SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metagenomic analysis of sediments along a uranium gradient

Surface sediment from a billabong in the Northern Territory of Australia was collected and spiked with uranyl sulfate at 6 different concentrations (0 - 4,000 mg/ kg). The sediments were then re-deployed at the site and left in these natural environmental conditions for 5 months. DNA was extracted from the sediments and submitted for metagenomic sequencing on the Illumina HiSeq 2500 instrument.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes.

Seawater was filtered from different depths to retain small cell sizes (Bacteria Organisms). The DNA was extracted and submitted to high throughput sequencing.

Biome: root:Environmental:Aquatic:Marine
metagenomic analysis of human gut microbiome

metagenomic analysis of human gut microbiome

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Analysis of sample SRA022105 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)

The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data. 

Biome: root:Environmental:Aquatic:Marine:Oceanic
Analysis of sample SRA022106 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)

The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data. 

Biome: root:Environmental:Aquatic:Marine:Oceanic
Analysis of sample GS112 take in the Indian Ocean

The comparative study of metagenomas arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude.

Biome: root:Environmental:Aquatic:Marine:Oceanic
non corroding sheet piles in the soil.

We have investigated the community composition and their metabolic potential of samples from sheet piles in soil. Samples were taken from the soil and soil attached to the sheet piles. The sheet piles were not corroded and showed a mineral coating. The metagenomes were sequenced  by the  Illumina Miseq technique.

Biome: root:Environmental:Terrestrial:Soil
cattle and buffalo based on roughage based diet

Analysis of rumen microbiome from cattle and buffaloes which were fed with same roughage diet using metatranscriptomics approache

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Sao Paulo Zoo Lake Study

Sao Paulo Zoo Lake Study

Biome: root:Environmental:Aquatic:Freshwater:Lake
Microbial diversity and isolation of novel hydrolases from the Kudu Rumen

Rumen of various angulates contain a variety of microbes that aid with the digestion of consumed plant material. These microbes have proved to be an important source of hydrolytic enzymes such as cellulases that are of immense importance in the emerging biofuels industry. This study seeks to understand the diversity and function of the Kudu rumen microflora and isolate its novel hydrolases.

Biome: root:Host-associated:Mammals
Metagenomic analysis of the Binga Hot Springs in Zimbabwe for Microbial Diversity and Hydrolytic Enzymes

Hot springs are an important source novel thermostable industrial enzymes. This study is seeks to use bioinformatics to analyze the metagenome derived from the Binga Hotsprings in Zimbabwe. The analysis will focus on microbial diversity  and function prediction of genes encoding Novel hydrolases of industrial importance

Biome: root:Environmental:Aquatic:Thermal springs
Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis

Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier, and assemble a pathogen?s draft genome using SOAPMeta.

Biome: root:Host-associated:Human:Digestive system
Metagenomics of Spartina anglica phyllosphere

Spartina anglica phyllosphere was investigated using metagenomics and metaproteomics in order to investigate bacterial Dimethylsulphide degradation associated with Spartina anglica in more detail.  DNA from Spartina anglica phyllosphere was extracted and used for metagenomics using the Nextera XT Kit (Illumina). Sequencing was carried out on the Illumina MiSeq. (2 x 301 bp paired end reads)

Biome: root:Host-associated:Plants:Phylloplane
Evidence for salt tolerance in the human gut mobilome and potential mechanisms.

The human gut microbiome and its associated mobilome is critical to health and wellbeing. It hosts a complex ecosystem comprising a multitude of bacterial species, which contributes functionality that would otherwise be absent from the host. Transient and commensal bacteria in the gut must withstand many stresses. The influence of mobile genetic elements, such as plasmids, in stress adaptation within the ecosystem is relatively unknown. We found evidence for plasmid mediated osmotolerance as a phenotype amongst the Proteobacteria in healthy faecal slurries. A transconjugant carrying multiple plasmids acquired from healthy faecal slurry demonstrated increased osmotolerance in the presence of metal salts, particularly potassium chloride, which was not evident in the recipient. Sequencing and analysis of the total plasmid DNA demonstrated the presence of plasmid-borne osmotolerance systems (including KdpD and H-NS) which may be linked to the observed phenotype.  This is the first report of a transferable osmotolerance phenotype in gut commensals and may have implications for the transfer of osmotolerance in other niches.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
BASE - Biomes of Australian Soil Environments

The samples in this study were collected as part of the BASE (Biomes of Australian Soil Environments) project, which is developing a database of Australian soil microbial diversity. The soil ecosystem is critical for ecosystem functioning, affecting human health and food supply, animal and plant health, edaphic factors and climate. The Base project has sampled soils from across a wide range of ecosystem types on the Australian continent and collected both contextual and DNA based data that are publically available and form a base line database of Australian soil microbial biodiversity. More information about BASE can be found at http://www.bioplatforms.com.au/special-initiatives/environment/soil-biodiversity. Collected here is Illumina shotgun sequencing data from these soils.

Biome: root:Environmental:Terrestrial:Soil
Synthetic community metagenomes study

Sequencing was carried out using Illumina MiSeq 2 x250bp sequencing.

Biome: root:Engineered:Modeled
Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries looking at the ecological communities.

Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries (Logan, Maroochydoore and Noosa). The study is looking at the ecological communities in each of these systems, and how they are impacted by pollution and environmental conditions.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Elixir marine metagenomics pilot - towards user centric service

Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research.  The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting.  Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms.  The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a "user community" for marine metagenomics analysis in ELIXIR

Biome: root:Environmental:Aquatic:Marine
Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories

Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Enriched Hetertrophic-Methantrophic Cultures from Different Soils (amplicon)

The project aimed to develop a robust consortia for oxidizing methane from possible emission sources e.g. coal mine and landfills. Different soil/sediments were collected and enriched under 20% methane atmosphere for more than 100 days and DNA were extracted for metagenomic studies. Methane oxidation potentials of each enrichments were analysed and byproducts were screened. Further testings were on-going using the enriched cultures for biofilter applications to treat continuous emissions of methane from point sources.

Biome: root:Environmental:Terrestrial:Soil
Metagenomics of a freshwater pond in Sheffield, UK.

The microbial community used in the microcosm study was obtained from this pond. The inoculums were subjected to nutrient enrichment studies.

Biome: root:Environmental:Aquatic:Freshwater:Lentic
Hydrocarbon Metagenomics Project

Metagenomics for Greener Production and Extraction of Hydrocarbon Energy:
Creating Opportunities for Enhanced Recovery with Reduced Environmental Impact

Biome: root:Environmental:Aquatic:Freshwater
Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris

Secondary metabolites like pyrrolizidine alkaloids (PAs) act as defense compounds against aboveground and belowground attackers. We studied to get a better understanding of relevance of microbial diversity in the rhizosphere for plant growth and behavior, specifically related to secondary metabolites production. We made soil dilution to compare the composition of soil microbial communities of soil suspension, incubation and rhizosphere soil by 16s rRNA high throughput pyrosequencing, as a consequence, to determine the effects on plant behaviors. The dilution procedure leads to reduction of the diversity of bacteria at the phylum level. After regrown, the structure of microbial community in the rhizosphere changed significantly as compared to the composition in the incubated soil. Jacobeae vulgaris as model plants growing in the soil where microbial diversity were decreased, had a higher biomass and higher amount of free base form of PAs? production, which indicates the reduction of soil microbial community in the rhizosphere shows significant feedback. Our study adds evidence that soil microbes may play a role in the evolution of plant secondary metabolites in plants.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Benchmark of metagenome analysis tools

A set of complex, realistic data sets were simulated based on real Illumina HiSeq 2000 data (100 bp PE reads). Two "conditions" consisting of 3 replicates each were used to evaluate the performance of a number of metagenome analysis tools.

Biome: root:Engineered:Modeled:Simulated communities (sequence read mixture)
Comparison of distal gut microbiota structure and function in US and Egyptian children

Cultural traditions, diet, and lifestyles of ethnic groups living in different geographic locations can serve as a source of variability in human gut microbiota. To examine the differences in gut microbiome of geographically distinct populations, we have carried out phylogenetic, functional, and metabolite analyses of the distal gut microbiota of healthy adolescents from United States and Egypt using next generation high-throughput sequencing.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Denovo test of eDNA sample

In this study we are going to establish the analyses of eDNA from sea water to identify macrofauna species from the North Sea.Instead of targeting single genes of taxa, we aim to sequence total DNA extracts. As a consequence, we expect to catch more diversity and to reduce the loss of information caused by unregularly binding of group specific primers.

Biome: root:Environmental:Aquatic:Marine
The fecal microbiome was studied in a group of IBD suffers and compared to a control group's fecal microbiome

Ten IBD and 10 healthy individual's fecal microbiomes were determined by NGS sequencing, to identify features that are unique to each group.  This was done using shot-gun metagenomics of DNA extracted from fecal samples and run on a HiSeq 2500.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Metagenomic exploration of Lasundra hot spring

Geothermal areas are the main permanent hot places of the world, and these areas are the major habitats of thermophilic bacteria. In culture independent method, metagenome was isolated using manual and kit based methods. The short gun sequencing of metagenome was performed using Ion torrent PGM platform. The analysis of sequencing data revealed that this spring is dominated by bacterial taxa. MG-RAST based community analysis showed that bacteria were found in dominancy with 99.2% in domain hit distribution. Firmicutes were found to be dominant in domain hit classification followed by proteobacteria. Moreover, unclassified sequences also found in this metagenome indicate there are possibilities of getting novel organisms.

Biome: root:Environmental:Aquatic:Thermal springs
A human gut microbial gene catalog established by deep metagenomic sequencing (MetaHIT)

A human gut microbial gene catalog established by deep metagenomic sequencing

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Reseq_Jan15 - Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories

Reseq_Jan15 - Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Metagenomes of hydrogen producing, xylan fed termites

Metagenome study with samples from the guts of termites (Nasutitermes exitiosus sp). The termites had xylan as their only carbon source and were raised at temperatures of 33, 40 and 45 degrees respectively while producing highly concentrated hydrogen.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Lacto broiler1d

To study the effect of feed additives on caecum microbiome

Biome: root:Host-associated:Birds:Digestive system:Ceca
Synthetic community metagenomes

Library methods comparison across illumina GAII, HiSeq, MiSeq using a synthetic community.
Four libraries methodology Nextera, NexteraXT, TruSeq, Low input have been used in this study

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Understanding the carriage dynamics of nasopharyngeal microbiota in Malawian children and adults: a metagenomic analysis.

This study was part of a project investigating the nasopharyngeal carriage of streptococcus pneumoniae in Malawian children and adults by microarray. Because the nasopharynx is colonised by several other microorganisms, we decided to investigate whether pneumococcal carriage dynamics was associated with carriage of particular microbial species. We collected nasopharyngeal swabs from children (n=51) aged 0-15 years and adults (n=55), all carriers of Streptococcus pnumoniae. DNA was extracted directly from the samples, followed by a PCR amplification of the 16S rRNA gene. The 16S amplicons were sequenced by 454 pyrosequencing.

Biome: root:Host-associated:Human
Elixir marine metagenomics pilot - towards user centric service - Gut samples

Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research. The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting. Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms. The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a "user community" for marine metagenomics analysis in ELIXIR

Biome: root:Host-associated
Marine metagenomes from 3 sediment samples along a pH gradient in Papua New Guinea

Sediment microbial communities are key players in biogeochemical cycling and the remineralization of organic matter on tropical reefs. To better understand the long-term effects of low pH conditions on sediment microbial communities, microbial diversity and community composition were investigated at naturally CO2-rich tropical coral reefs in Papua New Guinea. Metagenomic and metatranscriptomic analyses will reveal insights into the response of sediment microbial communities and their functions to low pH environments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Controlling enteric pathogens of poultry

There is rich genetic diversity in India?s native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ?thinning?, can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.

Biome: root:Host-associated:Birds:Digestive system:Ceca
metageomics 16S analysis

A metagenomics analysis and taxonomy 16S RNA

Biome: root:Environmental
Anopheles_Genome_Variation_Project

For information on this project, contributing investigators and studies, sample details, and data sharing policies please visit http://www.malariagen.net/node/287

Biome: root:Host-associated:Insecta
The comparison of gut microbiota obtained from centenarian, elderly, and adults living in southwestern longevity belt in Korea

Centenarians have lived for long ages and survived from various death causing factors. Several studies were analyzed the factors of health maintaining in centenarians, while the longevity factors are not completely understood. Recent analyses of gut microbiota have been reported the association of microbiota with health, and some studies were reported the alteration of gut microbiota with aging. In this study, we analyzed the gut microbiota of centenarians in particular regions of Korea to understand their longevity factors. The gut microbiota of centenarians (n=30) was compared with elderly (n=17) and adults (n=9) using pyrosequencing based on 16S rRNA gene. The relative abundance of Bacteroidetes was decreased, while those of Firmicutes and Proteobacteria were increased with aging. However, the proportion of Bacteroidetes was higher in centenarians than elderly subjects. The difference of gut microbiota composition between centenarians and elderly could be generated by diet patterns. Although additional studies such as functional analyses of microbiota between groups were need to understand, this study can provide the information of longevity factors of centenarians.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Changes imposed by Clostridium difficile infection on the human gut microbiome

Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious health problem.  In this study, we analyzed the metabolic changes associated to C. difficile infection in the human gut microbiota and its relation with the production or not of toxins A and B. In addition, we sequenced the amplicons of the 16SrDNA gene of the fecal samples to explore the effect of Clostridium difficile infection and toxin production on the intestinal microbial composition.

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