SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
16S rRNA amplicon sequencing from the Ocean Sampling Day (OSD) campaign June 2019

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. The OSD2019 event is a continuation of the successful OSD events of Micro B3 project (https://www.microb3.eu/osd.html).

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

Analysis of 16S DNA in Tara Oceans Polar Circle Prokaryotes size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small cell sizes. The DNA was extracted and amplified by PCR.

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

Analysis of 16S DNA in Tara Oceans Prokaryotes size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small cell sizes. The DNA was extracted and amplified by PCR.

Biome: root:Environmental:Aquatic:Marine
sponge metagenome genome assembly, odCliOrie1.metagenome

This project provides the full unbinned assembly of Cliona orientalis 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/).

Biome: root:Host-associated:Porifera
sponge metagenome genome assembly, odXesMuta1.metagenome

This project provides the full unbinned assembly of Xestospongia muta 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/).

Biome: root:Host-associated:Porifera
annelid metagenome genome assembly, wcBraLoba9.metagenome

This project provides the full unbinned assembly of Branchellion lobata 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/).

Biome: root:Host-associated:Annelida
sponge metagenome genome assembly, odAgeOroi1.metagenome

This project provides the full unbinned assembly of Agelas oroides 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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Mollusca
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/).

Biome: root:Host-associated:Mollusca
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/).

Biome: root:Host-associated:Annelida
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Mollusca
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Tunicates:Ascidians
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Fungi
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Porifera
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/).

Biome: root:Host-associated:Algae
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

Biome: root:Environmental:Aquatic:Marine
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

Biome: root:Host-associated:Plants:Rhizosphere:Soil
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.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
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.

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

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

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

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

Biome: root:Host-associated:Human:Skin
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

Biome: root:Engineered:Solid waste
Parfrey_euk_testing_samples_515_806

Comparison of different sample types using different primers and platforms

Biome: root:Mixed
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

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

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Archaea 16S 01-13 Genome sequencing and assembly

Archaea 16S rRNA gene

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Environmental:Aquatic:Marine:Coastal
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.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Metatranscriptomics analysis of bacterial comunities in two moss species

Metatranscriptomics analysis of bacterial comunities in two moss species

Biome: root:Host-associated:Plants:Phylloplane:Epiphytes
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

Biome: root:Environmental:Terrestrial:Soil
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.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
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

Biome: root:Environmental:Aquatic:Marine:Sediment
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.

Biome: root:Host-associated
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.

Biome: root:Environmental:Aquatic:Marine