SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Effects of organic matter manipulation on archaeal, bacterial, and fungal community assembly

Community assembly is not only important for community structure, it is also a strong predictor of ecosystem functioning. Understanding how communities initially form and colonize lake sediments – where essential functions like carbon cycling occur – is therefore important for whole-ecosystem processes. Here, we tested for the deterministic processes that drive assembly order. Is this order primarily determined by the sediment or by the lake conditions ? What influences how rapidly this environmental filtering occurs? Do communities become more interconnected with time because of the sediment or lake conditions? Artificial mesocosms were created with varying levels and types of terrestrial organic matter. The mesocosms were placed at the bottom of three lakes. We sampled the sediment monthly over a two-month period to characterize microbial communities.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
EMG produced TPA metagenomics assembly of PRJNA255918 data set (Fumarolic ice cave sediment Metagenome).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA255918, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Environmental:Aquatic:Sediment.

Biome: root:Environmental:Aquatic:Sediment
The microbiome of rock grains weathered in the soil environment.

Using a metagenomic and metatranscriptomic approach the study aims to investigate the differences and similarities between the microbial communities of basalt grains weathered in soil and its surrounding soil substrate. This will provide the foundation to characterise and harvest the full potential of the belowground microbiome to elevate rates of enhanced rock weathering (EW) and carbon dioxide removal (CDR) in agroecosystems, helping towards efforts to achieve negative C emission.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJEB4370 data set (A gnotobiotic mouse model of phage-bacterial host dynamics in the human gut).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB4370, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA598094 data set (Metagenomes of bacteria colonizing the gut of Apis mellifera and Apis cerana Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA598094, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA757579 data set (Adjunctive probiotic Lactobacillus rhamnosus Probio-M9 enhances the effect of anti-PD-1 antitumor therapy via regulating the gut microbiota damaged by antibiotics).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA757579, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA747837 data set (mouse gut metagenome of different environment).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA747837, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
Soil microbial communities in agricultural soils of Argentina

In this project we study soil bacterial and fungal communities under long-term agricultural management with contrasting fertilization, tillage and crop rotation practices.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Anaerobic microorganisms in rice fields

Enrichment and isolation of dehalogenating microorganisms in rice fields

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics assembly of PRJNA379709 data set (Species and functional composition of gut bacteria from TGF-Beta deficient H. hepaticus positive mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA379709, and was assembled with SPAdes v3.15.3, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
EMG produced TPA metagenomics assembly of PRJEB42296 data set (First expansion of the public Tomato brown rugose fruit virus (ToBRFV) Nextstrain build; inclusion of new genomic and epidemiological data).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42296, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of PRJNA755742 data set (Tomato rhizosphere microbiome in the pot experiment).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755742, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA725899 data set (Metagenomic sequencing of wild rodent colon, cecum and faeces).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA725899, and was assembled with unknown v0.0, metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of PRJNA766489 data set (Culture-independent analysis of rhizosphere microbial communities associated with tomato plants).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA766489, and was assembled with metaSPAdes v3.15.3, SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA755741 data set (Tomato rhizosphere microbiome in the belowground segregation experiment).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755741, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA590717 data set (Genome-resolved metagenomics to study the prevalence of co-infections and intraspecific heterogeneity among pathogen metapopulations within tomato and pepper fields).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA590717, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.

Biome: root:Host-associated:Plants:Phylloplane
EMG produced TPA metagenomics assembly of PRJNA645015 data set (Honeybee gut microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA645015, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA603603 data set (Soil and rhizospheric whole shotgun metagenomes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA603603, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere:Soil.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
EMG produced TPA metagenomics assembly of PRJNA597176 data set (global study of tomato bacterial wilt soil microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA597176, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.

Biome: root:Host-associated:Plants:Rhizoplane:Soil
EMG produced TPA metagenomics assembly of PRJNA653704 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_101317 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653704, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.

Biome: root:Host-associated:Plants:Rhizoplane:Soil
EMG produced TPA metagenomics assembly of PRJNA653703 data set (Soil microbial communities from Nachusa Grasslands, Illinois, United States - SOY_080817 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA653703, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizoplane:Soil.

Biome: root:Host-associated:Plants:Rhizoplane:Soil
EMG produced TPA metagenomics assembly of PRJNA539517 data set (Root nodule microbial communities collected in Santa Monica, California, United States - Edamame nodules 1 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA539517, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA655215 data set (Metagenomic analyses of soybean rhizosphere).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA655215, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJDB5626 data set (Microbial metagenome analysis of soybean root nodules).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB5626, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of PRJNA787435 data set (Geographical resistome profiling in honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA787435, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA371719 data set (Functional diversity within the simple gut microbiota of the honey bee).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA371719, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA784737 data set (Metagenomic detection of viral pathogens in Spanish honeybees).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA784737, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metatranscriptomics assembly of PRJNA318490 data set (RNA shotgun metagenomic sequencing in social and solitary wild bees Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA318490, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA642095 data set (Metagenome, bees, yeasts).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA642095, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA599288 data set (Cross-species colonization of Apis cerana and Apis mellifera gut bacteria).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599288, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metatranscriptomics assembly of PRJNA172020 data set (Honey bee (Apis mellifera) and an ectoparasitic mite of honey bee, Varroa destructor Transcriptome or Gene expression).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA172020, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA786615 data set (Characterization of gut bacteria of italian honey bee Apis mellifera (Apidae: hymenoptera)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA786615, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA253368 data set (Honey bee gut metatranscriptome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA253368, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metatranscriptomics assembly of PRJNA687318 data set (Metatranscriptome analysis of sympatric bee species identifies variants of bee infecting viruses, and a novel RNA virus primarily associated with Andrena).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA687318, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA400782 data set (A scientific note on the first detection of Israeli acute paralysis virus in honey bees (Apis mellifera) in Kenya using high-throughput sequencing).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA400782, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA481316 data set (honeybee viral metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA481316, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta.

Biome: root:Host-associated:Insecta
EMG produced TPA metagenomics assembly of PRJNA599289 data set (Gut microbiome of honey bees in china).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA599289, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA786261 data set (Geographical resistome profiling in honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA786261, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA473901 data set (Gut microbiota of honeybees Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA473901, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Insecta:Digestive system.

Biome: root:Host-associated:Insecta:Digestive system
EMG produced TPA metagenomics assembly of PRJNA750880 data set (Mouse intestinal phages-Health and alcohol feeding).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA750880, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA852525 data set (gut metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA852525, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA771488 data set (Dynamic impact of Blautia producta on gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA771488, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA841368 data set (C-section increases cecal abundance of the archetypal bile acid and glucocorticoid modifying Lachnoclostridium [Clostridium] scindens in mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA841368, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA828263 data set (Impact of a phage cocktail targeting Escherichia coli and Enterococcus faecalis as members of a gut bacterial consortium in vitro and in vivo).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA828263, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA705695 data set (Gut metagenomes of patients and mice with post-infection irritable bowel syndrome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA705695, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA776120 data set (Effectiveness of Jianpi Qushi Heluo formula (JQHF) in alleviating experimental passive Heymann nephritis in rats and its modulation effect on gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA776120, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA741607 data set (Inhibitory Effects of Lactulose on Colitis-Associated Carcinogenesis by Restoration of the Gut Microbiota in AOM/DSS Mouse Model).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741607, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA760892 data set (Fecal Whole Metagenomic Shotgun Sequencing on mouse).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA760892, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA844935 data set (The gut microbiome in age-related sepsis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA844935, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA753725 data set (Changes of intestinal resistance genome induced by diet).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA753725, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal