SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of PRJNA433811 data set (shotgun metagenome sequencing salmo salar gut microbiota).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA433811, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.

Biome: root:Host-associated:Fish:Digestive system
EMG produced TPA metagenomics assembly of PRJNA506751 data set (Puffer fish gut Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA506751, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system.

Biome: root:Host-associated:Fish:Digestive system
EMG produced TPA metagenomics assembly of the Oral microbiome Metagenome (human oral metagenome) data set.

The human oral metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA255922.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Oral.

Biome: root:Host-associated:Human:Digestive system:Oral
Bio-GO-SHIP: Global marine 'omics studies of repeat hydrography transects

The Global Ocean Shipboard Hydrographic Investigations Program (GO-SHIP) is a ship-based global survey of ocean hydrographic sections, which are repeatedly measured on a decadal time scale. The program covers a suite of physical (light, heat, currents, water column structure, etc.) and chemical (nutrients, oxygen, dissolved organic and inorganic carbon, pH, etc.) state variables over the full ocean water column, and in areas of the ocean inaccessible to other platforms. The principal scientific objectives for GO-SHIP are: (1) understanding and documenting the large-scale ocean water property distributions, their changes, and drivers of those changes, and (2) addressing questions of how a future ocean will increase in dissolved inorganic carbon, become more acidified and more stratified, and experience changes in circulation and ventilation processes due to global warming and altered water cycle.The vision of the biological GO-SHIP initiative, or "Bio-GO-SHIP," is to develop a deep understanding of the link between the physio-chemical environment and global ocean plankton diversity, abundance, and biogeochemical roles in the context of a changing ocean. This will be achieved through systematic, high-quality, and calibrated sampling of marine 'omics products.In this BioProject, we aim to provide a singular resource for Bio-GO-SHIP 'omics datasets. We also provide appropriate metadata such that the 'omics data may be linked to the broad range of state variables measured by GO-SHIP and associated oceanographic transects.

Biome: root:Environmental:Aquatic:Marine
metabarcoding of eDNAbyss sediment samples

Sediments were collected using multicore sampler, or simple cores when a submarine or a remote operated vehicle (ROV) were present. The cores were collected and sliced according to sediment depth and using a standardized scheme. Slices were preserved and treated individually. When hard substrate was collected, the gear ELFES designed on purpose to scratch and collect the surface of substrate, or bulk samples were retained after sieving communities. Nucleic acids (DNA or RNA) were extracted and submitted to a PCR-ligation protocols using 6 sets of primers pairs targeting metazoans (2 primer pairs targeting a fragment of Cytochrome Oxydase I and one of rDNA18S V1-V2), microeukaryotes (2 primer pairs targeting rDNA 18S V4 and V9) and prokaryotes (2 sets of primer pairs targeting rDNA16S V4-V5 respectively defined for prokaryotes in general, and archaebacterial in particular).

Biome: root:Environmental:Aquatic:Marine:Sediment
Metagenomes from an Argentine salt flat

Analysis of assembled metagenomes from an Argentine salt flat

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJEB11419 data set (American Gut Project).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB11419, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human.

Biome: root:Host-associated:Human
Extensive microbial novelty in the Hadza and Nepali gut microbiome reveals how lifestyle impacts composition and function

The gut microbiome has been identified as a key to immune and metabolic health, especially in industrialized populations. Non-industrialized individuals harbor more diverse microbiomes and distinct bacterial lineages, but systemic under-sampling has hindered insight into the extent and functional consequences of these differences. Here, we performed ultra-deep metagenomic sequencing and laboratory strain isolation on fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophage, and eukaryotes, and find that 43% are novel upon aggregating with existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, and high-resolution strain tracking reveal dynamics in the hunter-gatherer gut microbiome that are distinct from industrialized populations. Industrialized versus Hadza gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. We use phylogenomics to reveal that global spread of the spirochaete Treponema succinifaciens parallels historic human migration prior to its extinction in industrialized populations. When combined with a detailed definition of gut-resident strains that are vanishing in industrialized populations, our data demonstrate extensive perturbation in many facets of the gut microbiome brought on by the industrialized lifestyle.

Biome: root:Host-associated:Human:Digestive system
EMG produced TPA metagenomics assembly of the Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn''s disease (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 PRJNA321058. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Microbial composition of samples from infant gut

The microbial composition of the gut likely contributes to a wide-range of health and disease states including intestinal inflammation, atopic disease, and possibly diseases of adulthood, such as heart disease and obesity. The early establishment of the gut microflora is suspected to have a particularly profound impact protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. In contrast to the large-scale efforts of the Human Microbiome Project to characterize the microbial flora of healthy adults, relatively little has been accomplished to characterize the early establishment of the microbiota in infants.  The administration of antibiotics to infants has the capacity to profoundly affect the early acquisition, establishment, and natural maturation of commensal microflora. Prematurity is another major factor that is thought to influence 'normal' gut microbial composition in early life. A high number of pre-term infants receive antibiotic therapy prophylactically; the immediate and long-term effects of antibiotic treatment on infant and later health outcomes are unknown. We hypothesize that gestational age influences the ability to support 'normal' gut microbiota, and that antibiotic administration in the first few weeks of life can alter or delay the development of a 'normal' microbiota and may lead to adverse health outcomes. If we hope to promote the healthy establishment of early gut colonization and thereby improve health outcomes, we need to establish what 'normal' colonization looks like across gestational ages and apply this knowledge as a benchmark to understand the impact of antibiotic treatment in early postnatal life.  In this project, we propose to examine the microbiome in four cohorts ranging from extremely preterm to term, with birth weights appropriate for gestational age: Group 1) 23 to 27 weeks and extremely low birth weight [ELBW, <1000 grams]; Group 2) 28 to 32 weeks and very low birth weight [VLBW, >1000 to <1500 grams]; Group 3) 33 to 36 weeks and low birth weight [LBW, >1500 to <2500 grams]; and Group 4) term (37 to 42 weeks) and normal [>2500 to <4000 gram] birth weight. The infant gut microbiome will be assessed longitudinally in study infants from the first postnatal week to 18 months of age, and will include untreated and antibiotic-treated infants.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Dark ocean microbial diversity

The goal of the study is to assess the diversity of bacteria and archaea in the water masses of the open ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic
16S rRNA gene sequences from temperate soils Targeted Locus (Loci)

Both climate and pH are key in determining soil archaeal community structure and diversity

Biome: root:Environmental:Terrestrial:Soil
Peru margin subsurface

Investigation of the microbial diversity in subsurface sediments of Peru margin

Biome: root:Environmental:Aquatic:Marine:Sediment
Oral microbial changes in ASD children

This project depicts the characteristics of oral microbiome in autistic children.

Biome: root:Host-associated:Human:Digestive system:Oral
structural analysis of microbial community for feild soil and compost made from coffee lees

Our final end is to change organic agriculture to matter production system based on scientific basis by stationary measurement of soil microbial community.This year,We analyze bacteria and fungi community at feild soil fertilized by compost made from coffee lees.We also analyze compost made from coffee lees.

Biome: root:Environmental:Terrestrial:Soil
Universal metabarcoding of pico- mesoplankton reveals seasonal dynamics and a bacterial bloom

Most studies of biodiversity focus on either macroscopic or microbial communities, with little or no simultaneous study of eukaryotes and prokaryotes. We tested whether a universal metabarcoding approach could be used to study the total diversity and temporal dynamics of aquatic pico- to mesoplankton communities in a shallow temperate lake. The approach revealed significant changes in the relative abundance of eukaryotic and prokaryotic plankton communities over a period of three months. These patterns, based on sequencing reads, fit with counts using traditional methods. We also witnessed the bloom of a conditionally rare bacterial taxon belonging to Arcicella, a genus that has been largely overlooked in freshwaters. Our data demonstrate the potential of universal metabarcoding as a complement to traditional studies of plankton communities, and for long-term monitoring across a broad range of organisms.

Biome: root:Environmental:Aquatic:Freshwater:Lake
peptide incubation in GOM C6 seawater bacteria Metagenome

Study bacteria community changes in the peptide decomposition in different seawater

Biome: root:Environmental:Aquatic:Marine
Biogeography of pelagic bacterioplankton across an antagonistic temperature-salinity gradient in the Red Sea

The Red Sea is a unique marine ecosystem with contrasting gradients of temperature and salinity along its north to south axis. It is an extremely oligotrophic environment that is characterized by perpetual year-round water column stratification, high annual solar irradiation, and negligible riverine and precipitation inputs. In this study, we investigated whether the contemporary environmental conditions shape community assemblages by pyrosequencing 16S rRNA genes of bacteria in surface water samples collected from the northeastern half of this water body. A combined total of 1,855 operational taxonomic units (OTUs) were recovered as free-living and particle-attached bacterioplankton. Here, a few major OTUs affiliated with Cyanobacteria and Proteobacteria accounted for ~93% of all sequences whereas a tail of “rare” OTUs represented most of the diversity. OTUs allied to Surface 1a/b SAR11 clades and Prochlorococcus related to the high light-adapted (HL2) ecotype were the most widespread and predominant sequence types. Interestingly, the frequency of taxa that are typically found in the upper mesopelagic zone was significantly elevated in the northern transects compared to those in the central, presumably as a direct effect of deep convective mixing in the Gulf of Aqaba and waters exchange with the northern Red. Although temperature was the best predictor of species richness across all major lineages, both spatial and environmental distances correlated strongly with genetic distances. Our results suggest that the bacterial diversity of the Red Sea is as high as in other tropical seas and provide evidence for fundamental differences in the biogeography of pelagic communities between the northern and central regions.

Biome: root:Environmental:Aquatic:Marine:Pelagic
Alwernia Metagenome

Pyrosequencing of V3-V4 16S rRNA gene fragments amplified from metagenomic DNA isolated from heavy metals-contaminated soils collected near chromium green-producing facility in Alwernia, Poland.  Two samples of soils from Alwernia, Poland, collected at the vicinity of chromium green-producing factory.

Biome: root:Environmental:Terrestrial:Soil
Submarine Ligurian Canyons Water Prokaryotic and Protist Communities

Planktonic prokaryote communities in a submarine canyon system in the Ligurian Sea (NW Mediterranean)

Biome: root:Environmental:Aquatic:Marine
Marine sediment in Arctic Raw sequence reads

This study assessed the diversity and distribution of fungal communities associated with marine sediments in Arctic.

Biome: root:Environmental:Aquatic:Marine:Sediment
North Pacific Subtropical Gyre Microbial Community

16S amplicon libraries were collected as a portion of the Seasonal and decadal changes in temperature drive Prochlorococcus ecotype distribution patterns, also known as Prochlorococcus of Warming Ocean Waters (POWOW) Cruise series. The samples were collected in January 2013 (KM1301) and July 2013 (KM1312) in the Eastern North Pacific Ocean. The goal of this project was to characterize ecosystem scale changes associated with shifts in temperature.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine metagenome ICM_JRV

Microeukaryote diversity in the Gulf of Maine: Under-explored microbial diversity in a well-studied coastal marine ecosystem.

Biome: root:Environmental:Aquatic:Marine:Coastal
Diversity and structure of benthic bacterial community from South-Eastern Pacific Ocean, Targeted Locus (Loci)

Assessing diversity and structure of sediment microbial communities under the influence of the oxygen minimum zone of an Eastern Boundary Current ecosystem: the Humboldt marine ecosystem

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
EMG produced TPA metagenomics assembly of PRJEB54673 data set (Paediatric Oral Microbiome).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB54673, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.

Biome: root:Host-associated:Human:Digestive system:Oral
Picoplankton 16S rRNA gene sequences (DNA and RNA) from Vertical Profiles (surface to 4000m depth) sampled during the Malaspina 2010 circumglobal expedition

The study here includes 182 samples (91 DNA and 91 RNA) of the 16S from the Malaspina-2010 expedition. The samples were sequenced using Illumina MiSeq 2x250bp.

Biome: root:Environmental:Aquatic:Marine
Amplicon 18S rRNA Illumina TAGs from Malaspina Bathypelagic samples

Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the 18S rRNA gene
using primers XXXXX and XXXX. Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
eukaryotic diversity from bathypelagic samples and describe its
biogeography.

Biome: root:Environmental:Aquatic:Marine
Amplicon 16S rRNA Illumina TAGs from Malaspina Bathypelagic samples

Bathypelagic samples collected during the global
circumnavigation Expedition Malaspina 2010 were generated by
amplifying the V4 and V5 hypervariable regions of the 16S rRNA gene
using primers 515F-Y (5’-GTGYCAGCMGCCGCGGTAA-3’) and 926R
(5′-CCGYCAATTYMTTTRAGTTT-3′). Sequencing was performed in an Illumina
MiSeq platform (iTAGs) using 2x250 bp paired-end approach at
Genoscope. The data generated has been used mainly to describe the
bacterial diversity from bathypelagic samples and describe its
biogeography.

Biome: root:Environmental:Aquatic:Marine
Amplicon sequencing of Tara Oceans DNA samples corresponding to size fractions for protists.

Analysis of 18S DNA in Tara Oceans Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The DNA was extracted and amplified by PCR.

Biome: root:Environmental:Aquatic:Marine
Microbial communities of methane seeps in shallow, porous sands off Elba

The methane cold seeps near Pomonte (Elba) are unique ecosystems situated in very shallow and porous coastal sands. We investigated the influence on hydrodynamics on microbial community structure and function. Understanding these ecosystems is important to estimate their role in carbon cycling and their emission of methane to the atmosphere.

Biome: root:Environmental:Aquatic:Marine:Sediment
Global fungal diversity

This is a global dataset of unprecedented scope to disentangle the relative roles of climatic, edaphic, floristic, and spatial variables governing global-scale patterns of soil fungal diversity. We also address key macro-ecological phenomena such as latitudinal gradients of diversity and Rapoport’s rule (expansion of species’ latitudinal range with increasing latitude) as well as cross-biome and cross-continental biogeographic relationships in multiple phylogenetic and functional groups of fungi.

Biome: root:Environmental:Terrestrial:Soil
Diversity of Pico- to Mesoplankton Along the 2000 km Salinity Gradient of the Baltic Sea

Microscopic plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. Next Generation Sequencing (NGS) of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but also novel groups to the Baltic were observed, such as relatives to the coccolithophore Emiliana huxleyi in the northern Baltic Sea. The deep sequencing also enabled accurate enumeration of highly resolved (> 99% identity) operational taxonomic units, which revealed contrasting distribution profiles among closely related populations, reflecting niche partitioning into ecotypes. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.

Biome: root:Environmental:Aquatic:Marine
marine sediment metagenome Genome sequencing and assembly

To share species we detected in the South China Sea

Biome: root:Environmental:Aquatic:Marine:Sediment
Distinctive community structure and high diversity in particle-associated prokaryotes in tropical and subtropical Pacific Ocean surface seawater

The specific aim of this project was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the tropical and subtropical Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the Western Antarctic Peninsula

The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and materials flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters compared to lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We characterized bacterial, archaeal, and eukaryotic community diversity and composition from two depths (near surface and below the euphotic zone) at four sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern ones but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents but did vary with depth. Archaea were virtually absent in summer surface waters but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of “winter water” below the euphotic zone. Inter-domain heterotroph-phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in microbial communities may be assessed.

Biome: root:Environmental:Aquatic:Marine
Abalone seed nursing ecosystem Metagenome

In this study, using abalone seed nursing pond as a model system, we separately collected the time-series samples of three

Biome: root:Environmental:Aquatic:Marine