Datasets:
SantiagoSanchezF
/
mgnify_study_descriptions

Dataset card Data Studio Files
xet
Community
1
study_id
stringlengths
12
12
study_name
stringlengths
2
506
⌀
study_abstract
stringlengths
1
7.48k
⌀
lineage
stringclasses
298 values
MGYS00006597
sponge metagenome genome assembly, ooOscLobu1.metagenome
This project provides the full unbinned assembly of Oscarella lobularis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006596
mollusc metagenome genome assembly, xbBatBroo1.metagenome
This project provides the full unbinned assembly of Bathymodiolus brooksi and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Mollusca
MGYS00006595
mollusc metagenome genome assembly, xgAlvStru1.metagenome
This project provides the full unbinned assembly of Alviniconcha strummeri and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Mollusca
MGYS00006594
annelid metagenome genome assembly, wsLamColu1.metagenome
This project provides the full unbinned assembly of Lamellibrachia columna and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Annelida
MGYS00006593
sponge metagenome genome assembly, ohAphBeat7.metagenome
This project provides the full unbinned assembly of Aphrocallistes beatrix and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006592
sponge metagenome genome assembly, odPetFici3.metagenome
This project provides the full unbinned assembly of Petrosia ficiformis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006591
sponge metagenome genome assembly, odCraCram1.metagenome
This project provides the full unbinned assembly of Crambe crambe and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006590
mollusc metagenome genome assembly, xcSepLess1.metagenome
This project provides the full unbinned assembly of Sepioteuthis lessoniana and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Mollusca
MGYS00006589
sponge metagenome genome assembly, odAplAero1.metagenome
This project provides the full unbinned assembly of Aplysina aerophoba and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006588
sponge metagenome genome assembly, odSpoLacu1.metagenome
This project provides the full unbinned assembly of Spongilla lacustris and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006587
sponge metagenome genome assembly, odChoReni1.metagenome
This project provides the full unbinned assembly of Chondrosia reniformis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006586
Trididemnum clinides seq squirt metagenome assembly, kaTriClin1.metagenome
This project provides the sea squirt metagenome assembly of Trididemnum clinides. It contains the full unbinned assembly of Trididemnum clinides and associated organisms plus the MAGs and bins derived from this assembly. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Tunicates:Ascidians
MGYS00006585
sponge metagenome genome assembly, odSpoOffi2.metagenome
This project provides the full unbinned assembly of Spongia officinalis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006584
sponge metagenome genome assembly, odHalPani1.metagenome
This project provides the full unbinned assembly of Halichondria panicea and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006583
lichen metagenome genome assembly, glLicPygm2.metagenome
This project provides the genome assembly of lichen metagenome. The assembly is provided by the Darwin Tree of Life Project (https: //www.darwintreeoflife.org/). The data under this project are made available subject to the Darwin Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Fungi
MGYS00006582
sponge metagenome genome assembly, odEunFrag1.metagenome
This project provides the full unbinned assembly of Eunapius fragilis and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006581
sponge metagenome genome assembly, odXesBerg1.metagenome
This project provides the full unbinned assembly of Xestospongia bergquistia and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006580
sponge metagenome genome assembly, ooCorCand1.metagenome
This project provides the full unbinned assembly of Corticium candelabrum and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Porifera
MGYS00006579
algae metagenome genome assembly, uoEpiScrs1.metagenome
This project provides the full unbinned assembly of Epithemia sp. CRS-2021b and associated organisms. The assembly is provided by the Aquatic Symbiosis Genomics Project (https: //www.aquaticsymbiosisgenomics.org/). The data under this project are made available subject to the Tree of Life Open Data Release Policy (https: //www.darwintreeoflife.org/project-resources/).
root:Host-associated:Algae
MGYS00006577
Malaspina Expedition 2010 Microbial Vertical Profiles Metagenomes
Here we present a dataset of 76 microbial metagenomes of the picoplankton size fraction (0.2-3.0 μm) collected in 11 stations along the Malaspina Expedition circumnavigation (http://www.expedicionmalaspina.es; Duarte 2015) that cover vertical profiles sampled at 7 depths, from the surface to 4,000 m deep (or the sea floor in shallower waters), plus 5 additional metagenomes. This Malaspina Microbial Vertical Profiles metagenomes (MProfile) dataset produced 1.66 Tbp of raw DNA sequences. Six L seawater samples were collected and filtered through a 200 and a 20 μm mesh to remove large plankton, the prokarotic free-living size fraction (0.2 to 3.0 μm) was recovered in each sample by pumping water serially through 47-mm polycarbonate membrane filters of 3.0 μm and 0.22 μm pore sizes with a peristaltic pump. DNA was extracted using a standard phenol-chloroform protocol and was sequenced at the National Center for Genomic Analsis (CNAG-CRG. Barcelona, Spain; www.cnag.es), funded by project MALASPINOMICS (CTM2011-15461-E, led by Carlos M Duarte) on the Illumina HiSeq2000 sequencing platform utilizing a TruSeq paired-end cluster kit, v3, following a 2x100 indexed run recipe. References: Duarte CM. 2015. Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition. Limnology and Oceanography Bulletin 24:11-14; Sánchez, P. et al., 2023. Marine picoplankton metagenomes from eleven vertical profiles obtained by the Malaspina Expedition in the tropical and subtropical oceans. bioRxiv 2023.02.06.526790; doi: https://doi.org/10.1101/2023.02.06.526790
root:Environmental:Aquatic:Marine
MGYS00006578
Analisi metagenomica (16S) su suolo rizosferico di nocciolo
Piante di nocciolo di 4 anni di due varieta' diverse (Tonda di Giffoni e Mortarella) concimate con fertilizzante di sintesi (NPK), compost di sansa, zolfo e bentonite, zolfo e bentonite + compost di sansa
root:Host-associated:Plants:Rhizosphere:Soil
MGYS00006576
EMG produced TPA metagenomics assembly of PRJNA340003 data set (Metagenomic reconstruction of bacterioplankton community metabolism in the northern Gulf of Mexico Dead Zone).
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA340003, and was assembled with SPAdes v3.11.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary.
root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
MGYS00006574
EMG produced TPA metagenomics assembly of PRJEB42572 data set (Dental plaque microbiomes from hunter-gatherer and subsistence farmer populations in Cameroon).
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42572, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral.
root:Host-associated:Human:Digestive system:Oral
MGYS00001988
EMG produced TPA metagenomics assembly of the Gut microbial succession follows acute secretory diarrhea in humans (cholera_succession) data set
The cholera_succession Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB9150. This project includes samples from the following biomes : Human gut.
root:Host-associated:Human:Digestive system
MGYS00005023
EMG produced TPA metagenomics assembly of the The gut microbiome in Crohn's disease and modulation by exclusive enteral nutrition (123CD-metagenomics) data set.
The 123CD-metagenomics Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB15371. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.
root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002425
EMG produced TPA metagenomics assembly of the Metagenomic sequencing of preterm infant gut microbiota raw sequence reads () data set.
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA301903. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine.
root:Host-associated:Human:Digestive system:Large intestine
MGYS00006563
EMG produced TPA metagenomics assembly of PRJEB42399 data set (Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their adult caregivers).
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42399, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Skin.
root:Host-associated:Human:Skin
MGYS00002659
Bacteria exposure experiment North Sea
Bacterial sequencing (V3-V4 16S rDNA region) of plastic debris exposed for 5 or 10 months at the North Sea environment
root:Engineered:Solid waste
MGYS00002364
Parfrey_euk_testing_samples_515_806
Comparison of different sample types using different primers and platforms
root:Mixed
MGYS00000965
Soil bacteria (Pico de Aguila) Metagenome
In this study, the effect of deforestation and cultivation of maize (Zea mays L.) on the physicochemical characteristics and the bacterial community structure in soil were studied at the national park ‘Nevado de Toluca’ in Mexico. Soil was sampled from three forested areas in the national park with natural vegetation, and from three deforested areas cultivated with maize or grazed by animals and characterized while the bacterial community structure was investigated through 454 pyrosequencing of the 16S rRNA gene
root:Environmental:Terrestrial:Soil:Forest soil
MGYS00002519
Reciprocal transplantation experiment of salt marsh sediments Targeted loci
A reciprocal transplant experiment of rhizome associated bacterial communities between five salt marshes along the US East Coast to examine the roles that dispersal and environmental selection play in driving microbial community dynamics using bacterial v4v5 16S rRNA tag sequencing.
root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
MGYS00003993
Archaea 16S 01-13 Genome sequencing and assembly
Archaea 16S rRNA gene
root:Environmental:Aquatic:Marine:Sediment
MGYS00004044
16S rRNA Analysis of Osaka Bay Microbiomes
16S rRNA gene sequencing project for a time-series nine seawater samples from the 5 m depth at the entrance of Osaka Bay, Japan every 3 hours over a period of 24 h.
root:Environmental:Aquatic:Marine:Coastal
MGYS00004066
Deep-sea post-eruption "snowblower" microbial blooms raw sequence reads
Microbial community analysis of fluid samples and white flocculent material from active snowblower vents as well as orange flocculent material found on top of newly formed lava flows. Samples were collected following the 2011 eruption at Axial Seamount, an active volcano on the Juan de Fuca Ridge.
root:Environmental:Aquatic:Marine:Hydrothermal vents
MGYS00006572
Metatranscriptomics analysis of bacterial comunities in two moss species
Metatranscriptomics analysis of bacterial comunities in two moss species
root:Host-associated:Plants:Phylloplane:Epiphytes
MGYS00000437
The effect of different loading rates of biochar on soil microbes
Biochar and its applications in soil is involved in many aspects related to soil health and quality, for instance, chemical and physical changes in soil. However, the major aspect, which is still far from being understood and has so far received less attention than any other aspects, is the impact of biochar applications on soil microbes and how microorganisms in soil interact and adjust with biochar-modified soil environments
root:Environmental:Terrestrial:Soil
MGYS00002492
Metagenomes of Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools
The study focuses on Atlantis II and Discovery deeps brine pool sites, specifically sub-seafloor sediment.
root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004347
Surface sediment of Yellow Sea, Bohai Sea and north East China Sea Metagenome
This is a microbial assemblages study targeting the surface sediments of the northern part of Chinese marginal seas
root:Environmental:Aquatic:Marine:Sediment
MGYS00003722
3Soil16S
null
root:Environmental:Terrestrial:Soil
MGYS00002363
Song_2012_family_study
Human-associated microbial community composition is highly variable across host individuals, but the sources of this variability remain poorly understood. Previous studies have explored some possible contributing factors such as (genetic) relatedness, diet, and developmental stage. A likely additional cause is that our microbial communities are shaped by our unique surroundings, including the individuals with whom we interact at various stages of life. To quantify potential microbial exchange, we surveyed fecal, oral, and skin microbiota from 159 humans and 36 dogs across 60 families consisting of spousal units with children, dogs, both, or neither. Members of the same family, particularly couples, shared more of their microbiota than did individuals from different households, with an especially strong effect of co-habitation on skin compared to oral or fecal microbiota. Dog ownership, but not children, had a significant effect on the extent to which cohabiting adults shared skin (forehead and palm) microbiota, and dog-owning adults shared more microbial taxa with each other than with those who did not. Furthermore, adults shared more skin microbiota with their own dogs than with other dogs. These results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities.
root:Host-associated
MGYS00003117
uncultured marine eukaryote Targeted loci environmental
Identification of mixotrophic protists in Antarctic marine water samples based upon bromodeoxyuridine incorporation via grazing on labelled bacteria and subsequent 454 amplicon sequencing of the V9 region of the 18S ribosomal RNA gene.
root:Environmental:Aquatic:Marine
MGYS00003990
Marine subseafloor sediment Targeted Locus (Loci)
We examine the relationship between subseafloor microbial diversity and paleoceanographic conditions in samples from three sediment cores from the Eastern Mediterranean Sea and the Black Sea. All three cores record dramatic changes in oceanographic/limnic conditions resulting from oscillation between oligotrophic and euxinic condition, yet they also differ remarkably between sites. Our motivation for this study is based on the premise that paleoenvironmental conditions in the overlying water column are intimately linked to the composition of aquatic microbial communities and thus the inoculum for subseafloor communities. Our study will address the long-standing question to what degree the composition of subseafloor microbial communities is linked to paleoenvironmental conditions at time of deposition. The sample set at both Mediterranean sites is composed of carbonate-rich, organic-lean sediments and interspersed so-called sapropels, that is, organic-rich black layers that were deposited during climates that were probably warmer and more humid than today, when the Mediterranean was euxinic. The samples from the discovery basin are influenced by a highly saline brine and thus may select for halophilic sedimentary microbes. The Black Sea sample set is composed of organic-lean coccolith ooze deposited during the recent few thousand years, an organic-rich sapropel deposited during the early Holocene and below of sediment deposited during the late glacial/early Holocene when the Black Sea was still a freshwater lake. We examine both archaeal and bacterial diversity with a 454-based tag sequencing survey. We can address questions relating to the paleoenvironmental history at each site as well as to the relationship of microbial communities in sediments deposited during euxinic conditions at three sites along a salinity gradient remote to each other, in two different ocean basins. The sample set will be accompanied by an in-depth biogeochemical characterization of its sedimentary habitat. Sediment sampling and characterization are performed and mutually integrated on the same cruise (RV Meteor, M84-1, February 9-22, 2011) by the proponents of this proposal.
root:Environmental:Aquatic:Marine:Sediment
MGYS00001024
Environment Targeted Locus (Loci)
The application of fresh digestate, derived from the anaerobic treatment of animal wastes, is known to affect the short-term dynamics of microbial communities. A metagenomic study was carried out to test the effect of livestock-derived digestate amendment on an agricultural soil bacterial, yeasts and fungal community structure and dynamics.
root:Environmental:Terrestrial:Soil:Agricultural
MGYS00003091
Ocean crust Targeted Locus (Loci)
Much of the earth''s microbial biomass exists in the subsurface, and a sizable fraction of this is in oceanic igneous rocks. If microbial life in the igneous ocean crust extends to the depth of the ~120°C isotherm (the current upper temperature limit of life) then the volume of rock available for microbial colonization is about the same as the volume of the oceans. Most of this volume is difficult to sample but microorganisms have been identified from deep layers of the igneous ocean crust. Additional understanding of the deep igneous biome comes from microorganisms extracted from subsurface fluids; although unattached microorganisms in aquifer fluids are not necessarily representative of the microorganisms attached to the host rocks. Another difficulty is that the ocean crust is mineralogically heterogeneous typically on the 0.01 mm to 10 mm scale and if the mineralogy influences or controls the microbial communities, then the ocean crust is microbially heterogeneous on the 0.01 to 10 mm scale. Community structure that is determined from bulk crustal rock samples will not be informative about how communities are associated with crustal minerals. Also, molecular and sample processing methods are not currently available to determine the community structure of minerals in igneous rocks. In situ colonization of mono-mineralic substrates in the ocean crust is one method of determining microbial community structure of the minerals that make up the crust. We devised a method of incubating a wide variety of mono-mineral aggregates in the ocean floor simultaneously so that they all experienced the same temperature, water composition, and pressure. The mass of each incubated mineral was large enough to expect recovery of adequate amounts of DNA for analysis. The location chosen for this experiment was Integrated Ocean Drilling Program (IODP) borehole 1301A, which is located at 47° 45.210'' N, 127° 45.833'' W in 3.6 Ma old ocean crust in the northeast Pacific Ocean.
root:Environmental:Aquatic:Marine:Oceanic:Sediment
MGYS00004036
Bacterial population dynamics in a natural assemblage upon the addition of artificial alginate particles and alginolytic Alteromonas macleodii
Investigation of alginate degradation by marine bacterial communities from macroalgae-rich habitats in Southern California.
root:Environmental:Aquatic:Marine
MGYS00001008
CK1/MNPK1/NPK1 Targeted Locus (Loci)
The goal of present study is to examine what soil bacterial taxa were significantly affected by Cu amendments, and what taxa were the keystone organisms in Cu-contaminated soils using network analysis approach
root:Environmental:Terrestrial:Soil:Contaminated
MGYS00000725
soil metagenome Metagenome
Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (e.g. nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 varied Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP). Bacterial community composition of uncontaminated, diesel-contaminated, and diesel + MAP soils was assessed through multiplexed 16S rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by GC analysis. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future. Top 15 cm soils collected from across the Arctic, left untreated, or treated with diesel or diesel nutrients.
root:Environmental:Terrestrial:Soil
MGYS00000886
Arable soil Targeted Locus (Loci)
Manure unspiked and spiked with SDZ in two different concentrations was applied three times, and the bacterial community composition in soil was monitored over a period of 193 days. To differentiate between short and longer-term effects, the soil was sampled 3 and 60 days after each manure application, respectively.
root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004138
Diversity and abundance of Bathyarchaeota (MCG) in South China Sea sediments and the implication of its ecological roles
Diversity and abundance of Bathyarchaeota
root:Environmental:Aquatic:Marine:Sediment
MGYS00002660
Diet analysis of Pacific Bluefin Tuna larvae
Metagenetic analysis on gut contents of Pacific Bluefin Tuna larvae and planktons in environmental water
root:Environmental:Aquatic:Marine
MGYS00000426
Changes in microbiota composition in colitis-prone mdr1a mice
The symbiotic relationship between gut microbiota and the host is necessary for intestinal homeostasis. Loss of tolerance to the gut microbiota results in chronic inflammatory bowel diseases (IBD), such as Crohn’s disease and Ulcerative colitis. The microbiota resides in two compartments-the gut lumen and mucus layer. Most published findings focus on luminal microbial communities in IBD pathogenesis with much less being understood about the bacteria resident in the mucus layer that abuts the epithelium. Thus, the precise interactions between microbiota and the intestinal mucosa during IBD development are still unknown. To address this, we investigated colitis progression in the mdr1a-/- spontaneous model of colitis. We examined microbiota composition in the mucus and lumen in mdr1a-/- mice and wild-type littermate controls at an early pre-colitic and a later post-colitic stage. We aim to identify if bacterial differences in specific niches precede IBD development and progression. Our study provides valuable insight in microbiota-host interactions in normal and diseased states, revealing new approaches for the management of IBD.
root:Host-associated:Mammals:Digestive system:Large intestine
MGYS00004568
Marine metagenome ICM_BSR
Examining the Free-Living and Particle-Associated Bacterial Community in the Black Sea''s Suboxic Zone.
root:Environmental:Aquatic:Marine
MGYS00002773
Microbial Processes and Biodiversity: OCEAN
Study of microbial communities (16S rRNA and 18S rRNA genes) in two coastal oceans observatories located in contrasting latitudes: (i) Equatorial Atlantic Ocean - Equatorial Atlantic Microbial Observatory (EAMO) and (ii) Mediterranean Sea - Blanes Bay Microbial Observatory (BBMO).
root:Environmental:Aquatic:Marine:Coastal
MGYS00004032
Diversity of Microbial Eukaryotes in Sea Waters From Fildes Peninsula,King George Island, Antarctica
To investigate molecular diversity of microbial eukaryotes in sea water from Greatwall cove and Ardley cove, Fildes Peninsula, ten water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013. After pyrosequencing and analysis, the molecular diversity of microbial eukaryotes of sea water from Greatwall cove and Ardley cove was generally achieved.
root:Environmental:Aquatic:Marine:Coastal
MGYS00002554
Nutrient addition mesocosm experiment Targeted Locus (Loci)
Amplicon sequencing of environmental planktonic organisms to assess the interactions during a nutrient addition experiments.
root:Environmental:Aquatic:Marine:Coastal
MGYS00002523
South China Sea interfaces 16S amplicon sequencing
16S amplicon sequencing of microbial communities at geological interfaces in South China Sea marine sediments sampled during IODP expedition 349.
root:Environmental:Aquatic:Marine:Sediment
MGYS00000961
Arable and pasture soils spiked with anthracene Metagenome
Two soils were contaminated with 500 mg anthracene using acetone. Five different treatments were applied to the anthracene-contaminated soil. In a first treatment, soil was amended with two adult Eisenia fetida earthworms (0.35 g) and with a developed clitellum. The earthworms were fed 60 g carrot every two weeks. In a second treatment, soil was amended with 60 g organic material (carrot) every two weeks. As such, the effect of the earthworms on the removal of anthracene could be differentiated from that of the organic material applied. In a third treatment, soil was mixed for 10 min every 7 days. In a fourth treatment, soil was amended with 24.9 g kg-1 soil surfactant Surfynol® 485 and mixed. In a fifth treatment, soil was left unamended and served as control so that remediation capacity of the autochthonous microorganisms could be determined. Two more treatments were used in this study. In a first additional treatment, both soils were applied with the same amount of acetone used as carrier to contaminate the soil with anthracene and in a second additional treatment, unamended soil was used and served as control.
root:Environmental:Terrestrial:Soil
MGYS00002518
Marine planktonic ciliates: SSU rDNA
Diversity and biogeography of marine planktonic ciliates in the NW Atlanctic Ocean
root:Environmental:Aquatic:Marine:Oceanic
MGYS00001791
Benthic microbial communities associated with hypoxia on the Black Sea shelf break (NW Crimea)
The effect of varying oxygen conditions on benthic microbial communities was investigated at the North Western Crimean shelf break (Black Sea), at water depths between 105-207 m. Sampling was performed with a TV-MUC on April-May 2010 on board of the RV Maria S. Merian (Cruise MSM 15-a) along gradient of oxygen bottom water concentrations between oxic (150 μmol L-1, station 464), variable hypoxic (3-60 μmol L-1 O2, stations 487 and 393) and anoxic, sulfidic conditions (station 448).
root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001602
Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms
The nitrogen cycling bacterial community at 100 m depth in crystalline bedrock groundwater was investigated using nitrate and ammonium as substrates in a stable isotope probing study. The bacterial community was enriched with 15N ammonium or nitrate for 28 days after which the enriched community and the nitrogen assimilating communities were compared using 454 amplicon sequencing of the 16S rRNA genes
root:Environmental:Aquatic:Freshwater:Groundwater
MGYS00004673
Study on bacterial diversity and functionality in the Adriatic Sea
Study on bacterial diversity and functionality in the Adriatic Sea. PCR amplified 16S rRNA genes from an inoculum in the Adriatic Sea and bacterial communities incubated in continuous cultures with different treatments.
root:Environmental:Aquatic:Marine:Coastal
MGYS00003076
Red Sea marine sponges and seawater Targeted Locus (Loci)
The genes and transcripts of 16S rRNA were amplified from seawater, S. carteri, and X. testudinaria DNA (originating the following datasets: WTD1-WTD3, ASD1-ASD3, and AXD1-AXD3; respectively) and cDNA (originating the following datasets: WTR1-WTR3, ASR1-ASR3, and AXR1-AXR3; respectively). Purified amplicons were pooled equally and sequenced on a Roche 454 GS FLX Titanium platform. Sponge samples from the species Stylissa carteri and Xestospongia testudinaria were collected. Seawater samples were collected during the same dive. Sample location is: Fsar reef (22°23'N; 39°03'E) at the coast of Thuwal, Saudi Arabia. Depth was at 8.5-12 meters.
root:Mixed
MGYS00006571
EMG produced TPA metagenomics assembly of PRJEB34453 data set (Atlantic Ocean Metagenomes).
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34453, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.
root:Environmental:Aquatic:Marine
MGYS00004465
Marine fungi Raw sequence reads
biogeography and seasonality of benthic fungi
root:Environmental:Aquatic:Marine:Oceanic
MGYS00004064
Surfactant-associated bacteria in the near-surface layer of the ocean
Certain marine bacteria found in the near-surface layer of the ocean are expected to play important roles in the production and decay of surface active materials; however, the details of these processes are still unclear. Here we provide evidence supporting connection between the presence of surfactant-associated bacteria in the near-surface layer of the ocean, slicks on the sea surface, and a distinctive feature in the synthetic aperture radar (SAR) imagery of the sea surface. From DNA analyses of the in situ samples using pyrosequencing technology, we found the highest abundance of surfactant-associated bacterial taxa in the near surface layer below the slick. Our study suggests that production of surfactants by marine bacteria takes place in the organic-rich areas of the water column. Produced surfactants can then be transported to the sea surface and form slicks when certain physical conditions are met. This finding has potential applications in monitoring organic materials in the water column using remote sensing techniques. Identifying a connection between marine bacteria and production of natural surfactants may provide a better understanding of the global picture of biophysical processes at the boundary between the ocean and atmosphere, air-sea exchange of greenhouse gases, and production of climate-active marine aerosols.
root:Environmental:Aquatic:Marine:Oceanic
MGYS00004201
22V-SMAR-TVG01 Targeted Locus (Loci)
Analyzing the microbial diversity of the sediment
root:Environmental:Aquatic:Marine:Sediment
MGYS00004017
Aarhus Bay Station M5 sediment metagenome sequencing
ANME-1 draft genome binned from Aarhus Bay M5 sediment metagenome samples (Bioproject PRJNA305566)
root:Environmental:Aquatic:Marine:Sediment
MGYS00002591
Spirulina necromass degradartion in arctic marine sediments
Reveal the identity and population dynamics of responders to spirulina and acetate amendments to arctic marine sediments.
root:Environmental:Aquatic:Marine:Sediment
MGYS00003468
EMG produced TPA metagenomics assembly of the A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning () data set.
The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB1220. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.
root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00002952
Microbial communities in marine surface water
To investigate the biogeographic patterns of microbial communities in surface water from Indian Ocean to Chinese marginal seas
root:Environmental:Aquatic:Marine
MGYS00001003
16s rRNA profiling of Park Grass microbial community
16s rRNA amplicon sequencing of DNA isolated from the Park Grass soil
root:Environmental:Terrestrial:Soil:Grasslands
MGYS00005156
Flores_forehead_EBI
Forehead skin samples from Flores_SMP for submission to EBI
root:Host-associated:Human:Skin
MGYS00004102
marine sediment metagenome Raw sequence reads
null
root:Environmental:Aquatic:Marine:Sediment
MGYS00002896
Diversity of SE Pacific benthic Bacteria and Archaea communities Targeted Locus (Loci)
Characterization of the benthic bacteria and archaea communities their inferred functions and biotechnological potential.
root:Environmental:Aquatic:Marine:Oceanic:Benthic
MGYS00001456
Sediment microbial diversity from samples of the lagoons of the Amvrakikos Gulf (Ionian Sea, Western Greece)
The aim of the present study was to explore the biodiversity patterns of microorganismic assemblages and to examine whether these patterns are associated with those of the contextual environmental parameters. For this purpose, sediment samples were collected from five lagoons (Rodia, Tsoukalio, Tsopeli, Mazoma, Logarou), located in Amvrakikos Gulf (Ionian Sea, Western Greece). In each lagoon, two sampling stations were chosen, with different connectivity degree with the sea. A number of abiotic parameters were measured for every station, including the sediment concentrations of heavy metals and elements. Microbial DNA was extracted from the sediment upper layer (0-2cm) and was further processed through deep sequencing of the V5-V6 region of the 16S rRNA gene by next generation sequencing.
root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004452
Marine sediment microbial communities in the presence of macrophytes
In this study we examined the sediment microbial communities in the absence and presence of two marine macrophytes (Zostera muelleri - Zm, and Caulerpa taxifolia - Ct), and at low (L) and high (H) densities of the macrophytes.Three independent and randomly obtained samples were taken from each of the five treatment groups (absent, Zm-L, Zm-H, Ct-L, Zm-H), genomic DNA extracted and PCR conducted targeting the V4 region of the 16S gene. PCR amplicons were sequenced using Illumina MiSeq 2x250 bp, with paired-end sequencing.
root:Environmental:Aquatic:Marine:Coastal:Sediment
MGYS00004169
Microbial eukaryotes present in a Norwegian coastal ecosystem and in the gut content of Calanus copepods from Raunefjorden
Use metabarcoding to characterize the diversity of Calanus prey relative to the total microbial eukaryote diversity in the co-occurring seawater habitat
root:Environmental:Aquatic:Marine
MGYS00004171
marine metagenome Raw sequence reads
Microbial diversity in coastal areas of Sichang island in Thailand
root:Environmental:Aquatic:Marine
MGYS00000789
Geothermal Springs Targeted Locus (Loci)
Studies to date suggest that this temperature-diversity gradient relationship is weak or nonexistent for Bacteria and Archaea. To test the impact of temperature as well as pH on prokaryotic diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study.
root:Environmental:Terrestrial:Soil
MGYS00003984
marine sediment metagenome Targeted Locus (Loci)
The microbiological objectives of IODP Expedition 347 Baltic Sea Paleoenvironmentfocused on 1) how the phylogenetic diversity of the deep biosphere in this intracontinental sea differs from that of deep-ocean communities, and 2) are microorganisms that presently live in the deep sediments remnants of limnic and marine populations, or does the modern sedimentary environment select for thecommunity. The Expedition took place September 16, 2013 – November 1, 2013 on board the IODP Mission-Specific Platform Greatship Manisha. Cores were advanced for microbiological sampling at 4 locations: BSB-1, BSB-3, BSB-7, and BSB-9 (Figure 1) using Advanced Piston Coring (APC) and checked for contamination using perfluorcarbon tracers (PFTs).
root:Environmental:Aquatic:Marine:Sediment
MGYS00004164
Seawater coastal British Columbia
Examine the distribution of specific markers genes over time
root:Environmental:Aquatic:Marine
MGYS00004158
16S rRNA genes Random survey
Sequencing of 16S genes from fractions of 15N and 13C SIP experiments
root:Environmental:Aquatic:Marine
MGYS00004589
Diversity of archaeal amoA gene
Diversity of Archaeal amoA genes in sea water samples from Ardley cove, Fildes Peninsula, Antarctica
root:Environmental:Aquatic:Marine
MGYS00004581
Arabian Sea OMZ nirS Metagenome
nirS amplicon sequences from the Arabian Sea
root:Environmental:Aquatic:Marine
MGYS00004208
1)sediments; 2) coral floc Metagenome
Deep-sea sediments and coral flocculant material (floc) collected from a coral community impacted by the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of oil-degrading genes
root:Environmental:Aquatic:Marine:Sediment
MGYS00004277
sediment metagenome Raw sequence reads
microbe community and funtion
root:Environmental:Aquatic:Marine:Sediment
MGYS00005234
Goodrich_TwinsUK_Miseq_2
second half of Goodrich_MiSeq for EBI submission
root:Host-associated:Human:Digestive system:Large intestine:Fecal
MGYS00001561
Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time and seeded with either acclimated or non-acclimated sludge
In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the effect of solids retention time (SRT) on the diversity and dynamics of total, dominant and rare bacterial taxa in eight replicate lab-scale sequencing batch reactors (SBRs) operated for a period of 78 days and seeded with either acclimated or non-acclimated sludge. Rank-abundance curves showed strong abundance of few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2d vs. 10d) on Shannon diversity index and OTU richness of both dominant and rate taxa. Nonmetric Multidimensional Scaling (NMDS) analysis showed that the total, dominant and rare bacterial taxa were highly dynamic during entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media. Moving-window analysis, Global ANOSIM and NMDS analysis revealed that the bacterial community structure in replicate SBRs seeded with acclimated or non-acclimated sludge was reproducible. Overall 16S rRNA gene pyrosequencing could reveal the dynamics of rare bacterial taxa that are normally left out using conventional molecular biology methods.
root:Engineered:Bioreactor:Continuous culture
MGYS00003002
Marine sediment metagenome ICM_FIS
Sands as microbial biodiversity hotspots: Investigating the effect of grain size and biofilm formation.
root:Environmental:Aquatic:Marine:Coastal
MGYS00000812
Antarctic soil watering experiment across a natural salinity gradient
The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change induced disturbances including the melting of massive buried ice, cutting through permafrost by streams, and warming events. These processes are increasing moisture across the landscape altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition (16S rRNA genes) and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment.
root:Environmental:Terrestrial:Soil
MGYS00005075
NEON Surface Water Microbe Marker Gene Sequences - 2014
This study provides the sequence data for the NEON data product, Surface water microbe marker gene sequences (NEON.DP1.20282). The goal of this project is to track changes in the diversity and composition of bacteria, archaea and fungi in planktonic aquatic ecosystems through space and time. NEON collects water column microbes from various depths at numerous sites distributed across the United States. Total genomic DNA is extracted and the 16S and ITS regions of the rRNA cistron are sequenced using high-throughput methods. For additional details and data, visit the NEON Data Portal at http://data.neonscience.org.
root:Environmental:Aquatic:Marine:Oceanic
MGYS00004383
Oxygen minimal zone Targeted loci environmental
To study diversity of microbe community including bacteria, dizotrophs, and protist.
root:Environmental:Aquatic:Marine:Oceanic
MGYS00005093
Effect of long term fertilization strategies on soil bacterial communities
Effect of long term fertilization strategies on soil bacterial communities
root:Environmental:Terrestrial:Soil:Agricultural
MGYS00004195
La Medee sediment - Extracellular Metagenome Metagenome
SSU 16S pyrosequencing project of the extracellular DNA metagenome of a DHAB sediment (La Medee) from the Eastern Mediterranean.
root:Environmental:Aquatic:Marine:Sediment
MGYS00000955
Arbuscular mycorrhizal fungi from soil samples Targeted Locus (Loci)
Sequence arbuscular mycorrhizal fungi from soil samples from the Andean region
root:Host-associated:Plants:Rhizosphere:Soil
MGYS00002527
Diversity of archaeal and bacterial 16S rRNA gene in marine sediment in Aarhus Bay
This project is to study the diversity of Archaeal and bacterial 16S rRNA gene in marine sediments in Aarhus Bay.
root:Environmental:Aquatic:Marine:Sediment
MGYS00002997
nifH diversity in the North Pacific Ocean
This study was performed to elucidate community structure of nitrogen fixing bacteria in the North Pacific Ocean
root:Environmental:Aquatic:Marine:Oceanic
MGYS00002812
Equatorial Pacific Ocean Targeted loci environmental
To (i) document vertical distributions of bacterial diversity and community composition, (ii) investigate how these communities vary from one oceanographic region to another, and (iii) test the extent to which bacterial communities of deep subseafloor sediment may originate in the water column, we used 454 pyrosequencing technology and the v4-v6 hypervariable region of the bacterial 16S rRNA gene to examine bacterial community composition (presence/absence and relative abundance) in the water column, near-seafloor sediment (5 cm), and subseafloor sediment at three environmentally distinct Pacific sites: the very high-productivity eastern equatorial upwelling region (EQP1), the moderately high-productivity open-ocean central equatorial upwelling region (EQP8) and the very low-productivity northern gyre (EQP11) (Figure 1).
root:Environmental:Aquatic:Marine:Oceanic
MGYS00002490
Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Indian Ocean 2015
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 Bay of Bengal in Auguest-September 2015 to examine phytoplankton community diversity.
root:Environmental:Aquatic:Marine
MGYS00002476
Comparative study in validity of three regions of 18S-rRNA for eukaryote amplicon sequence analyses
In the present study, we performed a detailed investigation of the 18S-rDNA, namely, numbers of registered sequences, frequencies of amplification success, the amplicon sequence variability among three regions containing V1-V3, V4-V5 and V7-V9 regions using in silico PCRs based on public databases, and the identification power by NGS-based environmental surveys of planktonic eukaryote community. Although the number of registered sequences in V4-V5 regions was remarkably higher than other regions, the identification power in NGS-based environmental surveys was lowest in V4-V5 regions due to the lowest sequence variability. The number of registered sequences in V1-V3 region was ca. two times smaller than V7-V9 region, and the sequence variability in V1-V3 region was significantly higher than that in V7-V9 region. Then, the identification power was not significant between these two regions, implying identification power is affected by combination of numbers of registered sequences and the sequence variability. We therefore believe V1-V3 region will be the best one for applying to NGS-based monitoring of planktonic eukaryote community in the near future as the number of sequences deposited increases in public databases.
root:Environmental:Aquatic:Marine:Coastal