SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Microbial biogeography of 925 geothermal springs in New Zealand

Geothermal springs are model ecosystems to investigate microbial biogeography as they represent discrete, relatively homogenous habitats, are distributed across multiple geographical scales, span broad geochemical gradients, and have reduced metazoan interactions. Here, we report the largest known consolidated study of geothermal ecosystems to determine factors that influence biogeographical patterns. We measured bacterial and archaeal community composition, 46 physicochemical parameters, and metadata from 925 geothermal springs across New Zealand (13.9100.6 C and pH <19.7). We determined that diversity is primarily influenced by pH at temperatures <70 C; with temperature only having a significant effect for values >70 C. Further, community dissimilarity increases with geographic distance, with niche selection driving assembly at a localised scale. Surprisingly, two genera (Venenivibrio and Acidithiobacillus) dominated in both average relative abundance (11.2% and 11.1%, respectively) and prevalence (74.2% and 62.9%, respectively). These findings provide an unprecedented insight into ecological behaviour in geothermal springs, and a foundation to improve the characterisation of microbial biogeographical processes.

Biome: root:Environmental:Aquatic:Thermal springs
Nasal Microbiome Samples from NYU-Rutgers Cohort

The nasal lavage samples

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal:Nasal cavity
EMG produced TPA metagenomics assembly of the Hospital Metagenomics (Colonization and Succession of Hospital-Associated Microbiota) data set.

The Colonization and Succession of Hospital-Associated Microbiota Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13117.  This project includes samples from the following biomes: Engineered,Built environment.

Biome: root:Engineered:Built environment
EMG produced TPA metagenomics assembly of the Gut microbiota of 10 pairs of Chinese infant twins (Gut microbiota of 10 pairs of Chinese infant twins) data set.

The Gut microbiota of 10 pairs of Chinese infant twins Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12669.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the Metagenomics of BMS sulfide deposits (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5792.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Hydrothermal vents, Sediment.

Biome: N/A
EMG produced TPA metagenomics assembly of the Metal availability predicts community metallogenomes in marine oxygen minimum zones (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA254808.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: N/A
EMG produced TPA metagenomics assembly of the Marine microbial communities from Deepwater Horizon Oil Spill, sample DHOS BM58 plume metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336904.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.

Biome: N/A
EMG produced TPA metagenomics assembly of the metagenomic data for ekhotsk sea () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA398459.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: N/A
EMG produced TPA metagenomics assembly of the Red Sea metagenomes (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA289734.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: N/A
EMG produced TPA metagenomics assembly of the Marine sediment microbial communities from Kolumbo Volcano mats, Greece - white/grey mat metagenome (marine sediment metagenome) data set.

The marine sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA337731.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Hydrothermal vents, Microbial mats.

Biome: N/A
Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 2 metagenome


Biome: N/A
EMG produced TPA metagenomics assembly of the Marine microbial communities from expanding oxygen minimum zones in Line P, North Pacific Ocean - fosmids plate 2 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330364.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of the Oral microbiome samples from the Philippines (Phillipines oral microbiome) data set.

The Phillipines oral microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14383.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral, Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of the Marine microbial communities from Deepwater Horizon Oil Spill, sample DHOS OV011 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336903.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Oceanic, Oil-contaminated.

Biome: N/A
Estuarine microbial communities from the Columbia River estuary - Flood tide non-ETM metaG S.733 metagenome

Sequencing of microbial communities from the Columbia River estuary to analyze effect of nutrient fluxes

Biome: N/A
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Flood tide non-ETM metaG S.733 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365284.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
EMG produced TPA metagenomics assembly of the Pediatric Fecal Metagenome (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 PRJNA215106. 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 stool samples Raw sequence reads (stool) data set

The stool Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA363080. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the A metagenome-wide association study of gut microbiota in type 2 diabetes. (gut metagenome) data set.

The gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA422434.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.

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

Functional metagenomic selections were performed from various pediatric fecal metagenomes, enriched for children in the first two years of life. A major goal was to understand how antibiotic resistance genes establish and propagate among developing intestinal microbiomes.  Fecal metagenomic DNA was cloned into an E. coli library and subjected to selections for antibiotic resistance. After selection, resistance-conferring fragments (the only fragments conferring survival to E. coli in the presence of the drugs) were PCR-amplified, sequenced, and assembled.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
stool samples Raw sequence reads

stool and meconium 16s RNA samples Raw sequence reads

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Roux-en-Y gastric bypass surgery of morbidly obese patients shows swift and persistent changes of the individual gut microbiota (GBP) data set

The GBP Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12947. This project includes samples from the following biomes : Human gut.

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

Gut microbiome diversity

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Rapid evolution of the human gut virome (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 PRJNA196801. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the Human gastric microbiome metagenome (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 PRJNA297869. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Intestine
Human gastric microbiome metagenome

Human gastric microbiome

Biome: root:Host-associated:Human:Digestive system:Large intestine
Rapid evolution of the human gut virome

Longitudinal characterization of intestinal viral particles from WGS sequence.

Biome: root:Host-associated:Human:Digestive system
Metagenome sequencing of the Hadza hunter-gatherer gut microbiota.

By human microbiome sequencing we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that align with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little to no antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with environment and lifestyle, and how complexity from the exogenous environment is matched by endogenous homeostasis. The Hadza gut metagenome structure allows to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the Metagenomes from human infant fecal samples with and without necrotizing enterocolitis (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: PRJNA273761.  This project includes samples from the following biomes: Host-associated, Animal, Digestive system, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
human gut and groundwater harbor non-photosynthetic bacteria

S. C. Di Rienzi, I. Sharon, K. C. Wrighton, O. Koren, L. A. Hug, B. C. Thomas, J. K. Goodrich, J. T. Bell, T. D. Spector, J. F. Banfield, and R. E. Ley, The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria., Elife, vol. 2, pp. e01102e01102, Jan. 2013.

Biome: N/A
EMG produced TPA metagenomics assembly of the human gut and groundwater harbor non-photosynthetic bacteria (metagenome) data set.

The metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321218.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
EMG produced TPA metagenomics assembly of the seawater metagenome Genome sequencing and assembly (seawater metagenome) data set.

The seawater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA329908.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of the human gut metagenome in RA (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: PRJNA356102.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.

Biome: root:Host-associated:Human:Digestive system
seawater metagenome Metagenomic assembly

ESRF shotgun metagenomics project

Biome: root:Environmental:Aquatic:Lentic:Brackish
human gut metagenome in RA

Gut microbiome make contributions to human host, and intestinal dysbiosis is associated with rheumatoid arthritis. Here we firstly demonstrated that the human gut microbiome related to rheumatoid arthritis could be divided into subtyping groups under different human enterotypes, which indicate the associations between rheumatoid arthritis and gut microbiome were diverse. In rheumatoid arthritis-related microbiota, Prevotella could be an indicator of early rheumatoid arthritis patients but insufficient to differentiate RA patients from healthy controls, and Bacteroides coprocola enriched in group 3 and Bacteroides dorei enriched in group 4 were considered to be as indicators of serious rheumatoid arthritis patients. Our findings provide additional evidences supporting that rheumatoid arthritis is a heterogeneous disease. Thus, the study of association between disease and gut microbiome should be conducted under different human gut enterotypes.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the sludge metagenome Metagenomic assembly (sludge metagenome) data set.

The sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA427366.  This project includes samples from the following biomes: Engineered, Wastewater, Water and sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Identification of fungi and ameba from human wound genomic sequencing (human wound) data set

The human wound Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA344941. This project includes samples from the following biomes : Human skin.

Biome: root:Host-associated:Human:Circulatory system
Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn''s disease

This is an uncontrolled, prospective open-label study of FMT from healthy donors to subjects with active CD. A single FMT was performed via colonoscopy. Stool samples were collected prior to FMT and at two time points, four and eight weeks after FMT. Recipients microbial diversity, mucosal T-cell phenotypes and clinical and inflammatory parameters were measured over 12 weeks, and safety over 26 weeks.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
sludge metagenome Metagenomic assembly

Sludge from the petroleum refinery having phenol-degrading bacteria for the study of genetic evolution in bacteria

Biome: root:Engineered:Wastewater:Activated Sludge
Identification of fungi and ameba from human wound genomic sequencing

Hypothesis-free detection of pathogens directly in sample material from patients with infectious diseases of unknown origin using next generation sequencing (NGS) is an important goal of diagnostic research. However, NGS is highly susceptible to contamination, which complicates the interpretation of diagnostic results from samples with (poly-)microbial contamination. The potential of NGS for hypothesis-free diagnostic approaches of such difficult sample material is examined in the study presented here, using the example of formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and invasive amebiasis.

Biome: root:Host-associated:Human:Circulatory system
Metagenomes from human infant fecal samples with and without necrotizing enterocolitis

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. This study compares microbial communities of 10 co-hospitalized infants, five of which had a diagnosis of necrotizing enterocolitis.  Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, a genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants that developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically-relevant time scales.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the A DSS colitis mouse model was used to assess the microbial metabolic landscape during inflammation. (Metagenomic sequencing of cecal microbiota from DSS colitis mouse model) data set.

The Metagenomic sequencing of cecal microbiota from DSS colitis mouse model Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15095.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the WGS of Acinetobacter baumannii ATCC 17978 passaged in presence of antibiotics in mouse model () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA485355.  This project includes samples from the following biomes: Host-associated, Mammals, Respiratory system.

Biome: root:Host-associated:Mammals:Respiratory system
EMG produced TPA metagenomics assembly of the Sheep faecal microbiota (Sheep faecal microbiota) data set.

The Sheep faecal microbiota Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14312.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Midgut
EMG produced TPA metagenomics assembly of the PRJNA477326 data set (Identification of bloodstream pathogens in the gut microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA477326.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Identification of bloodstream pathogens in the gut microbiome

Identify enteric strains matching patient bloodstream isolates.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Sheep faecal microbiota

In this study, faecal 16S rDNA (V4) profile, metagenome and metaproteome were analyzed from five lactating Sarda sheep coming from the same flock, free-grazing and with no evidence of clinical symptoms. DNA sequences were obtained using an Illumina HiScan instrumentation.

Biome: root:Host-associated:Mammals:Digestive system:Midgut
Sus scrofa domesticus Metagenome

We describe here the metagenomics-derived viral sequences found in fecal samples collected from adult pigs with diarrhea in China. Feces can be the source of numerous viral infections in humans and animals. A library was then constructed using Nextera XT DNA Sample Preparation Kit (Illumina) and then sequenced using the Miseq Illumina platform with 250 bases paired ends with a distinct molecular tag .

Biome: N/A
EMG produced TPA metagenomics assembly of the Sus scrofa domesticus Metagenome (Sus scrofa domesticus) data set.

The Sus scrofa domesticus Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA475617.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
A DSS colitis mouse model was used to assess the microbial metabolic landscape during inflammation.

A total of 24 C57BL6 mice were used for this analysis. Six mice received dextran sodium sulfate (DSS) (3%) in their drinking water ab libitum. In addition to DSS treatment 6 mice were given sodium tungstate (0.2%) or sodium tungstate plus DSS in their drinking water ab libitum. A control group was included where 6 mice were given untreated water. All animals received their treatments for a total of 9 days.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
WGS of Acinetobacter baumannii ATCC 17978 passaged in presence of antibiotics in mouse model

Acinetobacter baumannii ATCC17978 was infected oropharyngeally into Balb/c mice or in Balb/c mice depleted of neutrophils by cyclophosphamide treatment. Mice were treated with various antibiotics, and infection was allowed to proceed for 24 hours before lungs were removed and bacteria were pooled. The pooled bacteria were either sequenced en masse, or used to reinfect mice to enrich for bacteria resistant to the antibiotic. At least three parallel lines of bacteria were maintained during the sequential passaging in either the neutrophil replete or depleted mice. Data deposited are the total sequencing reads of the pool to identify mutants that arose after each passage, the relative abundance of each of the mutants. Passage number refers to the number of sequential passages. Cyclophosphamide refers to neutrophil depleted mice.

Biome: root:Host-associated:Mammals:Respiratory system