SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Metabarcoding Eukaryotic plankton  time series samples from long-term ecological research site MareChiara (LTER-MC)

Metabarcoding analysis of a 48 sample time series from Jan 2011 to Dec 2013 targeting 18S V4 rRNA of Eukaryotic plankton from the Long-Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples, Mediterranean Sea. For DNA extraction, about 3 liters of surface sea-water sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were stored at −80°C. Nextera dual index approach and 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform.

Biome: root:Environmental:Aquatic:Marine
Temporal diversity and community structure of the planktonic protist assemblage at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples(Mediterranean Sea) assessed using V4 Illumina sequencing.

We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using V4 Illumina sequencing. Samples for metabarcoding analyses were collected from surface waters at the LTER-MC station on eight dates from February to December 2011. The dates were selected based on light microscopy phytoplankton data, which were used as proxies for the seasonal phase and trophic status of the system.  For DNA extraction, about 3 litres of surface sample (0.5 m) was filtered under mild pressure on each of two cellulose ester filters (47 mm diameter, 1.2 μm pore-size, EMD Millipore, USA). Filters were immediately frozen with liquid nitrogen and stored at −80◦C. Nextera dual index approach and to 2 × 250 bp were applied for V4 region sequencing on a MiSeq platform.

Biome: root:Environmental:Aquatic:Marine
SOLA sampling point Raw sequence reads

Raw environmental eukaryotic samples from the SOLA (Service d'Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2015 to 2017.

Biome: root:Environmental:Aquatic:Marine
SOLA Raw sequence reads

Raw environmental eukaryotic samples from the SOLA (Service d''Observation Laboratoire Arago) sampling point, in the North Western Mediterranean sea. These samples are part of a time series, from 2007 to 2015, that is investigating the seasonal reoccurrence of rhythmic species.

Biome: root:Environmental:Aquatic:Marine
Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

The deep-sea provides global vital functions such as sequestration of carbon from the atmosphere. The increased anthropogenic pressures and interest in expanding deep-sea fisheries makes this pristine ecosystem particularly vulnerable, whose conservation largely depends on rapid knowledge acquisition. In view of the limitations of traditional methods to explore the biodiversity of this vast ecosystem, the analysis of traces of macroorganismal DNA released into the water column arises as a cost-effective, non-invasive alternative. Yet, the success of this approach requires understanding of the stratification of DNA traces in the ocean. This study provides evidence that fish DNA traces can be used to establish depth-specific fish diversity and abundance throughout the water column, opening a promising avenue for gathering knowledge about the deep-sea ecosystem.

Biome: root:Environmental:Aquatic:Marine
Marine fish eDNA metabarcoding


Biome: root:Environmental:Aquatic:Marine
Time series of Synechococcus diversity at the SOMLIT-ASTAN station

The genetic diversity of Synechococcus population in the English Channel off Roscoff was assessed every two weeks by sequencing the high resolution petB gene marker at the long-term coastal observatory SOMLIT-ASTAN station from July 1st 2009 to December 19th 2011.

Biome: root:Environmental:Aquatic:Marine
Dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea

Here we report a comprehensive dataset covering spatiotemporal variations in prokaryotic and eukaryotic microbial communities and physicochemical parameters in the Baltic Sea. Within 13-months (Jan 2019-Feb 2020), we took 346 water samples during monthly cruises at 19 stations along the salinity gradient. We performed 16S and 18S DNA metabarcoding and microscopy based counting, and saw that both salinity and season are strongly reflected in the dataset. 
It provides unique opportunities for both technical and ecological analyses, and is valuable for both environmental monitoring and as a biodiversity reference for future studies, in the context of eutrophication and the prospect of climate change.

Biome: root:Environmental:Aquatic:Marine
Blanes Bay Microbial Observatory (BBMO) time-series 18S rRNA gene pico- and nano-plankton (10 years monthly samples)

This study includes 18S rRNA-gene sequences (V4 region) of pico- and nanoplankton from Blanes Bay Microbial Observatory (BBMO) monthly sampled during 10 years. It contains 120 pico-samples and 120 nano-samples.

Biome: root:Environmental:Aquatic:Marine:Coastal
16S rRNA gene amplicon time-series in Blanes Bay Microbial Observatory (BBMO)

This study includes 16S rRNA-gene sequences (V3-V4 region) of bacterioplankton monthly sampled from the Blanes Bay Microbial Observatory (BBMO). It contains 11 years of samples from the 0.22-3 μm  size fraction and 10 years from the 3-20 μm size fraction.

Biome: root:Environmental:Aquatic:Marine:Coastal
Bacterial diversity of marine planktonic size-fractionated samples

16S rRNA sequencing of a 2-years temporal serie in Blanes Bay Microbial Observatory.

Biome: root:Environmental:Aquatic:Marine:Coastal
Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis

Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases with controversial reports about the vaginal microbiota diversity. We determined the vaginal microbial community in patients with VVC, bacterial vaginiasis (BV), and mixed infection of VVC and BV using the Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed an increased order from normal control, VVC only, mixed infection of BV and VVC, to BV. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV. Detailed comparison showed that while the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern with relatively higher abundance of Lactobacillus than the BV group but higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. The VVC-only group, however, could not be described by any single profile. They spanned from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC showed inconsistent changes of vaginal microbiota, with four BV/VVC samples recovered to a higher Lactobacillus level while many VVC-only patients did not. These results will be useful for future study about the role of vaginal microbiota in VVC and related infectious diseases.

Biome: root:Host-associated:Human:Reproductive system:Vagina
16S metabarcoding of bacteria associated with cultured strains of the brown alga Ectocarpus sp.

We examined the bacterial flora associated with 20 cultured strains of Ectocarpus sp. from different locations, and recorded both the bacterial diversity associated directly to the alga and that found in the culture medium. Experiments were carried out to amplify an approximately 400 bp fragment of the bacterial 16S comprising the V3 and V4 regions and sequenced on the Illumina MiSeq platform using V2 reagents ( 2x250 bp reads).

Biome: root:Host-associated:Algae:Brown Algae
EMG produced TPA metagenomics assembly of the Gut microbial dysbiosis in young adults with obesity (Gut microbial dysbiosis in young adults with obesity) data set.

The Gut microbial dysbiosis in young adults with obesity Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12123.  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
Oil spill dispersant strategies and bioremediation efficientcy

After accidental oil spills to seawater from production or transport facilities the oil will be spread on the water surface and in the water column, and a number of weathering processes will appear. Typical operational methods to remove the oil from the sea surface include physical limitation of the surface spreading with booms and collection of the oil by skimmers. An alternative method to remove surfaced oil is to use chemical dispersants. These chemicals create a more hydrophilic oil surface, resulting in the generation of small droplets by wave actions, which are spread into the water column. The generation of small droplet dispersions may increase the natural biodegradation of the oil in the seawater column. Recently, dispersant methods have also been used for sub-surface oil spills (blow-outs). The Norwegian Research Council and several oil companies have funded this research project in order to improve our knowledge and understanding about the effects of dispersant strategies on oil biodegradation and the microbial communities and processes involved. The data from this project will contribute to the optimization of dispersant strategies. The project will include experimental studies simulating both surface and subsurface oil discharges. The focus will be molecular microbiology analyses and bioinformatics, including phylogenetic characterization of microbial communities (characterization of 16S rRNA genes) and investigations of biochemical pathways associated with degradation of alkanes and aromatic oil compounds. Metagenomic and metatranscriptomic studies may be expected to be part of this work. Finally, generated experimental data should be incorporated into OSCAR model, a industry standard model for predicting the fate of the oil in the marine water column after an accidental oil spill.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
nifH gene in KH-11-10 and KH-13-7 cruises

This study aims to describe diazotroph community structure in the euphotic zone in the western and eastern subtropical South Pacific

Biome: root:Environmental:Aquatic:Marine
Baltic Sea

This is a 16S rRNA pyrosequencing study of ferruginous surface sediment samples collected from the Skagerrak (North Sea) and Bothnian Bay (Baltic Sea area).

Biome: root:Environmental:Aquatic:Marine:Sediment
Temperate forest soil Metagenome

The overall aims of this study were (1) to explore soil bacterial communities in four typical temperate forest types from Changbai Mountain (Broad-leaved Korean pine mixed forest, Secondary poplar-birch forest, Spruce-fir forest, and Larch forest) with newly developed bar-coded 454 pyrosequencing method; (2) to elucidate the biotic and abiotic factors controlling the abundance, diversity and composition of soil bacterial communities; (3) to test if the differentiation of soil bacterial communities in these temperate forests support the copiotroph/oligotroph functional classification model and the non-random co-occurrence patterns. This study will provide the first glimpse at the potential role of above-ground vegetation in allowing niche differentiation of soil bacterial communities in natural temperate forests situated in Changbai Mountain, and tries to reveal the intrinsic mechanism of such differentiation.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Marine metagenome ICM_AWP

Variation of Microplanktonic Communities Composition with Depth in an area under a Meddy Influence.

Biome: root:Environmental:Aquatic:Marine
Marine subseafloor sediment Targeted Locus (Loci)

We propose to apply 454-based tag pyrosequencing to investigate how microbial communities change with depth, lithology, and porewater geochemistry in the sediment that underlies one of the highest productivity regions in the world ocean. To accomplish this goal, we propose to analyze extracted DNA from 16 samples taken in high resolution in conjunction with detailed porewater geochemistry. This dataset will provide an unprecedented insight into the microbial ecology of a highly productive open ocean site (35 cm/k.y) to a sediment depth of 750 m and an age of 2.1 Ma. We anticipate that through this use of next-generation sequencing technology in combination with biogeochemical and cell count data sets collected during IODP expedition 323, we will obtain significant insight into this previously uncharted ecosystem.

Biome: root:Environmental:Aquatic:Marine:Sediment
Macroalgal Morphology affects composition and settlement of microbial communities

Macroalgae (seaweeds) have an intimate relationship with their microbial symbionts. Microbial communities associated with macroalgal surfaces (epibiota) are generally host-specific and, historically, there has been great interest in the role of biological compounds and chemical warfare in  microbial community assembly on seaweeds. However, the interaction between seaweeds and their environment may also influence community assembly of their microbiota. In this experiment, I ask whether the interaction between water flow and seaweed morphology affects the settlement and structure of microbial biofilms. I test whether three common algal morphologies select for differential biofilm communities using artificial macro algae units (AM units) made out of latex. I find that morphology does affect initial microbial settlement and community structure, but that eventual dominance of substrate specialists (in our case, a latex degrader) swamps the influence of morphology in long-term biofilms.

Biome: root:Environmental:Aquatic:Marine
Interferon-lambda and interleukin-22 cooperate for the induction of interferon-stimulated genes and control of rotavirus infection

The epithelium is the major entry point for many viruses but the processes protecting barrier surfaces against viral infections are incompletely understood. We identify interleukin (IL)-22 produced by group 3 innate lymphoid cells (ILC3s) as an amplifier of interferon (IFN)-lambda signaling, a synergism required to curtail replication of rotavirus, the leading cause of childhood gastroenteritis. Cooperation between IL-22 and IFN-lambda receptors, both of which are preferentially expressed by intestinal epithelial cells, was required for optimal STAT1 transcription factor activation and expression of interferon-stimulated genes. This data suggests that epithelial cells are protected against virus replication by co-opting two evolutionarily related cytokine networks. These data may inform the design of novel immunotherapies of virus infections that are sensitive to IFNs.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Baselines Initiative 16S rRNA gene dataset: Baselines Amplicon Release 1 (R1) Caribbean Sea near Curacao (including saline pond samples in Curacao) 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 Caribbean Sea near Curacao (and saline ponds in Curacao as well) in April 2015 to examine phytoplankton community diversity.

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

Analysis of RNA tags in Tara Oceans Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The RNA was extracted, cDNA prepared then amplified by PCR.

Biome: root:Environmental:Aquatic:Marine
Successional trajectories of coastal bacterioplankton communities in response to co-exposure of cadmium and phenanthrene

Coexistence of multiple contaminants in coastal aquatic ecosystems can lead to complicated circumstances in ecotoxicological assessment for biological communities due to potential interaction between contaminants. We chose cadmium (Cd) and phenanthrene (PHE) as representatives of heavy metals and polycyclic aromatic hydrocarbons, respectively. Contamination process was mimicked using coastal water microcosms contaminated by Cd (1 mg/L), PHE (1 mg/L), and their mixture over two weeks.

Biome: root:Environmental:Aquatic:Marine:Coastal
Nuunat- ORMS formation during oil biodegradation at low temperature

Biodegradation study of chemically dispersed oil and ORMS formation in cold local (5C) Norwegian seawater over 64 days incubation period containing natural microbial community and selected diatom population of Fragilariopsis cylindrus.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
Flores_fecal_EBI

Fecal samples from Flores_SMP for EBI submission

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
PETROMAKS E#9

Biodegradation study was conducted with two different oils (naphthenic and asphaltenic) at two different temperatures (5C and 13C). The aim of the study was to evaluate differences in biodegradation and microbial community dynamics between two oils at different temperatures.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
Planktonic bacterial communities in the arctic Canada Basin and
                Kongsfjorden

Planktonic bacteria play key role in biogeochemical cycles and energy
                flow in marine ecosystems. However, our knowledge of the extent and character of
                bacterial diversity in polar marine environments is still limited. Here we present
                the use of high throughput DNA pyrosequencing and statistical inference to assess
                the diversity of planktonic bacteria in the arctic Canada Basin, and Kongsfjorden in
                Spitsbergen. The V3 region of the 16S rRNA gene was amplified from seawater samples
                collected from the upper water column. The number of bacterial 16S rRNA sequences
                obtained from each sites varied from 7433 to 9218. In the Canada Basin, the most
                abundant bacterial groups in two sites of water at 10m depth were the Proteobacteria
                (mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria.
                Different bacterial communities were observed in the deeper water (80 or 100m depth)
                at the two sites. The Proteobacteria and Bacteroidetes also formed the dominant
                bacterial groups in surface water of Kongsfjorden. However, Gammaproteobacteria
                accounted for more than 90% of the Proteobacteria.

Biome: root:Environmental:Aquatic:Marine
marine sediment metagenome Targeted Locus (Loci)

Site U1387 offers a chance to study the response of microbial assemblage to specific seafloor events such as contourite depositions, changes in bottom current energy, shifts in organic matter deposition rates, and geochemical changes that are representative of seafloor processes during rapid climate change.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial community structures of chimney in DODO and Solitaire hydrothermal fields

Difference of microbial diversity by the 16S rRNA gene in chimney structures between two hydrothermal fields on central Indian Ridge.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
WGS of bacterial strains from food industry

In this study, strains were isolated from different points of the food industry and characterized by classical microbiological methods. DNA was then extracted and sequenced by shotgun technology to assess metabolic potential.

Biome: root:Engineered:Food production
EMG produced TPA metagenomics assembly of PRJEB31095 data set (The intestinal microbiome from two ecotypes of Atlantic cod and three additional Gadidae species.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB31095, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine.

Biome: root:Host-associated:Fish:Digestive system:Intestine
EMG produced TPA metagenomics assembly of PRJNA482836 data set (Gut microbiome from Piaractus mesopotamicus Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA482836, 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 PRJEB42464 data set (Gut Microbiomes of European Farm Rainbow Trout).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB42464, and was assembled with megahit v1.2.9, 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 PRJEB19833 data set (Mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diet).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19833, and was assembled with metaSPAdes v3.15.3, megahit v1.2.9. 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 PRJNA663846 data set (Metagenomic analysis of stomach contents of Acanthopagrus latus).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA663846, 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 PRJEB29346 data set (Metagenomic shotgun sequencing of the Atlantic cod intestinal microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB29346, and was assembled with unknown v0.0. This project includes samples from the following biomes: root:Host-associated:Fish:Digestive system:Intestine.

Biome: root:Host-associated:Fish:Digestive system:Intestine
EMG produced TPA metagenomics assembly of PRJEB19785 data set (Metagenomics of the mid- and hind-gut of rainbow trout gastrointestinal tract (GIT) fed alternative protein diets).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB19785, 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 PRJNA434147 data set (Delta Smelt gut content study).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA434147, 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 PRJEB30661 data set (TO INVESTIGATE THE MICROBIAL COMMUNITY ASSOCIATED WITH FISH GUT).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB30661, 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