SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease

Coronary heart disease (CHD) is top risk factor for health in modern society, causing high mortality rate each year. However, there is no reliable way for early diagnosis and prevention of CHD so far. So study the mechanism of CHD and development of novel biomarkers is urgently needed. In this study, metabolomics and metagenomics technology are applied to discover new biomarkers from plasma and urine of 59 CHD patients and 43 healthy controls and trace their origin. We identify GlcNAc-6-P which has good diagnostic capability and can be used as potential biomarkers for CHD, together with mannitol and 15 plasma cholines. These identified metabolites show significant correlations with clinical biochemical indexes. Meanwhile, GlcNAc-6-P and mannitol are potential metabolites originated from intestinal microbiota. Association analysis on species and function levels between intestinal microbes and metabolites suggest a close correlation between Clostridium sp. HGF2 and GlcNAc-6-P, Clostridium sp. HGF2, Streptococcus sp. M143, Streptococcus sp. M334 and mannitol. These suggest the metabolic abnormality is significant and gut microbiota dysbiosis happens in CHD patients.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia

This is a longitudinal collection of stool samples from infants at risk for disease. Approximately 1,000 newborns were recruited to the birth cohort as part of the international DIABIMMUNE Study (http://www.diabimmune.org/) for which the consent rate was 80% in Tartu, Estonia, 59% in Espoo, Finland, and 24% in Petrozavodsk, Russia. Recruitment took place between September 2008 and May 2010 in Estonia and Finland, and between September 2008 and July 2011 in Russia. Follow-up was completed in April 2013 in Estonia and Finland, and in October 2013 in Russia. The final number of children included in the present study was 74 from each country. Inclusion criteria included positive cord blood testing for HLA DR-DQ alleles conferring increased risk for autoimmunity. The participating children were monitored prospectively for infections, use of drugs including antibiotics, and other life events.

Biome: root:Host-associated:Human:Digestive system
Gut microbiota of 10 pairs of Chinese infant twins

Early colonization of intestinal microflora in the human gut is a complex process. It remains unclear when intestinal microflora colonization occurs and how it proceeds. we recruited 10 healthy pairs of twins, including five monozygotic(MZ) and five dizygotic(DZ) twin pairs,who ranged in age from 0 to 6 years old.We performed shotgun metagenomic sequencing on 20 samples and generated averaged data output of 2G per sample.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbial dysbiosis in young adults with obesity

Obesity has become a global epidemic as a high risk factor for type 2 diabetes, cardiovascular diseases and cancer. Besides human genetics, our gut microbiome is another contributor to human obesity. Here we perform metagenome-wide association studies (MGWAS) on fecal samples from a case-control cohort including 95 Chinese young adults with obesity and 105 normal-weight controls, and 23 obese patients after weight-loss treatment. We discover and validate microbial species deregulated in obesity, and show the changes of gut microbial composition after weight-loss treatment.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Marine microbial community from La Parguera, Puerto Rico - BB Mangrove A Liquid metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336672.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Mangrove swamp.

Biome: root:Environmental:Aquatic:Marine
C.diff FMT


Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Uncultured Antibiotic Resistance Genes from Grassland and Agricultural Soil (soil metagenome) data set

The soil metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA244044. This project includes samples from the following biomes : Grassland, Soil.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of the Acid sulfate soil microbial profile - pre-investigation (Acid sulfate soil microbial profile - pre-investigation) data set.

The Acid sulfate soil microbial profile - pre-investigation Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB6384.  This project includes samples from the following biomes: Environmental, Terrestrial, Soil.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
EMG produced TPA metagenomics assembly of the The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics. (Antibiotic resistance within the preterm infant gut.) data set.

The Antibiotic resistance within the preterm infant gut. Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15257.  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
EMG produced TPA metagenomics assembly of the Lab-scale EBPR reactor Metagenome (bioreactor sludge metagenome) data set.

The bioreactor sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA254356.  This project includes samples from the following biomes: Engineered, Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the Richness of human gut microbiome correlates with metabolic markers (MetaHIT-Richness) data set.

The MetaHIT-Richness Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB4336.  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 Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel (Gut microbiota and motility) data set.

The Gut microbiota and motility Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB9169.  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 Comparison of meta-barcoding and shotgun metagenomic analysis of fungi associated with spontaneous wine fermentation (food metagenome) data set.

The food metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA305659.  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 Bioreactor inoculated with sediment Metagenome (bioreactor metagenome) data set.

The bioreactor metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA158439.  This project includes samples from the following biomes: Engineered, Bioreactor, Continuous culture, Marine sediment inoculum, Wadden Sea-Germany.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine sediment inoculum:Wadden Sea-Germany
EMG produced TPA metagenomics assembly of the Wastewater bioreactor microbial communities from Cape Town, South Africa - Thiocy_expt_500_biof metagenome (wastewater metagenome) data set.

The wastewater metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA377111.  This project includes samples from the following biomes: Engineered, Wastewater.

Biome: root:Engineered:Wastewater
EMG produced TPA metagenomics assembly of the Core genomes of cosmopolitan surface ocean plankton (jcvi_gos_circumnavigation) data set

The jcvi_gos_circumnavigation Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB8968. This project includes samples from the following biomes : Marine.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Photic zone
EMG produced TPA metagenomics assembly of the Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2014 (2014 'Omics from the diffuse hydrothermal vents of Axial Seamount) data set

The 2014 'Omics from the diffuse hydrothermal vents of Axial Seamount Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB12000. This project includes samples from the following biomes : Hydrothermal vents.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
EMG produced TPA metagenomics assembly of the Metagenomic characterization of three Swedish sewage treatment plants (Swedish STPs) data set

The Swedish STPs Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14051. This project includes samples from the following biomes : Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
EMG produced TPA metagenomics assembly of the Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life (InfantGut) data set

The InfantGut Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6456. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
EMG produced TPA metagenomics assembly of the mouse gut metagenome Raw sequence reads (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: PRJNA386849.  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 PRJEB2280 data set (Viral metagenomic study of two freshwater Lakes.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB2280.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of the Shotgun sequencing on multiple activated sludge samples (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 PRJNA288131. This project includes samples from the following biomes : Sludge.

Biome: root:Engineered:Wastewater:Activated Sludge
Rabbit INRA sire line 1001 cecal microbiota

Experiment based on a cross fostering between a rabbit line selected for lower residual feed intake and a non-selected control line to study direct and maternal effects of feed efficiency

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
Turkey intestinal contents Raw sequence read

Turkeys were fed an antibiotic (bacitracin methylene disalicylate (BMD)) at sub-therapeutic (50g/ton of feed) or therapeutic (200g/ton) concentrations for 14 weeks, and its effect on turkey intestinal microbial communities were evaluated by 16S rRNA gene analysis.

Biome: root:Host-associated:Birds:Digestive system
16S rRNA Marker-gene survey Two-sample titration dataset

16S rRNA marker-gene survey assessment dataset generated using mixtures of human stool DNA extracts. We used samples collected from participants in an Enterotoxigenic Escherichia coli (ETEC) vaccine trial. A two-sample titration mixture design was used where DNA from stool samples collected prior to ETEC exposure were titrated into stools samples collected after exposure, in effect diluting the amount of ETEC in the mixed sample. Independent titration series were produced using samples from five trial participants. The titration series consisted of 9 samples including the unmixed samples. Four 16S PCR replicates were generated for each titration. The PCR products were sent to two independent laboratories for library preparation and sequencing. The libraries were sequenced twice at each laboratory resulting in four sequencing datasets.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
High temporal resolution study of coastal marine microbial communities Raw sequence reads

Weekly microbial time-series sampling was conducted at two coastal sites in Sydney, Australia based on their exposure to high (Foreshore Beach) and low (Maroubra Beach) stormwater and sewage pollution. Foreshore Beach, within Botany Bay is frequently exposed to stormwater input, as well as periodic sewage overflows released from upstream overflow outlets and discharged into Botany Bay. Maroubra Beach is east facing, exposed to the Tasman Sea, where water quality is less impacted by stormwater input.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Microbial drivers of the human pharyngeal microbiome are associated with age-related macular degeneration

While the etiology of age-related macular degeneration (AMD), a major blinding disease, remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with Neisseria meningitidis, a bacterial colonizer of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. Shotgun sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 260 AMD patients and 386 controls.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
A Multi-Omic Association Study of Trimethylamine N-Oxide

Trimethylamine N-Oxide (TMAO) is a circulating metabolite that has been implicated in the development of atherosclerosis and cardiovascular disease. Manor et al. identify blood markers, metabolites, proteins, gut microbiota patterns, and diets that are significantly associated with levels of plasma TMAO.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
human gut metagenome Raw sequence reads

Raw sequence reads of human gut metagenome

Biome: root:Host-associated:Human:Digestive system
Who eats the tough stuff  DNA stable isotope probing (SIP) of bacteria and fungi degrading 13C-labelled lignin and cellulose in forest soils

Decomposition and storage of plant-derived carbon has become a hot topic in environmental research. Since carbon dioxide has been detected as one of the most relevant drivers of global climate change, its potential storage and fate in soils has become key for predicting climate scenarios. Unfortunately, studies with a focus on the decomposition and driving factors are still lacking for precise modelling of the fluxes in a changing world. The main actors of carbon degradation in soils have not been fully identified, especially in regard to bacteria very little is known about their contribution to degradation of persistent carbon components. In the present study, the active microbial community involved in degrading 13C-labelled cellulose and lignin in forest soils was identified using a DNA stable isotopic probing (SIP) approach. Microbial activity assessed by measurements of 13CO2 increased with labelled substrate addition, during a 28 days incubation period. Within the vast microbial communities, bacterial and fungal members specialized in degrading cellulose (e.g. Devosia (Rhizobiales), Sebacinales), lignin (e.g. Sphingopyxis (Sphingomonadales), Paucibacter (Burkholderiales), Xylariales, Auriculariales, Helotiales), and both substrates (e.g. Caulobacter (Caulobacterales), Schizoporaceae, Orbiliales) have been identified. Over the course of the experiment, a successional shift from early degrading colonizers (e.g. Brevundimonas (Caulobacterales), Trichosporonales, Hymenochaetales, Gomphales) to late stage beneficiary microorganisms (e.g. Sphingopyxis (Sphingomonadales), Devosia (Rhizobiales), Orbiliales) became evident. These results provide novel insights into the degradation processes of woody plant debris in soil, disentangling the active microbial degraders from the beneficiaries, within the vast complexity of the soil microbiome.

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
16s rRNA sequencing of mice fecal microbiota

Mouse gut microbiota diversity under conditions of different feed was sequenced using a HiSeq 2500 platform.

Biome: root:Host-associated:Mammals:Digestive system
Influence of maternal microbiology on the microbiological and immunological health of the developing bovine intestinal tract.

Digesta and epithelial scrapings from domestic cattle between birth and 21 days of age.

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

Characterization of the bacterial communities associated with the rhizosphere and soils surrounding Arabidopsis and Brachypodium

Biome: root:Host-associated:Plants:Rhizosphere
Fecal microbiota of patients over time at one long-term acute care hospital

Multidrug-resistant organisms (MDROs) pose an increasing public health threat, particulary in healthcare-associated environments. One such organism of increasing concern are the carbapenemase-producing Enterobacteriaceae (CPE), for which few effective antibiotics exist. Because gastrointestinal tract colonization precedes infection in many patients, preventing initial acquisition in the GI tract is one potential strategy to limit this serious disease. This longitudinal study aimed to identify risk factors associated with acquisition of CPE, including patient clinical variables and the resident gut microbiota throughout patient stay, at one longterm acute care hospital.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.

It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal adenomatous polyps, we compared change in the microbiome composition after a 3-year intervention in a subset of participants randomized to oral UDCA at 8-10 mg/kg of body weight per day (n = 198) or placebo (n = 203). Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This reflected a UDCA-associated shift in microbial community composition (P < 0.001), independent of sex, with no evidence of a UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P > 0.05) in men or women. Separate analyses of microbial networks revealed an overrepresentation of Faecalibacterium prausnitzii in the post-UDCA arm and an inverse relationship between F prausnitzii and Ruminococcus gnavus. In men who received UDCA, the overrepresentation of F prausnitzii and underrepresentation of R gnavus were more prominent in those with no adenoma recurrence at follow-up compared to men with recurrence. This relationship was not observed in women. Daily UDCA use modestly influences the relative abundance of microbial species in stool and affects the microbial network composition with suggestive evidence for sex-specific effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.[This text is derived from our Open Access publication of the same title as this project.]

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
the upper respiratory tract microbiome of chronic rhinosinusitis patients

Swab samples were taken from the anterior nares (nose), nasopharynx, maxillary sinus and ethmoid sinus of 200 patients with chronic rhinosinusitis. Bacterial DNA was extracted, the V4 region of the 16S rRNA gene was amplified by PCR and the libraries were sequenced on an Illumina MiSeq machine. Samples were sequenced on five different runs.

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

We developed an open-source R package, decontam, to identify and remove contaminating DNA sequences from marker-gene and metagenomics datasets. We validated decontam on a 16S rRNA gene oral mucosa microbiome dataset generated in our laboratory, and on additional datasets derived from previous studies.

Biome: root:Host-associated:Human:Digestive system:Oral
Arable land and chronosequenced forest land soil from different depth Raw sequence reads

Our study's aim was to investigate the vertical assembly of soil microbiomes at a fine scale during the successional development of restored ecosystems, and their contribution to soil ecosystem multi-nutrients cycling at subsurface profiles.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Raw sequence reads

CA Study

Biome: root:Host-associated:Human:Digestive system
Body site is a more determinant factor than human population diversity in healthy skin microbiome

To characterize the diversity of cutaneous microbiomes in different ethnic groups.

Biome: root:Host-associated:Human:Skin
Corbiculate bee gut amplicons Raw sequence reads

16S rRNA amplicons from corbiculate bee gut community

Biome: root:Host-associated:Insecta:Digestive system
Soil microbial distribution

Soil microbial distribution in agricultural lands

Biome: root:Environmental:Terrestrial:Soil:Agricultural