SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.

The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1461.  This project includes samples from the following biomes: Host-associated, Mammals, Digestive system, Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2_B C12 SIP DNA metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340517.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_A C12 SIP DNA metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340512.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Hong Kong - AD_UKC115_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340750.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from Japan - AD_JPNNA7_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340768.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from USA - AD_UKC075_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340774.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.4.yng.040610 metagenome (rhizosphere metagenome) data set.

The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406163.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.

The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1464.  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 Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.2.yng.030610 metagenome (rhizosphere metagenome) data set.

The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406161.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Col.3.yng.040610 metagenome (rhizosphere metagenome) data set.

The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406162.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the Arabidopsis rhizosphere microbial communities from North Carolina - M.Cvi.2.old.130510 metagenome (rhizosphere metagenome) data set.

The rhizosphere metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406144.  This project includes samples from the following biomes: Host-associated, Plants, Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the Mouse cecum microbial communities from Vienna, Austria - Mucus amended microcosms incubated with D2O metagenome (mouse gut metagenome) data set.

The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375354.  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 Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.

The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1463.  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 Metagenome analysis of fecal microbiota from mouse which was promoted longevity, spatial learning and memory (mouse gut metagenome) data set.

The mouse gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB1460.  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 Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-5-D metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366884.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_92 metaG metagenome (plant metagenome) data set.

The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444456.  This project includes samples from the following biomes: Host-associated, Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - RS_213 metaG metagenome (plant metagenome) data set.

The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444455.  This project includes samples from the following biomes: Host-associated, Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of the Switchgrass associated microbial communities from Austin, Texas, USA, to study host-microbe interactions - LS_167 metaG metagenome (plant metagenome) data set.

The plant metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA444459.  This project includes samples from the following biomes: Host-associated, Plants.

Biome: root:Host-associated:Plants
EMG produced TPA metagenomics assembly of the Ionic liquid and high solid enriched microbial communities from the Joint BioEnergy Institute, USA - AR20-1-D metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366880.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Biogas fermentation microbial communities from Germany - Plant 4 DNA1 metagenome (biogas fermenter metagenome) data set.

The biogas fermenter metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA311376.  This project includes samples from the following biomes: Engineered, Biogas plant.

Biome: root:Engineered:Biogas plant
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550B-02 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367302.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1550B-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367300.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1370A-02 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367270.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R1_A C13 SIP DNA metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340510.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Chrysochromulina tobin associated microbial communities from unialgal haptophyte culture, Seattle, Washington, USA - P5_0mM MetaG metagenome (mixed culture metagenome) data set.

The mixed culture metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406749.  This project includes samples from the following biomes: Environmental, Aquatic, Lentic, Brackish.

Biome: root:Environmental:Aquatic:Lentic:Brackish
EMG produced TPA metagenomics assembly of the Anaerobic biogas reactor microbial communites from Washington, USA - Biogas_R2_B C13 SIP DNA metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340515.  This project includes samples from the following biomes: Engineered, Biogas plant.

Biome: root:Engineered:Biogas plant
EMG produced TPA metagenomics assembly of the Analysis of Microbial Diversity of Kombucha () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA382626.  This project includes samples from the following biomes: Engineered, Food production, Fermented beverages.

Biome: root:Engineered:Food production:Fermented beverages
EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from British Columbia, Canada, to study Microbial Dark Matter (Phase II) - Dewar Creek DC2 2012 metaG metagenome (sediment metagenome) data set.

The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375326.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Sediment.

Biome: root:Environmental:Aquatic:Thermal springs:Sediment
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - metaG 1449B-3 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA367276.  This project includes samples from the following biomes: Environmental, Aquatic, Estuary.

Biome: root:Environmental:Aquatic:Estuary
Inflammation, Antibiotics, and Diet as Concurrent Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease

Dysbiosis in the human intestines, an alteration in the normal composition of the microbiota, characterizes a wide spectrum of diseases, such as infections, irritable bowel syndrome, Crohn's disease. Dysbiosis has been studied extensively but typically characterized cross-sectionally and as alterations in bacterial taxonomic proportions.  The longitudinal contributions of diet, antibiotic use, and inflammation on the evolution of dysbiosis during therapy for Crohn's disease have not been well characterized. Here we used shot-gun metagenomic sequencing of fecal samples collected from a longitudinal prospective cohort of pediatric Crohn's disease subjects to analyze the representation and gene content of all types of organisms present, including bacteria, fungi, archaea and viruses.  Patients initiated treated with either antibodies directed against tumor necrosis factor alpha or enteral nutrition per the treating physician.  Multivariate analysis showed that microbiome composition was associated with three environmental stressors--intestinal inflammation, antibiotic use, and diet.  Bacterial gene signatures suggested that communities in Crohn's samples were responding to oxidative stress. Antibiotic use was associated with a more dysbiotic composition of the bacterial microbiota as well as a distinctive increase in fungal organisms and human DNA content. In contrast, the abundance of tailed phage and archaea was similar in feces of children with Crohn's disease and healthy controls.  Composition of the bacterial and fungal communities were highly correlated. Dysbiosis in bacterial and fungal communities was reduced in patients with reduction of intestinal inflammation by either therapy. Diet had an independent and rapid effect on gut microbiota composition within one week of initiation. Evidently dysbiosis characteristic of Crohn's disease results in part from inflammation and antibiotic use, and involves correlated changes in bacterial and eukaryotic community members.  Notably, the three stressors were independently associated with different bacteria and different gene pathways, reflecting concurrent disruption of normal homeostasis by multiple mechanisms. Thus, while dysbiosis in general is common to multiple disease states, the nature of the dysbiosis is unique to the environmental stressor.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
WINOGRADSKY PLASTIC LOWER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY PLASTIC UPPER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY MONOCROTOPHOS LOWER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY MONOCROTOPHOS UPPER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY QUINALPHOS LOWER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY QUINALPHOS UPPER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY CONTROL LOWER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
WINOGRADSKY CONTROL UPPER LEVEL

The Winogradsky column is a simple device for culturing a large diversity of microorganisms.

Biome: root:Engineered:Lab enrichment:Defined media
METAGENOMIC STUDY OF WAF

The Indian wild ass (Equus hemionus khur) also called the Ghudkhur, Khur or Indian onager in the local Gujarati language, is a subspecies of the onager native to Southern Asia. It is currently listed as Near Threatened by IUCN.

Biome: root:Engineered:Lab enrichment:Defined media
SHEEP FAECAL METAGENOME

Sheep wool has a distinctive "dry" texture, a little like linen, typical of wool from this area.  Because the wool yarn is hand spun, the cloth has a wonderfully irregular texture, full of movement.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
METAGENOME ANALYSIS OF SABARMATI RIVER

The Sabarmati river is one of the major west-flowing rivers in India. It originates in the Aravalli Range of the Udaipur District of Rajasthan and meets the Gulf of Khambhat of Arabian Sea.

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Low land river systems
KHAJOD WASTE WATER

Wastewater is any water that has been affected by human use. Wastewater is "used water from any combination of domestic, industrial, commercial or agricultural activities, surface runoff or stormwater, and any sewer inflow or sewer infiltration". Therefore, wastewater is a byproduct of domestic, industrial, commercial or agricultural activities. The characteristics of wastewater vary depending on the source. Types of wastewater include: domestic wastewater from households, municipal wastewater from communities (also called sewage) or industrial wastewater from industrial activities. Wastewater can contain physical, chemical and biological pollutants.

Biome: root:Engineered:Wastewater
COW DUNG ANALYSIS

GIRCOW DUNG HOST ORGANISMS ANALYSIS

Biome: root:Host-associated:Mammals:Digestive system:Fecal
(1) Personalized microbiome and host features resist gut mucosal colonization by empiric probiotics; (2) Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT

Abstract (1):Empiric probiotics are commonly consumed in healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo, demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured a person-, region- and microbial-specific mucosal colonization patterns, hallmarked by differential baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, highly-individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.Abstract (2):Probiotics are widely prescribed for prevention of antibiotics-associated dysbiosis and related adverse effects. However, probiotic impact on post-antibiotic reconstitution of the gut mucosal host-microbiome niche remains elusive. We invasively examined the effects of multi-strain probiotics or autologous fecal microbiome transplantation (aFMT) on post-antibiotic reconstitution of the murine and human mucosal microbiome niche. Contrary to homeostasis, antibiotic perturbation enhanced probiotics colonization in the human mucosa, but only mildly improved colonization in mice. Compared to spontaneous recovery, probiotics induced a markedly delayed and persistently-incomplete indigenous stool/mucosal microbiome reconstitution and gut transcriptome recovery to steady-state configuration, while aFMT induced a rapid and near-complete recovery within days of administration. In-vitro, Lactobacillus-secreted soluble factors contributed to probiotics-induced microbiome inhibition. Collectively, potential post-antibiotic probiotic benefits may be offset by a compromised microbiome and host recovery, highlighting a need of developing aFMT or personalized probiotic approaches achieving mucosal protection, without compromising microbiome recolonization in the antibiotics-perturbed host.

Biome: root:Host-associated:Human:Digestive system
Structure and function of picoplankton and virus communities along zonal gradients in the South Pacific Ocean

Picoplankton (0.2-2.7 µm fraction) and virus (<0.22 µm fraction) samples were obtained on the BiG-RAPA (Biogeochemical Gradients Role in Arranging Planktonic Assemblages) expedition in the late austral spring of 2010. Additional samples obtained during this expedition include whole community biomass (>0.22 µm fraction) samples that profile a deep (150 m) subsurface chlorophyll maximum in the South Pacific Gyre. High throughput, short read, shotgun sequencing was used to produce metagenomic data from the extracted DNA of these samples. These data enable the assessment of how picoplankton and viral populations are structured along strong physical and chemical gradients on a zonal transect from the upwelling along the western coast of South America to the oligotrophic gyre in the South Pacific.

Biome: root:Environmental:Aquatic:Marine