SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the Municipal Pensacola Beach Sand Metagenome (beach sand metagenome) data set

The beach sand metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA260285. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Sand
EMG produced TPA metagenomics assembly of the Gut metagenome from two premature infants (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA221723. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Oklahoma soil 10 year warming Metagenome (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA219368. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the DG Metagenome (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA188490. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Kansas, Cultivated corn soil metagenome reference core Project (402463) data set

The 402463 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP008742. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics assembly of the Central Alaskan Permafrost Metagenome (permafrost metagenome) data set

The permafrost metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA72925. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
EMG produced TPA metagenomics assembly of the DIPP Diabetes Microbiome (DIPP Diabetes Microbiome) data set

The DIPP Diabetes Microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set SRP006764. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Metagenomic, Metatranscriptomic and Metviriomic analysis of samples collected at four time points during a single day at the Gulf of Aqaba in the Red Sea. (Red Sea Diel) data set

The Red Sea Diel Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19060. This project includes samples from the following biomes : Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the Molecular study on haloarchaea producing industerially important enzymes (Molecular study on Haloarchaea) data set

The Molecular study on Haloarchaea Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB18746. This project includes samples from the following biomes : Aquatic.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline
EMG produced TPA metagenomics assembly of the Oyster and water samples from Texas bays. (Texas Bay Metagenomes) data set

The Texas Bay Metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB16362. This project includes samples from the following biomes : Marine, Mollusca.

Biome: root:Environmental:Aquatic:Marine:Coastal
EMG produced TPA metagenomics assembly of the Study of the changes in the metagenome of the groundwater community at (Metagenomics of a radioactive legacy site) data set

The Metagenomics of a radioactive legacy site Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14718. This project includes samples from the following biomes : Freshwater.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Contaminated
EMG produced TPA metagenomics assembly of the Comparison of two soil microbiomes with different organic matter content (Restinga experiment) data set

The Restinga experiment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12940. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Mining for novel cellulase genes from different ecosystem metagenomes (Mining for novel cellulase genes) data set

The Mining for novel cellulase genes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12864. This project includes samples from the following biomes : Aquatic.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline:Sediment
EMG produced TPA metagenomics assembly of the The Pig's other genome: a reference gene catalogue of the gut microbiome (A catalog of the pig gut metagenome) data set

The A catalog of the pig gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11755. This project includes samples from the following biomes : Mammal (non-human).

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Chinese Poyang Lake resistant genes from soil metagenome (Chinese Poyang Lake resistant genes from soil metagenome) data set

The Chinese Poyang Lake resistant genes from soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9412. This project includes samples from the following biomes : Freshwater.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Subseafloor microbes at Mid-Cayman Rise (Mid-Cayman Rise FS848 and FS856 metagenomes) data set

The Mid-Cayman Rise FS848 and FS856 metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9204. This project includes samples from the following biomes : Hydrothermal vents.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
EMG produced TPA metagenomics assembly of the Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient (Columbia River coastal margin 'omics) data set

The Columbia River coastal margin 'omics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9136. This project includes samples from the following biomes : Marine.

Biome: root:Environmental:Aquatic:Marine:Coastal
EMG produced TPA metagenomics assembly of the MiDAS DNA Extraction metagenomics and metatranscriptomics (ena-STUDY-AALBORG UNIVERSITY-27-02-2015-09:25:27:418-237) data set

The ena-STUDY-AALBORG UNIVERSITY-27-02-2015-09:25:27:418-237 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8669. This project includes samples from the following biomes : Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Forest harvesting reduces the soil metagenomic potential for biomass decomposition (Forest harvesting reduces the soil metagenomic potential for biomass decomposition) data set

The Forest harvesting reduces the soil metagenomic potential for biomass decomposition Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8420. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
EMG produced TPA metagenomics assembly of the The initial state of the human gut microbiome determines its reshaping by antibiotics (Impact of cefprozil on the gut microbiome of healthy individuals) data set

The Impact of cefprozil on the gut microbiome of healthy individuals Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8094. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the BASE – Biomes of Australian Soil Environments (BASE) data set

The BASE Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB7626. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Metagenomic analysis of sediments along a uranium gradient (Metagenomic analysis of sediments along a uranium gradient) data set

The Metagenomic analysis of sediments along a uranium gradient Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6942. This project includes samples from the following biomes : Freshwater.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
EMG produced TPA metagenomics assembly of the Metagenomic analysis of infant stool sample (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA60717. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
We employed shotgun metagenome and 16S rDNA gene amplicon sequencing to robustly compare the taxonomic and functional gene content variability between two key soil ecosystems for climate change, an Alaskan tundra permafrost (AK) and a natural prairie temperate soil in Oklahoma (OK).

Please see: Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Johnston et al. 2016. Frontiers in Microbiology.
doi: 10.3389/fmicb.2016.00579

How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1–2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100–530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
BBSRC Main Experiment Shotgun Study

There is rich genetic diversity in India's native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ‘thinning', can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.

Biome: root:Host-associated:Birds:Digestive system:Ceca
EMG produced TPA metagenomics assembly of the Lime was injected to acid sulfate soils with aim to balance the acidity. The indigenous microbial communities before and after injection were investigated. (Effects of lime injection on the microbial community in acid sulfate soils) data set

The Effects of lime injection on the microbial community in acid sulfate soils Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6125. This project includes samples from the following biomes : Grassland.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Raw reads of the microbiota of premature infant mouth, skin, and gut (human gut metagenome) data set

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA327106. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human
EMG produced TPA metagenomics assembly of the Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India (Antibiotic resistance genes in a polluted lake) data set

The Antibiotic resistance genes in a polluted lake Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6102. This project includes samples from the following biomes : Freshwater.

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of the Microbial Community of Mobilong Acid Sulfate Soil depth profile using Metagenomics (Mobilong Soil Profile) data set

The Mobilong Soil Profile Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB5872. This project includes samples from the following biomes : Grassland.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount, 2011-2012 (Axial Seamount Metagenomes 2011-2012) data set

The Axial Seamount Metagenomes 2011-2012 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB5293. This project includes samples from the following biomes : Hydrothermal vents.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
EMG produced TPA metagenomics assembly of the A human gut microbial gene catalog established by deep metagenomic sequencing (MetaHIT) data set

The MetaHIT Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB2054. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Symptomatic atherosclerosis gut metagenome. (gut metagenome) data set

The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA177201. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
Metagenomics of camel tuberculosis

Tuberculosis is the most important zoonotic disease in the world.

Biome: root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
microbiom of B. reticulatus

microbiom of B. reticulatus

Biome: root:Host-associated:Fungi
Desert Fairy Circles

The formation of fairy circles, circular patches without vegetation in the center but with perennial grasses at the margin, is investigated.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Study of the microbial assembly of lab-scale biofilter media

Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory or neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter media type) and stochastic forces. Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials and of the filter influent and effluent was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality.  The filter media communities seemed to be strongly assembled by selection rather than stochastic immigration, with only 28% of those OTUs shared with the source water detected on the filter media and following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water.

Biome: root:Environmental:Aquatic:Freshwater:Drinking water:Delivery networks
A large-scale field study of bacterial communities in cereal aphid across Morocco

Insects are frequently associated with bacteria that can have significant ecological and evolutionary impacts on their hosts. Much progress has been made to unravel the diversity and effects of obligate and facultative endosymbionts. Nevertheless, few studies have examined the influence of environmental factors to microbiome composition of aphids. The current work assessed the diversity of bacterial communities of five cereal aphid species collected across Morocco and covering a wide range of environmental conditions. Deep 16S rRNA sequencing enabled us to identify 17 bacterial Operational Taxonomic Units (OTU). Facultative endosymbionts were totally absent in D. noxia, R. maïdis and R. padi, whereas a high relative prevalence of R. insecticola and S. symbiotica was observed in S. avenae and S. maydis, respectively. In addition to these symbiotic partners, Pseudomonas, Acinetobacter, Pantoea, Erwinia and Staphyloccocus were also identified in the aphid species R. padi, R. maïdis and S. avenae, suggesting that the aphid microbiome is not limited to the presence of endosymbiotic bacteria. Beside the significant association between host species and bacterial communities, a significant inverse correlation was also found between altitude and α-diversity.

Biome: root:Host-associated:Insecta:Digestive system
First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages

In the present study we used Next Generation Sequencing (NGS) in 16S rRNA gene analysis to define whether the bacterial composition varies among the different developmental stages of H. carpathicus. We analyzed obtained microbiome profiles to verify the presence of known endosymbionts. Moreover, we delineate metabolic potentials of the microorganisms associated with different developmental stages of H. carpathicus.

Biome: root:Host-associated:Insecta
16S RNA  high-throughput sequencing of the gut microbiota from chronic exposed Sprague-Dawley rats.

A growing body of research suggests that dysbiosis of the gut microbiota induced by environmental pollutants, such as pesticides, could have a role in the development of metabolic disorders.  We have examined the long-term effects of 3 doses of the Roundup herbicide (made of glyphosate and formulants) on the gut microbiota in male and female Sprague-Dawley rats. A total of 141 bacteria families were identified by a high-throughput sequencing metagenomics approach. An OPLS-DA analysis revealed an increased Bacteroidetes family S24-7 and a decreased Lactobacillaceae in 8 out of the 9 females treated with Roundup. These effects were confirmed by repetitive sequence-based PCR fingerprinting showing a clustering of treated females. A traditional culture-based method showed that Roundup had a direct effect on rat gut microbiota. Cultivable species showed different sensitivities to Roundup, including the presence of a high tolerant strain identified as Escherichia coli by 16S rRNA sequencing. The high tolerance of this E. Coli strain was explained by the absence of the EPSPS gene (coding glyphosate target enzyme) as studied by DNA amplification. Overall, these gut microbiome disturbances showed a substantial overlap with those associated with liver dysfunction in other studies. In conclusion, we revealed that environmental concentrations of R have a sex-dependent impact on rat gut microbiome composition and thus warrant further investigations.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Microbiota broiler carcasses

Microbiota broiler carcasses

Biome: root:Host-associated:Birds