SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Human Microbiome Environment Metagenome

The samples within this Bioproject represent the third phase (Phase III) of metagenomic sequencing (whole genome shotgun (WGS) sequencing) of microbial communities from specimens collected as a part of the NIH-supported Human Microbiome Project (HMP Consortium A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209). The sample collection represents a unique reference resource of microbiome samples from healthy adults largely residing in the USA at the time of sample collection. In the HMP Phase III component the goal has been to supplement previous WGS sequencing by generating additional sequence from as many of the specimens in the HMP collection as possible that had not been sequenced in the previous HMP Phase I and Phase II sequencing. In Phase III, a focus was placed on six of the 18 body sites: Stool (gut), Buccal mucosa (oral), Supragingival plaque (oral), Tongue dorsum (oral), Anterior nares (nasal), Posterior fornix (vaginal) and the goal was to further capture as many of the longitudinal samples (second and third visits by the same individual) as possible. From genomic DNA extracted from the collected specimens, WGS sequence was produced from libraries constructed from using a NexteraXT library construction protocol. All libraries were sequenced using a 100bp paired end approach using the Illumina HiSeq 2000 platform.

Biome: root:Host-associated:Human
Uncultured fungus Targeted Locus (Loci)

Continental scale survey of soil fungi across North America using 454 pyrosequencing and extracellular enzyme assays to assess taxonomic and functional diversity.

Biome: root:Host-associated:Fungi
Fish gut metagenome Targeted loci environmental

Globally, marine species distributions are being modified as a result of rising sea surface temperature. On the west coast of Australia, the southern distributional limits of several tropical herbivorous fish species, including the rabbitfish Siganus fuscescens, have recently expanded into temperate regions. Microbes are fundamentally important to animal health, demanding an understanding of their variation in studies of animal adaption. Range-shifting S. fuscescens thus provide a unique opportunity to assess the stability of gastrointestinal microbes under varying environmental conditions. Here, the gastrointestinal microbial communities of S. fuscescens were characterised over 2000km of Western Australia's coastline, including in the species' historical and current southern range limit. MiSeq Illumina sequencing of the 16S rRNA gene demonstrated that the microbial community differed among populations, and there was a general decrease in hindgut microbial community similarity with distance. However, the population in the newly expanded range had similar hindgut microbial communities to one population in the historical range and levels of short chain fatty acids, an indicator of microbial fermentation activity, were similar among tropical and temperate locations. These data suggest that flexibility in the hindgut microbiome may play a role in enabling range-shifting herbivores to colonise new habitats.

Biome: root:Host-associated:Fish:Digestive system
Microbial communities of white band disease-infected Acropora cervicornis

Microbial communities of white band disease-infected Acropora cervicornis (WBD pools)

Biome: root:Host-associated:Cnidaria
Chicken cecal contents Metagenome

Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, particularly the ceca. Therefore a studly goal was to use in-depth metagenomics of the ceca to examine the microbial community from the ceca of a Broiler Chicken.

Biome: root:Host-associated:Birds:Digestive system:Digestive tube:Cecum
Uca urvillei Raw sequence reads

Uca urvillei gill microbiome

Biome: root:Host-associated:Arthropoda:Respiratory system:Gills
crustacean metagenome Targeted loci environmental

Bacterial assemblages from individual copepods (C. finmarchicus)

Biome: root:Host-associated:Arthropoda
Litopenaeus vannamei Metagenome

Pacific White Shrimps (Litopenaeus vannamei) are usually cultivated in large scale fisheries under less optimum conditions. Our study was aimed at finding any contaminants present inside the flesh of these commercially cultivated organisms that were imported to the USA.

Biome: root:Host-associated:Arthropoda
Helminth infections and gut microbiota  a feline perspective

The aim of this study was to investigate the qualitative and quantitative impact that infections by a widespread parasite of cats (i.e. Toxocara cati) exerts on the gut microbiota of feline hosts.

Biome: root:Host-associated:Animal:Digestive system:Fecal
Fecal bacteria of dogs and cats

The aim was to discover if the complex relationship between the host and Giardia are reflected in the faecal bacterial microbiome. Our hypothesis was that Giardia positive dogs and cats have a different microbiome structure and composition to Giardia uninfected animals. For this purpose, we used naturally infected cohorts of dogs and cats infected not only with Giardia, but also with hookworms and coccidia.

Biome: root:Host-associated:Animal:Digestive system
Marine invertebrates-associated Bacteria Raw sequence reads

An 8 week experiment was conducted to assess the changes in microbial communities from corals (Acropora millepora and Seriatopora hystrix), crustose coralline alga (Hydrolithon onkodes), foraminifera (Marginopora vertebralis and Heterostegina depressa) and sea urchin (Echinometra sp.) exposed to near-future climate change conditions, using next-generation amplicon sequencing.

Biome: root:Host-associated
BACTERIAL COMMUNITIES IN THE ACID AND THERMOPHILIC CRATER-LAKE OF THE VOLCANO "EL CHICHON", MEXICO


Biome: root:Environmental:Terrestrial:Volcanic
sediment metagenome Metagenome

To investigate the influence of birnessite-coated sand on sediment microbial communities.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
soil metagenome

The objectives of this investigation was to assess archaeal community and diversity in sediments from natural wetlands.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Boreal peatland bacterial 16S rRNA sequences Targeted Locus (Loci)

Defining bacterial community structure in the surface layers of three boreal peatland sites

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Moorland peat bacteria and fungi (16S and ITS)

We characterised the microbial communities in degraded moorland peat, and a variety of successful natural and managed restorations at a single site. Our hypothesis was that there is a dynamic interaction between soil microbes, edaphic factors, and vegetation in degraded peatlands which will be evidenced by changes in the soil microbial community associated with degradation and restoration. The results support our hypothesis and provide a basis to inform further studies which are needed to understand the roles of microbes in peatlands, and the impact of environmental change and management strategy upon their activities. We suggest that restoration success depends partly upon the readiness and response of below-ground microbial communities to the restoration activity, and that microbial community structure in peatlands may be diagnostic of future degradation risk or the progression of restoration.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Tibetan wetland soils Metagenome

The study is to investigate the methanogenic archaeal community by targeting the mcrA gene fragment, and to examine their link to environmental parameters

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Wetland soil Metagenome

The diversity of archaea in wetland in different seasons

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Chinampa wetland soil Metagenome

To know the bacterial diversity and variations of microbial communities in chinampa soil.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Fungi diversity in mangrove soils Targeted Locus (Loci)

This study goal is to investigate the diversity of fungi in mangrove soils in Bamen Bay, by 454 high through-put sequencing method.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Archaeal diversity in mangrove soils Targeted Locus (Loci)

To study the archaeal diversity in different sampling sites of mangrove soils in Bamen Bay by 454 high through-put sequencing

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Poyang Lake wetland soils Targeted Locus (Loci)

Reveal the relationships between bacterial community structure, composition and the geochemical factors.

Biome: root:Environmental:Terrestrial:Soil:Wetlands
T-W-B

Qinghai-Tibet wetland bacterial community

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Soils Random survey

To investigate the methanotrophs diversity in two wetlands in China

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Wetland samples Metagenome

To explore the microbial community composition and function in wetlands

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Wetland soil Metagenome

Study of microbial diversity under elevated CO2 and Nitrogen

Biome: root:Environmental:Terrestrial:Soil:Wetlands
Natural uranium-rich soils Targeted Locus (Loci)

High throughput pyrosequencing was used to assess the impact of uranium on bacterial communities by a comparative analysis of uranium-rich and control soil samples.  Soil samples with high and low uranium content were collected in the region of Bessines (Limousin, France), one of the most important natural uranium deposits in France.

Biome: root:Environmental:Terrestrial:Soil:Uranium contaminated
Soil microorganisms Targeted Locus (Loci)

Bacterial 16S sequences and fungal 18S sequences isolated from a wet tropical forest soil in Costa Rica

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Soil bacterial diversity beneath Atlantic Rainforest saprotrophic mushrooms

Sanger sequencing of isolated saprotrophic mushrooms and pyrosequencing of bacterial strains present in the mycospheres of each (mycospheric soil) and bulk soil samples.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Tropical soils Targeted Locus (Loci)

Tropical soil archaeal diversity and community structure.  Equatorial tropical biome at central and southern Malay Peninsula and Northern Borneo.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Malaysian Rainforest Soil Targeted Locus (Loci)

Spatial-scale independence of soil bacterial communities in Malaysian tropical forests

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
permafrost metagenome Targeted loci environmental

Analysis of microbial communities in thawing permafrost taliks of a thermokarst lake.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Arctic soil Metagenome

Sequencing of arctic soil samples on 454 platform for preliminary screening of most dominant bacteria and fungi before and after silver nanoparticles treatment

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Glacier forefield soils Targeted Locus (Loci)

Study of the diversity of soil microorganisms (bacteria, fungi, algae) along the chronosequences settled at two different glacier forefields of Southern Hemisphere, with different and contrasting environmental conditions

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Environmental Soil Sample

Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Study of microbial community structure of permafrost soil

The goal of this study is to uncover the inter-reflections between microbes and environment in continuous permafrost near bitumen in Qiangtang basin.  Organisms were grown in pure culture after isolation from permafrost soil.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Permafrost soil Metagenome

Sequencing of ITS hypervariable region to unravel fungal diversity in Siberian Arctic soil

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Arctic soils Metagenome

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. We hypothesize that warmer and therefore wetter conditions in polygonal tundra will lead to important changes in microbial processes, resulting in exacerbated carbon degradation under increasing anoxic conditions. To test this hypothesis, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Permafrost Metagenome Targeted Locus

DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal, and bacterial communities. In this study, we assess the small-scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1, and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, we sequenced control reactions to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance, and taxonomic diversity from the 12S, 16S, and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the Chi squared metric was used, however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil versus read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present day Yukon.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
High Arctic active layer and permafrost Targeted Locus (Loci)

Samples of active layer and permafrost were collected at the McGill Arctic Research Station, Axel Heiberg Island, Nunavut, Canada. The total community genomic DNA was extracted using PowerSoil DNA Isolation Kit. The V4 region of the bacterial 16S rRNA gene and the D1/D2 region of the fungal LSU rRNA were amplified and sequenced on a 454 Life Sciences Genome Sequencer FLX using Titanium chemistry.   Samples were collected at the McGill Arctic Research Station, Axel Heiberg Island, Nunavut, Canada. Active layer freezes and thaws every year. Active layer is underlain by permanently frozen soil (permafrost).

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Oil contaminated soils Targeted Locus (Loci)

Surveying microbial communities in desert soils polluted by oil

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Soil Targeted Locus (Loci)

The study has surveyed microbial communities in oil contaminated soils

Biome: N/A
Microbial Community in Petroleum Contaminated Soil Metagenome

Characterization of soil microbial community in a weathered petroleum hydrocarbon contaminated soil

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Oil contaminated soils Targeted Locus (Loci)

Diversity of microbial communities in oil contaminated soils from six oilfields in China

Biome: N/A
Soil sample Targeted Locus (Loci)

Oil contamination

Biome: root:Environmental:Terrestrial:Soil
Bacterial community of arable soil contaminated with diesel

Bacterial community was analyzed from arable soil contaminated with diesel. Red clay was added as a biostimulating agent. The results were compared between samples.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Changshu soil samples Metagenome

Organic-inorganic compound fertilizer is a novel fertilizer type in China. A field study was performed to evaluate the effect of organic-inorganic compound fertilizer to soil properties, microbial biomass, soil enzyme activity, functional genes and the bacterial community structure.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Soil and tailings Genome sequencing

Bacterial community research in metalliferous mine tailings, which was supported by National Natural Science Foundation of China

Biome: root:Environmental:Terrestrial:Soil:Mine drainage
soil metagenome Raw sequence reads

Profiling of Contaminated Soils in a Typical Antimony Mining Site

Biome: root:Environmental:Aquatic:Marine:Coastal
Stordalen mire environmental genomics 2 Targeted Locus (Loci)

Further to a previous submission SRP030775, more community composition analyses of Stordalen Mire''s thaw gradient.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Soil Random survey

Microbial response to climate warming

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Effects of N fertilization on arbuscular mycorrhizal fungal community in an alpine meadow on the Qinghai-Tibetan Plateau

Different forms and rates of nitrogen addition indirectly effect the arbuscular mycorrhizal fungal community primarily by altering soil characteristics

Biome: root:Environmental:Terrestrial:Soil:Grasslands
RaMPs 2006 tallgrass prairie soil fungi ITS1 locus sequencing

Responses of soil-borne fungi to environmental manipulations (elevated temperature and increased intervals between precipitation events) were evaluated through ITS1 locus sequencing.  The project explores fungal community shifts in response to manipulation of environmental conditions on an ecosystem level. 23 soil samples were collected, total DNA isolated and ITS1 targets sequenced.; Project type: Targeted Locus (Loci); Target description: A total of 23 soil samples were collected in June 2006 from the established rainfall manipulation (RaMPs) experiment. Total environmental DNA was extracted and fungal ITS1 regions PCR-amplified with target specific primers. The amplicons were sequenced on GS20 platform.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Prairie soil fungi, preindustrial-to-future CO2 gradient, Targeted Locus (Loci)

Soils sequester and release substantial atmospheric carbon, but the biological responses of soils to rising CO2 are not well understood. Studying fungal community responses to past and future CO2 concentrations should provide insights into how soils affect the path of rising atmospheric CO2. We studied fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250-500 ppm) on two soil types, a black clay and a sandy loam. The data uploaded are from 454 pyrosequencing of ITS-1 region rDNA, obtained from soil samples. The project is a collaboration between Duke University and the USDA-ARS Grassland, Soil and Water Research Laboratory in Temple, TX.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Kessler Farm Soil AOA communities Targeted Locus (Loci)

Ammonia oxidizing archaeal communities from a semi-arid tall grass prairies in Oklahoma were sequenced to gauge the diversity and response to climate warming.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
soil metagenome Targeted Locus (Loci)

In three California annual grassland soils, the present (DNA-based) and potentially active (RNA-based) soil bacterial and fungal communities were tracked over a summer field season and in response to a controlled rewetting of intact soil cores. Phylogenetic marker genes for bacterial (16S) and fungal (28S) RNA and DNA were sequenced and the abundance of these genes and transcripts were measured.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Soil Targeted Locus (Loci)

The goals of this study was to determine if there is a difference in bacterial community structure beneath beetle-killed trees as compared to healthy trees.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Hauturu temperate rainforest soil environmental sequencing using targeted loci (16S, 18S, ITS, COI and trnL)

From 20 soil samples we amplified DNA from five molecular markers (16S, 18S, ITS, COI and trnL) using targeted-locus next generation sequencing. Our aim was to evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life and compare these data to traditional biodiversity monitoring tools, including mist-netting and call counts for birds, vegetation surveys, and invertebrate collection with DNA barcoding. Our sampling regime consisted of ten 20x20 metre plots, each comprising sixteen 5x5 metre sub-plots along a 700 metre elevational gradient on a temperate island forest ecosystem (Hauturu, New Zealand).

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Effects of forest managements on soil fungi

Central objective of this study was to analyze forest management effects on soil fungal community structure

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Clearcut and forest ectomycorrhizal root tip communities Metagenome

Different ectomycorrhizal fungi (EMF) colonize seedlings in clearcuts versus intact forests. We were curious whether the shift in EMF community was associated with a change in the ability to access nutrients from soil organic matter, as measured by extracellular enzyme (EE) activities. Previous work in our lab had demonstrated that EMF identity can be more important than soil nutrient status and site in determining EE activities of ectomycorrhizal roots. Hence, we hypothesized that EE profiles associated with seedlings regenerating naturally in clearcuts would differ from those in adjacent forests. To test this hypothesis, naturally-regenerated subalpine fir (Abies lasiocarpa) seedlings were reciprocally transplanted between three pairs of clearcut and forest plots. One growing season after transplantation, EMF communities on seedlings originating from clearcuts and forests still differed from each other, regardless of whether they had been transplanted into clearcuts or forests. Activities of eight EE were measured on randomly-selected, individual mycorrhizal tips of transplanted seedlings. Contrary to our hypothesis, enzyme profiles were most similar among seedlings planted in the same destination, regardless of origin. Given that the EMF community depended on the site of origin, our results suggest that ectomycorrhizas exhibit a range of physiological attributes with respect to EE activities.

Biome: root:Environmental:Terrestrial:Soil:Forest soil