SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
HoloFood Salmon Trial A+B Gut Metagenome

Metagenomic raw reads, assemblies, and bins derived from HoloFood salmon gut samples from trial A and B. The samples in this project contributed to the salmon MAG catalogue (project: PRJEB55376 [ERP140265]).

Biome: root:Host-associated:Fish:Digestive system:Intestine
Quantitative monitoring of environmental DNA using high-throughput sequencing

The goal of this project is to monitor the dynamics of environmental DNA (e.g., fish DNA found in a water sample) quantitatively. By adding internal standard DNA, a standard curve (i.e., the relationship between the number of DNA copy and sequence read) will be drawn. Based on the standard curve, sequence reads of unknown DNA (non-standard DNA) will be converted to the number of DNA copy. The environmental DNA metabarcoding combined with internal standard DNA will enable quantitative monitoring of multispecies environmental DNA.

Biome: root:Environmental:Aquatic:Marine
Compost microbe establishment and growth in agricultural soils

Compost application to soil has numerous agricultural benefits, but mechanistic understanding of benefits beyond fertility and organic matter gains – particularly those mediated by microbes such as disease suppression – is limited. Narrowing this uncertainty requires understanding which types of compost microbes will establish in agricultural soils, which types of soils will support compost microbes, and how soil microbial diversity may change following compost application. We tested the ability of plant invasion and diversity theories to address these questions. From a row crop experiment to which management treatments had been applied for 22 years, soil was collected from three systems representing different resource inputs: no input (low resource), conventional (moderate resource), and organic (high resource) systems. Live composted poultry manure was added to laboratory microcosms of these soils, and bacterial and archaeal communities were tracked using 16S rRNA sequencing of pre-invasion soils, pre-invasion compost, and the combined communities at 4 and 32 days post-invasion.

Biome: root:Environmental:Terrestrial:Soil
marine metagenome Raw sequence reads

Mariana Trench microbial eukaryotes

Biome: root:Environmental:Aquatic:Marine:Sediment
marine sediment metagenome Raw sequence reads

The Roseobacter group within the family Rhodobacteraceae consists of nearly 70 genera and app. 180 species. They thrive in a broad variety of marine habitats and were found free-living in seawater, associated with micro and macro algae, marine sponges and invertebrates as well as in biofilms, sea ice and sediments. n the present study, we describe the abundance, distribution and diversity of the Roseobacter group in rather oligotrophic deep-sea sediments derived from the Pacific Ocean as all other benthic studies were performed on relatively eutrophic coastal sites or high-energy systems.

Biome: root:Environmental:Aquatic:Marine:Sediment
Nitrogen cycling microbes in the surface sediments of the South China Sea


Biome: root:Environmental:Aquatic:Marine:Sediment
marine sediment metagenome Raw sequence reads

XSD marine sediment metagenome Raw sequence reads

Biome: root:Environmental:Aquatic:Marine:Sediment
ASU barcoding in 5 regional seas

Metabarcoding of metazoan taxa collected in Artificial Substrate Units in 5 regional seas.

Biome: root:Environmental:Aquatic:Marine
Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) North Pacific Line-67 2009

The overall objective of this project (Baselines Initiative) is to generate several 16S rRNA gene databases to establish robust baseline information on the biological communities in marine ecosystems. This field study was conducted in the North Pacific Line-67 in October 2009 to examine phytoplankton community diversity.

Biome: root:Environmental:Aquatic:Marine
seawater metagenome Raw sequence reads

This project is to study the diversity of AAPB in Zhoushan sea area.AAPB belonging to the unclassified dominated the column, followed by Roseobacter ?The cluster analysis results by phylum ranked top was unclassified, then the Proteobacteria, Firmicutes followed, and finally the planctomycetes. The proportion of each class (clear classified phylum) of AAPB were clearly indicating that a-Proteobacteria remained dominant ,then ?-Proteobacteria and unclassified, ß-Proteobacteria and Bacilli possessed the same proportion,Planctomycetia and d- Proteobacteria occupied the minimum percentages. Obviously, in addition to the unclassified bacteria, Proteobacteria was absolute dominant member of AAPB?

Biome: root:Environmental:Aquatic:Marine
Camargue soil and sediment 16S community profiling

Characterize microbiome from camargue region in france

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
Impact of offshore oil drilling operations on the diversity of marine benthic Foraminifera  - Raw sequence reads

Environmental impacts from offshore oil and gas activities are currently partly determined by measuring changes in macro-infaunal diversity determined using microscopy. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding (i.e. high-throughput sequencing of foraminiferal environmental DNA marker sequences). Sediment samples were collected along distance gradients from two oil platform wellheads (WHs) off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macro-infaunal composition analysed.Our results suggest that foraminiferal metabarcoding may provide a more accurate assessment of the conditions of environmental communities at the time of sampling than current methods based on morphological examination. These data highlight the potential of foraminiferal metabarcoding as an effective asset to existing monitoring techniques.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Gastric microbiota of 120 samples Raw sequence reads

This study presented gastric microbiota in patients with gastritis, intestinal metaplasia,early gastric cancer and advanced gastric cancer,respectively.

Biome: root:Host-associated:Human:Digestive system
Uncultured eukaryote community Targeted loci environmental

Small size fraction (0.2-3 um) microbial community sample from northern Baffin Bay.

Biome: root:Environmental:Aquatic:Marine
Red Sea Zooplankton Raw sequence reads

To assess the diversity of zooplankton in the Red Sea. Samples were taken along a depth profile as well as being temporally and spatially differentiated.

Biome: root:Environmental:Aquatic:Marine
Microbial community of apple replant soils treated with fumigation or seed meal

Brassicaceae seed meal (SM) formulations were compared with pre-plant 1,3-dichloropropene/chloropicrin (Telone-C17®) soil fumigation for the ability to control apple replant disease and to suppress pathogen/parasite re-infestation of organic orchard soils at two sites in Washington State. The study also examined capacity of the SM treatment to minimize re-establishment of the causal pathogen populations and the potential contribution of altered rhizosphere microbiology to disease suppression.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Marine sponges and seawater Targeted Locus (Loci)

Assessment of microbial diversity of marine sponges and seawater

Biome: root:Environmental:Aquatic:Marine
Sediment sample Metagenome

Given the complexity in microbial transformation of arsenic in deep aquifer sediment, we aim to shade light of indigenous bacterial community structure in arsenic-enriched deep aquifer sediment and how the communities changes under controlled redox condition favoring reductive dissolution and release of arsenic from the sediment.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2)

Biome: root:Environmental:Terrestrial:Soil
Grassland 16S amplicons

Evaluate the relative importance of soil characteristics, climate, and plant roots on rhizosphere community assembly.

Biome: root:Environmental:Terrestrial:Soil:Grasslands
BrdU_MAB_SS Metagenome

Marine bacterial communities of the Mid-Atlantic Bight and Sargasso Sea

Biome: root:Environmental:Aquatic:Marine
Diversity of bacteria, archaea, fungi and algae in coal mine drainage remediation systems treating elevated manganese

Water discharging from abandoned coal mines can contain extremely high manganese levels, and removing this metal is an ongoing challenge. Passive Mn remediation systems promote the growth of certain bacteria and fungi that catalyze the transformation of soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Mn-oxidizing organisms likely belong to complex communities that include algae and archaea, as well as bacteria and fungi that do not oxidize Mn. Community interactions could be modulating the efficiency of Mn oxidation in the treatment beds. Using a targeted sequencing approach, we aimed to determine the diversity and composition of microbial communities inhabiting several different Mn remediation systems, compared with surrounding uncontaminated soil, and to establish the abundance of known Mn-oxidizing microorganisms relative to the entire community. Four Mn treatment beds in Pennsylvania were selected, each treating metal-contaminated discharge from abandoned coal mines. Rock or sediment samples were collected near the influent, in the middle and near the effluent of each bed, as well as from surrounding uncontaminated soil. Amplicon pyrosequencing was carried out with primers targeting bacteria (small subunit rRNA), archaea (small subunit rRNA), fungi (internal transcribed spacer) and algae (plastid large subunit rRNA).

Biome: root:Environmental:Terrestrial:Soil
Soil bacterial and fungal community changes during primary succession on lava flows in Iceland

Soil microbial communities (SMCs) play a critical role in the cycling of carbon and nutrients in terrestrial ecosystems, as well as regulating plant productivity and diversity. However, very little is known about long-term (decades-centuries) structural changes in these communities. The development of aboveground-belowground linkages during century-scale succession is also poorly understood. This study investigates SMC and plant communities undergoing primary succession on an 850-year chronosequence of lava flows in Iceland. We hypothesised that communities of microfungi and bacteria would respond to progressive changes in vegetation and that SMC diversity would increase with terrain age. This project has implications for studies of primary succession and the biogeochemical impact of vegetation change in high-latitude ecosystems.

Biome: root:Environmental:Terrestrial:Soil
BSM marine Targeted Locus

To study the bacterial diversity - coastal marine water from Malaysia.

Biome: root:Environmental:Aquatic:Marine:Coastal
Marine metagenome ICM_ICR

The Indian Ocean Cooperative 454 Run Project

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_AGW

Amazon-Guianas Water bacterial communities of the Amazon-Guianas water-sediment system.

Biome: root:Environmental:Aquatic:Marine
Microbial diversity of the central Arctic Ocean

We aimed to explore the community composition and turnover of eukaryotic and bacterial
                microorganisms associated with ice-associated and sinking algal aggregates, as well as their similarity
                to potential source communities of sea ice, water and deep-sea sediments using Illumina tag sequencing.
                We sampled algae aggregates growing in melt ponds on sea ice, deposited algae aggregates at the seafloor
                in more than 4000 m water depth, sea ice, upper water column, sediment surface and the gut content of
                holothurians feeding on the deposits.

Biome: root:Host-associated:Algae
Seasonal assemblages and short-lived blooms in coastal northwest Atlantic Ocean bacterioplankton

Temperate oceans are inhabited by diverse and temporally dynamic bacterioplankton communities. However, the role of the environment, resources and phytoplankton dynamics in shaping marine bacterioplankton communities at different time scales remains poorly constrained. Here, we combined time-series observations (time scales of weeks to years) with molecular analysis of formalin-fixed samples from a coastal inlet of the northwest Atlantic Ocean to show that a combination of temperature, nitrate, small phytoplankton and Synechococcus abundances are best predictors for annual bacterioplankton community variability, explaining 38% of the variation. Using Bayesian mixed modeling we identified assemblages of co-occurring bacteria associated with different seasonal periods, including the spring bloom (e.g. Polaribacter, Ulvibacter, Alteromonadales, and ARCTIC96B-16) and the autumn bloom (e.g. OM42, OM25, OM38 and Arctic96A-1 clades of Alpha-proteobacteria and SAR86, OM60, and SAR92 clades of Gamma-proteobacteria). Community variability over spring bloom development was best explained by silicate (32%) – an indication of rapid succession of bacterial taxa in response to diatom biomass– while nanophytoplankton as well as picophytoplankton abundance explained community variability (16-27%) over the transition into and out of the autumn bloom. Moreover, the seasonal structure was punctuated with short-lived blooms of rare bacteria including the KSA-1 clade of Sphingobacteria related to aromatic hydrocarbon-degrading bacteria.

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of the Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease (CHD102-metagenomics) data set.

The CHD102-metagenomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15111.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia (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: PRJNA290380.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of PRJNA986291 data set (CForBio.metagenome).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA986291, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Loam:Forest soil.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Archaea Arctic Ocean Survey Targeted Locus (Loci)

Eukaryota microbial diversity in different regions of the Arctic Ocean (Hudson Bay, Baffin Bay, canadian Archipelago, Laptev Sea)

Biome: root:Environmental:Aquatic:Marine:Oceanic
Enrichment of abundant sedimentary Bathyarchaeota demonstrating organoautotrophic metabolic capabilities

Enrichment of Bathyarchaeota

Biome: root:Environmental:Aquatic:Marine
srb of salt marshes Targeted loci environmental

To investigate on the changes in the diversity, abundance and community structure of sulfate-reducing bacteria along a plant successional gradient in coastal salt marshes of China

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
marine zooplankton environmental sample Targeted Locus (Loci)

Amplicon sequencing of marine zooplankton in the Red Sea

Biome: root:Environmental:Aquatic:Marine
Loihi Seamount basalts Targeted Locus (Loci)

Extracellular enzyme activity (alkaline phosphatase and leucine aminopeptidase), qPCR for prokaryotic biomass and Ion Torrent pyrotags of the V6 hypervariable region of 16S rRNA were analyzed from basalt samples collected from Loihi Seamount, HI

Biome: root:Environmental:Aquatic:Marine:Sediment
DNA from FIT can replace stool for microbiota-based colorectal

Using DNA extracted from fecal immunochemical test cartridges rather than directly from stool for detecting colorectal cancer based on the gut microbiome.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human feces metagenome 16s rDNA sequencing

The precise effects of HIV-1 on the human microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV status and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 risk groups.This was a cross-sectional study where we first tested 129 HIV-1-infected subjects and 27 HIV-negative controls in Barcelona (BCN0). Findings were internally validated in 110 subjects from BCN0 providing a second fecal sample 1 month later. External validation was obtained in 77 HIV-1-infected and 7 non-infected subjects from Stockholm. In all study participants, we produced MiSeq 16S rRNA data on fecal microbiomes and collected comprehensive metadata.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB32890 data set (The integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 high-quality metagenome-assembled genomes (MAGs)  linked to reconstructed full-length 16S rRNA gene sequences).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB32890, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
EMG produced TPA metagenomics assembly of PRJEB40358 data set (Dysbiotic Lesional Microbiome with Filaggrin Missense Variants Associate with Atopic Dermatitis in India).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB40358, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the C.diff FMT (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: PRJNA240307.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
16S sequencing of Malawian children

To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA+ bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss, and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition.

Biome: root:Host-associated:Human:Digestive system
Dewar Creek GAL08 Study Amplicons

Sediment samples from Dewar Creek hot spring in British Columbia, Canada, we processed for 16S rRNA gene sequencing. The goal of this project was to access the abundance of GAL08 (Acidobacteria) at Dewar Creek at varying temperatures over multiple sampling seasons.

Biome: root:Environmental:Aquatic:Thermal springs
EMG produced TPA metagenomics assembly of PRJEB27928 data set (Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB27928, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Host lifestyle affects human microbiota on daily timescales

Background,disturbance to human microbiota has been associated with numerous pathologies. Yet, we lack a comprehensive understanding for how human health and lifestyle affect the dynamics of human-associated microbial communities. Results, we link over 10,000 longitudinal measurements of host wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time-series show overall microbial communities to be stable for months. However, rare events in each of the subjects life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically-similar species. Still, even during periods of overall community stability, we could associate the dynamics of select microbial taxa to specific host behaviors. Most prominently, changes in host fiber intake correlated with next-day abundance changes among 15 percent of gut microbiota members.Conclusions,our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiota of Juvenile Idiopathic arthritis

Characterization of gut microbiota in Juvenile Idiopathic arthritis and comparison with healthy subjects.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiota of stroke patients differentiates from healthy controls

Gut microbiota of stroke patients differentiates from healthy controls

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