SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomic characterization of the human intestinal microbiota in faecal samples from STEC-infected patients

The human intestinal microbiota is a homeostatic ecosystem with a remarkable impact on human health and the disruption of this equilibrium leads to an increased susceptibility to infection by numerous pathogens. In this study, we used shotgun metagenomic sequencing and two different bioinformatics approaches, to investigate possible changes in the composition of the intestinal microbiota in samples from patients with STEC infection compared to healthy and healed controls, collected during an outbreak caused by a STEC O26:H11 infection. Regardless of the bioinformatic procedure used, a good resolution of the taxonomic profiles of the samples was achieved. The faeces collected from the STEC infected patients showed a lower intestinal abundance of the beneficial microorganisms Bifidobacterium and Clostridiales spp. in comparison to controls where those microorganisms predominated. These differences were observed with both bioinformatic approaches used and seemed to be related with the STEC infection although the variation in the relative abundance of the members of the Bifidobacterium genus could have also been associated with the dysbiotic status following the diarrhoea.Finally, the metagenomic sequencing allowed to identify in the STEC positive samples, all the virulence traits present in the genomes of the STEC O26 that caused the outbreak. The results shown represent a first evidence of the changes occurring in the intestinal microbiota of children in the course of STEC infection and indicate that metagenomics may be a promising tool for the culture-independent clinical diagnosis of the infection.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Blue Mountains Swamp Bacteria

Blue Mountains Swamp Bacteria

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Swamp
EMG produced TPA metagenomics assembly of the Linking Lifestyle to the Oral and Gut Microbiota in a Large Prospective Cohort (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 PRJNA188481. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system
Metagenome Analysis of palm oil mill effluent

Metagenome Analysis of palm oil mill effluent

Biome: root:Engineered:Wastewater:Industrial wastewater:Agricultural wastewater
16S rRNA gene sequencing (Primers 518F and 806R, Illumina MiSeq 150pb-PE) of SIP fractions following glucose amendment in Organic vs Conventional management systems and annual vs perennial crops.

16S rRNA gene sequencing (Primers 518F and 806R, Illumina MiSeq 150pb-PE) of SIP fractions following glucose amendment in Organic vs Conventional management systems and annual vs perennial crops.

Biome: root:Environmental:Terrestrial:Soil:Crop
characterization of gut microbiota profiles in nod2-/- and nod2+/+ mice and effect of genotype and environment on severity of colitis

characterization of gut microbiota profiles in nod2-/- and nod2+/+ mice and effect of genotype and environment on severity of colitis

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Microbial communities in drinking water systems

Microbial communities in drinking water systems

Biome: root:Environmental:Aquatic:Freshwater:Drinking water
metagenomes from three stations

metagenomes from three stations

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Shotgun Metagenomic Analysis of Microbial Composition of Kombucha

Shotgun Metagenomic Analysis of Microbial Composition of Kombucha

Biome: root:Engineered:Food production:Fermented beverages
New species of Methylomirabilis

New species of Methylomirabilis

Biome: root:Host-associated:Microbial
Dietary fat-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis

Dietary fat-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis

Biome: root:Host-associated:Mammals:Digestive system
Gut bacteria from giant stick insect guts

Gut bacteria from giant stick insect guts

Biome: root:Host-associated:Insecta:Digestive system
Library of 16S RNA, amplicon, from microbial community

Library of 16S RNA, amplicon, from microbial community

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Skin microbiota of Scinax alcatraz

Skin microbiota of Scinax alcatraz

Biome: root:Host-associated:Amphibia
soil microbiota in 2 different forest

soil microbiota in 2 different forest

Biome: root:Environmental:Terrestrial:Soil:Forest soil
skin microbiota in infected frogs

skin microbiota in infected frogs

Biome: root:Host-associated:Amphibia
Variations on the diversity of amphibian skin microbiota across forests fragments

Variations on the diversity of amphibian skin microbiota across forests fragments

Biome: root:Host-associated:Amphibia
Diversity of  Picoeukaryotic community in the Gulf of Gabès (south-eastern Mediterranean)

Diversity of  Picoeukaryotic community in the Gulf of Gabès (south-eastern Mediterranean)

Biome: root:Environmental:Aquatic:Marine
The rumen microbial metagenome associated with high methane production in cattle

The rumen microbial metagenome associated with high methane production in cattle

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
gut microbiota of mice treated with ag-nanoparticles

gut microbiota of mice treated with ag-nanoparticles

Biome: root:Host-associated:Mammals:Digestive system:Fecal
DeepHotMicrobe - genomic clues on microbial adaptation to life in deep bedrock

DeepHotMicrobe - genomic clues on microbial adaptation to life in deep bedrock

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Cave water
Metatranscriptome analysis of maize rhizosphere microbiome under nanosilver exposure

Metatranscriptome analysis of maize rhizosphere microbiome under nanosilver exposure

Biome: root:Host-associated:Plants:Rhizosphere
The diversity of bacteria in marine sediments of the Barents Sea

The diversity of bacteria in marine sediments of the Barents Sea

Biome: root:Environmental:Aquatic:Marine:Sediment
Hot water plumbing microbiome

Hot water plumbing microbiome

Biome: root:Engineered:Built environment
Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2015

Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount from 2015

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Diffuse flow
Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.

Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for small DNA viruses.

Biome: root:Environmental:Aquatic:Marine
Pilot Study DBT-BBSRC

Pilot Study DBT-BBSRC

Biome: root:Host-associated:Birds
Classification and quantification of commensal lysogens and induced prophages in the gut bacterial and phage metagenomes

Classification and quantification of commensal lysogens and induced prophages in the gut bacterial and phage metagenomes

Biome: root:Host-associated:Mammals:Digestive system:Fecal
This project studies the global transcriptional changes of P. veronii 1YdBTEX once it is introduced in different soils which contain a establish resident microbial community. We would like to characterize the response from the resident community members to the introduced strain.

This project studies the global transcriptional changes of P. veronii 1YdBTEX once it is introduced in different soils which contain a establish resident microbial community. We would like to characterize the response from the resident community members to the introduced strain.

Biome: root:Environmental:Terrestrial:Soil
The influence of sludge retention time on the  expressed functional diversity of and biotransformation rates of micropollutants performed by a community originating from wastewater activated sludge

The influence of sludge retention time on the  expressed functional diversity of and biotransformation rates of micropollutants performed by a community originating from wastewater activated sludge

Biome: root:Engineered:Wastewater:Activated Sludge
Metagenomic study on pasturelands chronically exposed to pesticides

Metagenomic study on pasturelands chronically exposed to pesticides

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Correlation between gut microbiota and presence of fecal fungal isolates in Crohn's disease patients.

Correlation between gut microbiota and presence of fecal fungal isolates in Crohn's disease patients.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Host-microbiome interactions

Host-microbiome interactions

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
wastewater metagenomics Orsay site 01

wastewater metagenomics Orsay site 01

Biome: root:Engineered:Wastewater
Aortite

Aortite

Biome: root:Host-associated:Human:Circulatory system
16S data - Multi-omics Differentially Classify Disease State and Treatment Outcome in Pediatric Crohn's Disease

16S data - Multi-omics Differentially Classify Disease State and Treatment Outcome in Pediatric Crohn's Disease

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Benguela Upwelling sediments metagenome study

Benguela Upwelling sediments metagenome study

Biome: root:Environmental:Aquatic:Marine:Sediment
Small mammal faecal metagenome and its relevance in emerging zoonotic infections.

Small mammal faecal metagenome and its relevance in emerging zoonotic infections.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
A/B testing for colon model

A/B testing for colon model

Biome: root:Host-associated:Human
Respiratory tract metagenomics for Respiratory Disease Complex in Poultry

Respiratory tract metagenomics for Respiratory Disease Complex in Poultry

Biome: root:Host-associated:Birds:Respiratory system
Pesticide degrading bacterial populations on glacier

Pesticide degrading bacterial populations on glacier

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacier
ICU_metagenomics_Using_16S_rRNA_analysis_for_assessing_the_respiratory_bacterial_infection_threat_to_immunocompromised_patients_within_Intensive_Care_Units

ICU_metagenomics_Using_16S_rRNA_analysis_for_assessing_the_respiratory_bacterial_infection_threat_to_immunocompromised_patients_within_Intensive_Care_Units

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human fecal microbiome

Human fecal microbiome

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP)

Nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP)

Biome: root:Environmental:Aquatic:Marine
Bacterial communities in two seasons

Bacterial communities in two seasons

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Metagenomics 1st 5 data

Metagenomics 1st 5 data

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

The_mechanism_of_nutritional_therapy_for_Paediatric_Crohn_s_disease

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from Acid Mine Drainage

Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from Acid Mine Drainage

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Acid Mine Drainage
Effects of seasonality and previous logging on wild lemur gastrointestinal microbial composition, nematode infections and their interactions

Effects of seasonality and previous logging on wild lemur gastrointestinal microbial composition, nematode infections and their interactions

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Effects of milk on gut microbiome

Effects of milk on gut microbiome

Biome: root:Host-associated:Mammals:Milk
Euprymna scolopes accessory nidamental gland and egg jelly coat bacterial communities

Euprymna scolopes accessory nidamental gland and egg jelly coat bacterial communities

Biome: root:Host-associated:Mollusca
Community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction.

Community composition and ultrastructure of a continuous bioreactor enrichment culture, in which anaerobic methane oxidation (AOM) was coupled to nitrate reduction.

Biome: root:Engineered:Bioreactor:Continuous culture
Amplicon sequencing of 16S rRNA of bacterial communities from deep-sea surface sediments in pressure and food source experiments

Amplicon sequencing of 16S rRNA of bacterial communities from deep-sea surface sediments in pressure and food source experiments

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Modulation of the piglets' microbiota: differential effects by a high wheat bran maternal diet during gestation and lactation

Modulation of the piglets' microbiota: differential effects by a high wheat bran maternal diet during gestation and lactation

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka

Structure and function of epispheric microbial communities from Warszawa, Białowieża and Bóbrka

Biome: root:Host-associated:Plants:Phylloplane
the relationships between gut microbiome and environmental chemicals

the relationships between gut microbiome and environmental chemicals

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs

We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Metatranscriptome reveals the function shifts of the vaginal microbiome during the treatment of bacterial vaginosis

Metatranscriptome reveals the function shifts of the vaginal microbiome during the treatment of bacterial vaginosis

Biome: root:Host-associated:Human:Reproductive system:Vagina
TSLR sequencing of landsort deep oxycline

TSLR sequencing of landsort deep oxycline

Biome: root:Environmental:Aquatic:Marine
Metagenomic study from hydrothermal sediments retrieved from Menez Gwen and Rainbow deep-sea vents.

Metagenomic study from hydrothermal sediments retrieved from Menez Gwen and Rainbow deep-sea vents.

Biome: root:Environmental:Aquatic:Thermal springs:Sediment
Area of habitation strongly influences faecal microbial composition of wild lemurs

Area of habitation strongly influences faecal microbial composition of wild lemurs

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Study of bacteriome from urban sediment: behavior according chemical and physical variables

Study of bacteriome from urban sediment: behavior according chemical and physical variables

Biome: root:Environmental:Aquatic:Freshwater:Sediment
gut mcrobiome research

gut mcrobiome research

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells

Poly iron sulfate flocculant as an effective additive for improving the performance of microbial fuel cells

Biome: root:Engineered:Lab enrichment
16S rRNA gene amplicon sequences of high-pressure bioelectrode microbiotas

16S rRNA gene amplicon sequences of high-pressure bioelectrode microbiotas

Biome: root:Engineered:Bioreactor
Bacterial communities in kimchi manufacturing process

Bacterial communities in kimchi manufacturing process

Biome: root:Engineered:Food production:Fermented vegetables
Anaerobic digester microbiome in Stickney WRP

Anaerobic digester microbiome in Stickney WRP

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
Heterotrophic methanogens dominate in anaerobic digesters

Heterotrophic methanogens dominate in anaerobic digesters

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
Evaluation of the potential for ammonia biofiltration using mature composts based on bacteriome analyses targeting 16S rRNA genes

Evaluation of the potential for ammonia biofiltration using mature composts based on bacteriome analyses targeting 16S rRNA genes

Biome: root:Engineered:Solid waste:Composting
Effects of NaCl concentrations on anode microbes in microbial fuel cells inoculated with mangrove soils

Effects of NaCl concentrations on anode microbes in microbial fuel cells inoculated with mangrove soils

Biome: root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum
Bacterial community of Korean traditional fermented foods

Bacterial community of Korean traditional fermented foods

Biome: root:Engineered:Food production:Fermented vegetables
food metagenome Metagenome

food metagenome Metagenome

Biome: root:Engineered:Food production:Fermented seafood
4 samples from Pacific Ocean uncultured phage metagenome

 Anaerobic oil degrading sediment metagenome - anaerobic subsurface sediments containing Monterey Formation oil and hydrocarbon gasses; sample description: Shane Seep; Coal Oil Point hydrocarbon seep field, offshore Goleta, CA.  0.22 micron filtered; CsCl-gradient; DNAse treatment.      <p>  ANME metagenome - carbonate mound formed by hydrate crystalization and expansion;  actively releasing methane from sediments; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment, amplified via MDA with phi29 polymerase.     <p>  Methanogenic sediments metagenome - anoxic sediments from center of Santa Barbara Basin. Basin water exhibits suboxic conditions at sampling depth.  Subsurface environment detailed in refs 1&2.  Methanogenesis confirmed through intermittent incubation headspace analyses; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment.     <p>  Benthic methanotrophic mats metagenome - sample cultivated ~1 month above active hydrocarbon gas vent; sample description: 0.22 micron filtered; CsCl-gradient; DNAse treatment.   

Biome: root:Environmental:Aquatic:Marine:Oceanic
Bioreactor scalability: laboratory-scale bioreactor design influences bioreactor performance, ecology and community physiology in expanded granular sludge bed bioreactors

Feasibility studies of new biotechnologies inevitably begin with laboratory-scale trials however rarely do we determine whether laboratory-scale results reflect full-scale performance or ecology. This study aims to bridge that knowledge gap using the expanded granular sludge-bed bioreactor (EGSB), a high-rate anaerobic digester type, as a model for study.Two laboratory-scale idealizations of the EGSB – a one-dimensional and a three- dimensional scale-down of a full-scale design – were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays and a range of physical and chemical monitoring methods.SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale.  We observed that bioreactor idealization at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance.

Biome: root:Engineered:Bioreactor:Continuous culture
The microbial content of raw and pasteurised cow's milk as determined by molecular approaches including sequencing

The microbial composition of raw and pasteurised milk is assessed by industry on a daily basis. However, many such tests are culture-dependent and thus bacteria that are present at sub-dominant levels and/or that cannot be easily grown in the laboratory may be overlooked. To address this potential bias, we have employed a number of culture-independent techniques, including flow cytometry, real-time qPCR and high throughput sequencing, to assess the microbial population of milk from a selection of commercial milk producers, pre- and post-pasteurisation. The combination of techniques employed reveals the presence of a previously unrecognised and diverse bacterial population in unpasteurised cow's milk. Most notably, the use of high throughput sequencing resulted in a number of bacterial genera being identified in milk samples for the first time. These included Bacteroides, Faecalibacterium, Prevotella and Catenibacterium. Our culture-independent analyses also indicate that the bacterial population of pasteurised milk is more diverse than previously appreciated but that non-thermoduric bacteria within these populations are likely to be in a damaged, non-culturable form. It is thus apparent that the application of state-of-the-art approaches can provide a detailed insight into the bacterial composition of milk and could potentially be employed in the future to investigate the factors that influence the composition of these populations.

Biome: root:Engineered:Food production:Dairy products
Volatile fatty acids (VFAs) production through anaerobic fermentation

Volatile fatty acids (VFAs) production through anaerobic fermentation is an effective way. Microbes in active sludge play key roles in VFAs production. In present study, VFAs were produced by sludge from five representative waste organic materials. We investigated prokaryotic community structure and diversity in sludge samples using 454 pyrosequencing technique based on 16S rRNA gene. Samples were collected as replicate samples for every waste organic material.

Biome: root:Engineered:Wastewater:Activated Sludge