun sequences were obtained from the Illumina instruments.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
EMG produced TPA metagenomics assembly of PRJNA419239 data set (Microbial communities in two hot springs sediments derived from the Kamchatka peninsula).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA419239, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Microbial communities in two hot springs sediments derived from the Kamchatka peninsula


Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
SSU rRNA amplicon of the Arctic Ocean during Winter-Spring Transition

One of the main concerns about the Arctic Ocean has been the changing sea ice regime with a reduction in the summer sea ice extent and a shift in dominance from thicker, perennial multiyear ice towards thinner, first-year ice. As the dietary basis of marine food webs and central players of biogeochemical cycles, microbial communities play an irreplaceable role when evaluating the ecological impact of the Arctics thinner ice regime. During the Norwegian young sea Ice cruise 2015 (N-ICE2015), that took place in drifting pack ice north of Svalbard between January-June 2015, seawater was collected, at 5, 20 or 50, 250 m depth in 9th March, 27th April and 16th June, together with physical and biogeochemical data. Through the massively parallel sequencing of SSU rRNA amplicon we expect to get a snapshot of the Arctics microbiota diversity and structure through the dark-light transition.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Shotgun Metagenomic Sequencing of the Arctic Ocean during Winter-Spring Transition

One of the main concerns about the Arctic Ocean has been the changing sea ice regime with a reduction in the summer sea ice extent and a shift in dominance from thicker, perennial multiyear ice towards thinner, first-year ice. As the dietary basis of marine food webs and central players of biogeochemical cycles, microbial communities play an irreplaceable role when evaluating the ecological impact of the Arctics thinner ice regime. During the Norwegian young sea Ice cruise 2015 (N-ICE2015), that took place in drifting pack ice north of Svalbard between January-June 2015, seawater was collected, at 5, 20 or 50, 250 m depth in 9th March, 27th April and 16th June, together with physical and biogeochemical data. Through the massively parallel sequencing of environmental DNA (metagenomics) we expect to get a snapshot of the Arctics microbiome structure, key functions and dynamic through the dark-light transition.

Biome: root:Environmental:Aquatic:Marine:Oceanic
1) Fungi, 2) Perscribed Burning, 3) Soil Targeted Locus (Loci)

We Ion Torrent sequenced Internal Transcribed Spacer Region 1 (ITS1) amplicons to interrogate soil fungal community responses to long-term prescribed fire treatments in a loblolly pine forest on the Piedmont of Georgia. Our deep sequence data are largely congruent with previous studies and indicate that frequent fire recurrence (3 year fire interval) leads to shifts in soil fungus communities whereas infrequent fires (6 year fire interval) permit system resetting to a state similar to that without prescribed fire. Our results suggest that shifts in the vegetation community, which are the management goal of frequent prescribed fire, accompany changes in the soil fungal community. However, these changes do not occur when the interval between fires is longer.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Switchgrass rhizosphere

Characterization of bacterial and fungal communities in switchgrass rhizosphere

Biome: root:Host-associated:Plants:Rhizosphere
Soil marker gene sequences across the Nutrient Network

Raw microbial marker gene sequences (16S rRNA and ITS) from soil samples across the Nutrient Network

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Varennes Communities in Contaminated Soils

In this study, 16S and ITS primers were used to amplify the bacterial and fungal populations, respectively, in both contaminated and uncontaminated soils that had been planted with willows. The goal was to see how willows and contaminants combined to shape microbial community structure.  Uncontaminated or petroleum contaminated soils from the site of a former oil refinery in Quebec.

Biome: root:Environmental:Terrestrial:Soil
The Island Project - Fungal communities in boreal forest soils

This project investigates fungal communities in fine-scaled organic soil profiles in a long-term chronosequence of boreal forests. The forests are situated on 30 islands in the two lakes Hornavan and Uddjaure, in northern Sweden. The islands have burned with different frequency due to their different area to intercept lightning, and the forests represent a successional gradient ranging from 50 to 5000 years in age. The current project seeks to unravel the mechanisms for the observed long-term build-up of carbon in the organic soil profiles in the islands. It is highly relevant to increase understanding of these mechanisms to be able to adequately predict effects of climate change, forest management practices and other environmental changes on the large carbon stocks currently stored in boreal forest soils.  Fungal ITS2 amplicons from organic soil profiles from boreal forest chronosequence.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Sharing of diverse mycorrhizal and root-endophytic fungi between dominant and subordinate plant species in an oak-dominated forest

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through the below-ground plant_fungal association, dominant plants can benefit by interacting with host-specific mutualistic fungi, while subordinate plant species may persist by sharing other sets (ecotypes) of fungal symbionts with each other. Therefore, the host preference of root-associated fungi is the key to understand plant community structure and dynamics. Based on 454-pyrosequencing, we revealed the root-associated fungal community on co-occurring 36 plant species in an oak-dominated forest in northern Japan, and statistically evaluated the host preference of diverse mycorrhizal and root-endophytic fungi. The analysis of 278 fungal taxa indicated that several taxa in the ectomycorrhizal family Russulaceae and the ecologically-diverse ascomycete order Helotiales had significant host preference for the dominant oak (Quercus) species. On the other hand, arbuscular-mycorrhizal fungi were shared mainly among subordinate plant species. While these fungi with host preference contributed to compartmentalize the below-ground plant_fungal associations, diverse clades of ectomycorrhizal fungi and possible root-endophytes associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant and subordinate plant species can host different subsets of root-associated fungi, while diverse clades of generalist fungi can counterbalance the compartmentalization of plant_fungal associations. Such insights into the overall structure of plant_root-associated fungal associations will enable us to understand the mechanisms that facilitate the co-existence of plant species in natural communities.

Biome: root:Host-associated:Plants
Microbial assemblages associated to crop residues

Crop residues are a crucial ecological niche having significant impact on agricultural ecosystems. Here, we investigated  the dynamics of these communities in three plots during a two-year wheat-oilseed rape rotation experiment. We demonstrated that crop residues are a pivotal, shifting platform that should be took into account as a whole microbial ecosystem to manage residues-borne disease.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJEB8094 data set (The initial state of the human gut microbiome determines its reshaping by antibiotics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8094, and was assembled with metaSPAdes v3.13.0. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal,root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal