SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJNA755346 data set (Intestinal Virome Diversity Correlates with Intestinal Microbiome Diversity in ob and Apoe mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755346, 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 PRJNA748686 data set (mouse gut metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA748686, 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 PRJNA753312 data set (Mastitis microbiomes of cow and mouse Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA753312, 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
EMG produced TPA metagenomics assembly of PRJNA838940 data set (Metagenomic sequencing of colon contents from gnotobiotic mice harboring the altered Schaedler flora).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA838940, 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 PRJNA785116 data set (Metagenomic sequencing).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA785116, 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 PRJNA738554 data set (The influence of the low-iron diet and the protective effect of Lactobacillus casei Zhang from the perspective of gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA738554, 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 PRJNA712972 data set (PIGA gene responsible for GPI anchor biosynthesis : knockout leads to gut microbiome dysbiosis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA712972, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA802607 data set (Genesis of fecal floatation is causally linked to gut microbial colonization in mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA802607, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA771420 data set (28-day gavage of Blautia product on gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA771420, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA704567 data set (Nicotinamide Riboside-Conditioned Microbiota Deflects High-Fat Diet-Induced Weight Gain in Mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA704567, 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 PRJNA693108 data set (Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA693108, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJNA734104 data set (Antibiotic-induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA734104, 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 PRJNA730805 data set (Integrative Analysis of the Western Diet-Induced Metabolic Phenotype and Microbiota Changes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA730805, 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 PRJNA732220 data set (Gut microbiota of pregnant C57BL/6J mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA732220, 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
EMG produced TPA metagenomics assembly of PRJNA646095 data set (Collaborative Cross founders mouse gut metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646095, and was assembled with 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
EMG produced TPA metagenomics assembly of PRJNA719224 data set (Shotgun Metagenomic Analysis of Dose-Dependent TCDD-elicited Effects on Cecal Gut Microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA719224, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
EMG produced TPA metagenomics assembly of PRJNA815731 data set (mouse gut metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA815731, 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 PRJNA389470 data set (Mus musculus Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA389470, 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
EMG produced TPA metagenomics assembly of PRJNA703330 data set (Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA703330, 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 PRJNA691897 data set (Generation-scale evolution of the gut resistome under selective antibiotic pressure).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA691897, 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 PRJNA646351 data set (Metagenomic data of mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646351, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA694540 data set (Effect of amylin on intestinal microflora in mice).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA694540, 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 PRJNA657446 data set (Alteration of gut microbiota by dietary change in mouse).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA657446, 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
Impact of organic management in soil borne bacterial communities

Evaluation of compost application, winter cover crops and no-tillage in an organic system for soybean, maize and wheat crop rotation in Argentina

Biome: root:Environmental:Terrestrial:Soil:Crop:Agricultural land
Metagenomics of Washed Rind Cheese Communities

We used short and long read metagenomics to look at the microbial diversity of cheese rind biofilms from several washed rind cheeses. Short reads were assembled with metaSPAdes 3.15.3. Oxford Nanopore reads were assembled with metaFlye 2.9.1 and polished with medaka 1.7.2. The following samples were sequenced with both Illumina and Oxford Nanopore Technologies and are samples from the same style of cheese sampled at different times throughout the aging process (early, middle, and late timepoints spanning the standard aging time for each cheese style):
EL2W, EL4W, EL12W (2, 4, 12 weeks)
OM2W, OM4W, OM8W (2, 4, 8 weeks)
WH1M, WH2M, WH4M (1, 2, 4 months)

Biome: root:Engineered:Food production:Dairy products
EMG produced TPA metagenomics assembly of PRJEB52004 data set (Tetracyclines effect on microbiome with and without Influenza infection in mouse.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB52004, 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 PRJNA783624 data set (A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA783624, 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 PRJNA812410 data set (Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA812410, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA799796 data set (Mouse fecal sample Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA799796, 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:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA851186 data set (Outer Membrane Vesicles from the gut microbiome contribute to tumor immunity by eliciting cross-reactive T cells.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA851186, and was assembled with 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:Fecal
EMG produced TPA metagenomics assembly of PRJNA755428 data set (Green tea polyphenols modulate gut virome diversity).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA755428, and was assembled with metaSPAdes v3.15.3, unknown v0.0. 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 PRJEB40312 data set (Analysis of longitudinal shotgun gut metagenomes and gut metabolites on co-housing treatment to examine link between host metabolism and gut microbes relevant to the pathology of PCOS.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB40312, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA691798 data set (Fecal samples of Listeria monocytogenes infected mice metagenomes Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA691798, 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 PRJNA649861 data set (mouse metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA649861, and was assembled with 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 PRJNA843121 data set (Mouse gut metagenome in early life exposure to cyanotoxin.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA843121, 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
Gut microbiome of IBS patients with personalized dietary intervention

In this study the efficacy of AI-based personalized microbiome diet in patients with IBS-Mix is investigated. 25 IBS-M patients (n=25, 19 females) according to Rome IV criteria were enrolled. Fecal samples were obtained from all patients twice (pre- and post intervention) and high-througput 16S rRNA sequencing was performed.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJEB39685 data set (Gut Microbiomes of European Turkey and Veal Calf Herds).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB39685, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Animal:Digestive system:Fecal.

Biome: root:Host-associated:Animal:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJEB49834 data set (The occurrence, prevalence and fate of antibiotic resistant genes and microbial community in Ili river).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB49834, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lotic.

Biome: root:Environmental:Aquatic:Freshwater:Lentic
Holofood Salmon 16S amplicon sequencing

Holofood Salmon 16S amplicon sequencing

Biome: root:Host-associated:Fish:Digestive system
Longitudinal Multi'omics of the Human Microbiome in Inflammatory Bowel Disease

The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi'omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn's disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects' medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
MIMS Environmental/Metagenome sample from human gut metagenome

201 Italian elderly EU FP7 NU-AGE project

Biome: root:Host-associated:Human:Digestive system
16S amplicon sequences of Crete soil meta genomes

Comparison of soil community structure and functional composition across Crete's  vegetation types and ecological zones.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJEB30074 data set (Comparative metagenome analysis of normal and arsenic contaminated soils from ballia district, Uttar Pradesh, India).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30074, and was assembled with SPAdes v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJNA646227 data set (Samples from fecal pellets of two strains of mouse (HLB444 and Black 6); DNA extractions and mWGS sequences.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA646227, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB9443 data set (Integrated microbiome and host profiling in a mouse model of colitis suggests host immune activity drives changes in the gut micro-environment that influence both microbial community structure and gene expression).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9443, 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 PRJEB50255 data set (Mouse gut metagenomes at the early stage after weaning).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB50255, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB44042 data set (Kefir ameliorates specific microbiota-gut-brain axis impairments in a mouse model relevant to autism spectrum disorder).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB44042, 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:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJNA739153 data set (Aging male C57bl/6 mouse gut microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA739153, and was assembled with 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:Fecal