SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the PRJEB8245 data set (Metagenomic sequencing revealed altered microbiota in microscopic colitis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8245.  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
EMG produced TPA metagenomics assembly of the PRJEB9524 data set (Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9524.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Expanded Enteric Virome and Altered Bacterial Microbiome in Acquired Immunodeficiency Syndrome

The effect of HIV on the enteric DNA virome and bacterial microbiome is incompletely characterized. Here we sequenced virus-like particles and bacterial 16S ribosomal RNA genes in stool from 40 HIV-negative subjects, 42 HIV-infected subjects and 40 HIV-infected subjects on anti-retroviral therapy (ART) living in Uganda. CD4 T cell counts inversely correlated with plasma soluble CD14 (sCD14) levels, suggesting increased translocation of pro-inflammatory microbial products across the enteric mucosa with worsening immunodeficiency. Low CD4 T cell counts were associated with expansion of the eukaryotic DNA virome including adenoviruses and Anelloviruses and changes in the bacterial microbiome including increases in Enterobacteriaceae members and decreases in Ruminococci. Thus immunodeficiency in progressive HIV infection is associated with significant alterations in the human enteric virome and bacterial microbiome. These changes may contribute to acquired immunodeficiency syndrome (AIDS) enteropathy, translocation of pro-inflammatory materials across the intestinal mucosa and systemic inflammation associated with progression to AIDS.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJNA397990 data set (Georgia Aquarium Sulfur Denitrification Reactor).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA397990.  This project includes samples from the following biomes: root:Engineered:Bioreactor.

Biome: root:Engineered:Bioreactor
Georgia Aquarium Sulfur Denitrification Reactor


Biome: root:Engineered:Bioreactor
Strain-level typing, community shifts and evidence of co-infection derived from metagenomic investigation of two Salmonella outbreaks

We applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) outbreaks, where the etiologic agents were identified as distinct strains of Salmonella enterica serovar Heidelberg by culture-dependent methods.

Biome: N/A
EMG produced TPA metagenomics assembly of the Strain-level typing, community shifts and evidence of co-infection derived from metagenomic investigation of two Salmonella outbreaks () data set.

The  Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321753.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the ISS Metagenomes (PRJNA438545) data set.

The PRJNA438545 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA438545.  This project includes samples from the following biomes: root:Engineered:Built environment.

Biome: root:Engineered:Built environment
408169 Genome sequencing and assembly

Genome of Marine Group A-SAR406.

Biome: N/A
EMG produced TPA metagenomics assembly of the PRJNA374409 data set (408169 Genome sequencing and assembly).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA374409.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the PRJNA485056 data set (Metagenomic sequencing of stool samples from rural communities from north-eastern Madagascar).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA485056.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJEB27445 data set (Deterministic microbial communities dynamics in salterns exposed to different light intensities).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB27445.  This project includes samples from the following biomes: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
EMG produced TPA metagenomics assembly of the PRJEB19522 data set (Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB19522.  This project includes samples from the following biomes: root:Host-associated:Plants:Phylloplane.

Biome: root:Host-associated:Plants:Phylloplane
Deterministic microbial communities dynamics in salterns exposed to different light intensities

Microbial communities thriving in salterns are influenced by high salinity and high light irradiation. Here, short read metagenomes (Illumina) were sequenced from 3 different ponds. One was applied as control with no environmental stress applied. The other pond was covered with a plastic mess decreasing the environmental light intensity.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Salt crystallizer pond
Metagenomic sequencing of stool samples from rural communities from north-eastern Madagascar

Stool samples from 112 individuals (two villages) in two rural communities of north-eastern Madagascar. Samples were collected by the Madagascar Health and Environmental Research (MAHERY) initiative between 2013 and 2014, and sequenced with Illumina HiSeq 2500.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify.

Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by nitrogen isotope determinations of fern biomass and detection of N2O released. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct near full-length Rhizobiales genomes were identified from leaf-pocket enriched samples from ditch grown A. filiculoides. Annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface sterilized ferns with the Rhizobiales. N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.

Biome: root:Host-associated:Plants:Phylloplane
EMG produced TPA metagenomics assembly of the PRJEB9818 data set (The gut DNA viromes of Malawian twins discordant for severe acute undernutrition).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9818.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Baltic Sea reference metagenome assembly and data sets; transect and redoxcline.

Two out of three datasets (the first one already published with Hugerth et al 2015) included in the Baltic Sea reference metagenome assembly. The assembly include herein is a coassembly of all three datasets, complete with annotated genes to facilitate further studies of the Baltic Sea with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly.

Biome: root:Environmental:Aquatic:Marine:Oceanic
The gut DNA viromes of Malawian twins discordant for severe acute undernutrition

The bacterial component of the human gut microbiota undergoes a definable program of postnatal development. Evidence is accumulating that this program is disrupted in children with severe acute malnutrition (SAM) and that their persistent gut microbiota immaturity, which is not durably repaired with current ready-to-use therapeutic food (RUTF) interventions, is causally related to disease pathogenesis. To further characterize gut microbial community development in healthy versus malnourished infants/children, we performed a time-series metagenomic study of DNA isolated from virus-like particles (VLPs) recovered from fecal samples collected during the first 30 months of postnatal life from eight pairs of mono- and dizygotic Malawian twins concordant for healthy growth, and 12 twin pairs discordant for SAM (either marasmus or kwashiorkor). Both members of discordant pairs were sampled just prior to, during and after treatment with a peanut-based RUTF. Using Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that distinguish different assembly stages of the gut microbiota in the concordant healthy twin pairs. This normal developmental program was impaired in both members of SAM discordant pairs and not repaired with RUTF. Phage plus viruses belonging to the Anelloviridae and Circoviridae families of single-stranded eukaryotic viruses discriminate  discordant pairs from concordant healthy pairs. These results disclose that apparently healthy co-twins in discordant pairs have viromes indicative of familial risk for SAM and provide a human model for delineating normal versus perturbed postnatal acquisition and retention of the gut microbiotas viral component in populations at risk for malnutrition.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Bariatric surgery induces long-term changes on the gut metagenome contributing to fat mass regulation

Bariatric surgery is the most effective procedure for the treatment of obesity. Given the role of the gut microbiota in regulating host metabolism and adiposity, we investigated the long-term effects of bariatric surgery on the human gut metagenome in patients randomized to Roux-en-Y gastric bypass and vertical banded gastroplasty. Genera of the Proteobacteria were specifically enriched after bypass, and the abundance of genes for fatty acid metabolism, nitrogen metabolism and two-component systems was increased after both procedures nine years after surgery. Through colonization of germ-free mice with stools from the patients we demonstrated that the altered gut microbiota promoted reduced fat deposition in recipient mice. Recipients of bypass microbiota also had a lower respiratory quotient, indicating decreased utilization of carbohydrates as fuel. Our results suggest that the gut microbiota may play a direct role in the reduction of adiposity observed after bariatric surgery.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Metagenomic sequencing revealed altered microbiota in microscopic colitis

Microscopic colitis (MC) is a disorder characterized by chronic non-bloody diarrhea predominantly affecting elderly smoking women. Since an altered microbiota is reported in several immune mediated diseases and since MC affects the gut, our hypothesis was that the microbiota would be altered in patients with MC. The bacterial microbiomes was analysed by DNA sequencing (Illumina Hiseq2000). Patients with MC had a marked reduction of Veruccomicrobia (Akkermansia spp) compared to healthy individuals. Specific Akkermansia spp PCR performed on the 10 patients and 7 controls and on an additional 5 female MC-patients confirmed the decreased levels of Akkermansia in MC patients.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the PRJNA231909 data set (A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA231909.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the human gut metagenome 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: PRJNA356225.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.

Biome: root:Host-associated:Human:Digestive system
human gut metagenome Metagenome

This study presented the bacterial diversity of human stool sample from the Vogt-Koyanagi-Harada disease patients in Chinese population

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the PRJEB12124 data set (Gut microbiome-dependent stratification of patients for anti-diabetic treatment).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12124.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJEB9576 data set (Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9576.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Human gut metagenome and metatranscriptome raw sequence reads. (256318) data set.

The 256318 Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA354235.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJEB26427 data set (Understanding the microbial basis of body odor in teenagers and kids).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB26427.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the PRJNA266117 data set (Human skin bacterial metagenome and Virome Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266117.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the PRJNA300541 data set (Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA300541.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJNA275349 data set (Human Microbiome Environment Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA275349.  This project includes samples from the following biomes: root:Host-associated:Human.

Biome: root:Host-associated:Human
Culture-independent assessment of oral microbiota composition in pet reptiles

Culture-dependent surveys of the oral cavity of snakes have found a wide array of potential human pathogens, hence bacterial infections secondary to snakebites and cases of salmonellosis have been linked to the oral microbiota of reptiles. Further, another set of literature records demonstrate that reptile oral bacteria are attributable to prey feces. Here, we used culture-independent16S rDNA amplicon sequencing to characterize the oral microbiota of snakes and other common pet reptiles and to test for the proportion of bacteria reported in literature. In our oral samples the vast majority of reported bacteria were either absent or present in very low proportions. We found strong differences between the taxonomic groups of reptiles, suggesting a highly specific and unique microbiota structure. Moreover, the oral microbiome of snakes was very different from the fecal microbiota reported for mice. Our study provides a first comprehensive survey with next-generation sequencing investigating the oral microbiota of snakes and reptiles in general and points out that it is important to readdress the current knowledge with culture independent techniques.

Biome: root:Host-associated:Reptile:Oral cavity
Soil fungal communities of Chilean temperate rainforests

Soil fungal communities of Chilean temperate rainforests were elucidated by Illumina MiSeq sequencing of the ITS2 region.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America

Microbiome and resistome of human fecal and environmental microbiota from rural El Salvador and peri-urban Lima, Peru

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes

This is a prospective, longitudinal collection of stool samples from infants at risk for disease. Infants from Finland and Estonia were recruited at birth based on HLA risk genotyping. Parents collected their infants' stool at approximately monthly intervals and promptly stored the sample in the freezer prior to shipment for sample processing and sequencing. The cohort comprised of 33 infants, 11 of which seroconverted to serum autoantibody positivity and of those, four developed T1D within the three year time-frame of this study.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome

The gut microbiota has been typically viewed as an environmental factor for human health. Twins are well suited for investigating the concordance of their gut microbiomes and decomposing genetic and environmental influences. However, existing twin studies utilizing metagenomic shotgun sequencing have included only a few samples. Here, we sequenced fecal samples from 250 adult twins in the TwinsUK registry and constructed a comprehensive gut microbial reference gene catalog. We demonstrate heritability of many microbial taxa and functional modules in the gut microbiome, including those associated with diseases. Moreover, we identified 8 million SNPs in the gut microbiome and observe a high similarity in microbiome SNPs between twins that slowly decreases after decades of living apart. The results shed new light on the genetic and environmental influences on the composition and function of the gut microbiome that could relate to risk of complex diseases.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiome-dependent stratification of patients for anti-diabetic treatment

Dysbosis of intestinal microbiota could contribute to the pathogenesis of Type 2 Diabetes. It is yet to be known whether intestinal flora could be related to differential responds to antidiabetic therapies. This study, herein for the first time, metagenomic sequenced fecal samples from a randomized clinical trial on new onset untreated Type 2 Diabetes patients applied two treatment arms, Acarbose and Glipizide (Sulfonylurea) and analyzed the differential responses of intestinal flora in different groups. Results showed substantial impact of Acarbose on gut microbiota community but minor of Glipizide. Enterotypes with similar baseline clinical characteristics, had significant different pharmacologic respond to Acarbose on insulin resistance, gut hormones, bile acids and cardiovascular risks, indicating that different pattern of intestinal microbiota component could determine different responses of Type 2 Diabetes to antidiabetic pharmacological therapies.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A meta-analysis of the effect of high fat diet on the murine gut microbiome

This project contains sequencing data (primarily 16S rRNA amplicon) from multiple published studies which are not already publicly available in a demultiplexed standard format. Note: Samples from Turnbaugh 2008 and 2009 were given pseudo quality scores of 30 (?) and are not suitable for denoising approaches.

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