SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
EMG produced TPA metagenomics assembly of the PRJNA336829 data set (Thermophilic microbial communities from the Joint Bioenergy Institute, California, USA of rice/straw/compost enrichment - eDNA_2 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA336829.  This project includes samples from the following biomes: root:Engineered:Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the PRJNA480846 data set (Metagenome of biofouled reverse osmosis membranes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA480846.  This project includes samples from the following biomes: root:Engineered:Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the PRJNA392180 data set (Seasonal Cycling in the Gut Microbiome of the Hadza Hunter-Gatherers of Tanzania).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA392180.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the PRJEB22997 data set (Baltic Sea reference metagenome assembly and s; transect and redoxcline.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22997.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine:Oceanic
EMG produced TPA metagenomics assembly of the PRJNA413474 data set (MTR skin microbiome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA413474.  This project includes samples from the following biomes: root:Host-associated:Human:Skin.

Biome: root:Host-associated:Human:Skin
EMG produced TPA metagenomics assembly of the PRJNA255783 data set (Home Microbiome Metagenomes).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA255783.  This project includes samples from the following biomes: root:Engineered:Built environment, root:Host-associated:Mammals.

Biome: root:Engineered:Built environment
EMG produced TPA metagenomics assembly of the PRJNA271618 data set (Baboon feces Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA271618.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.

Biome: root:Host-associated:Mammals:Digestive system
EMG produced TPA metagenomics assembly of the PRJEB8939 data set (Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8939.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Stomach:Rumen.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
EMG produced TPA metagenomics assembly of the PRJDB5777 data set (Metagenome analysis of the trench microbiome project on Northwest Pacific Ocean).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5777.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
EMG produced TPA metagenomics assembly of the PRJNA266679 data set (Pelagic Microbial community sample from North Sea - COGITO 998_met_07 Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266679.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Pelagic.

Biome: root:Environmental:Aquatic:Marine:Pelagic
EMG produced TPA metagenomics assembly of the PRJNA406172 data set (Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.5.yng.040610 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406172.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the PRJNA479434 data set (NRC/UOttawa - Peace Athabasca Delta Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA479434.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lake.

Biome: root:Environmental:Aquatic:Freshwater:Lake
EMG produced TPA metagenomics assembly of the PRJEB13832 data set (Local surveillance of infectious diseases and antimicrobial resistance from sewage).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB13832.  This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.

Biome: root:Engineered:Wastewater:Water and sludge
EMG produced TPA metagenomics assembly of the PRJNA406152 data set (Arabidopsis rhizosphere microbial communities from North Carolina - M.Oy.2.old.250510 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406152.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the PRJNA321634 data set (mouse gut metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA321634.  This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Large intestine.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of the PRJNA406788 data set (Rhizosphere microbial communities from Sorghum bicolor, Mead, Nebraska, USA - 072115-113_1 MetaG metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406788.  This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere.

Biome: root:Host-associated:Plants:Rhizosphere
EMG produced TPA metagenomics assembly of the PRJNA266672 data set (Pelagic Microbial community sample from North Sea - COGITO 998_met_01 Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA266672.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the PRJEB25754 data set (Using salinity to select for progressive onset denitrifiers).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB25754.  This project includes samples from the following biomes: root:Engineered:Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the PRJNA405734 data set (Cellulose-adapted microbial communities from the Joint BioEnergy Institute, USA - Passage B1F01 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405734.  This project includes samples from the following biomes: root:Engineered:Bioreactor.

Biome: root:Engineered:Bioreactor
EMG produced TPA metagenomics assembly of the PRJNA405200 data set (Marine microbial communities from the Central Pacific Ocean - Fk160115 155m metaG metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA405200.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic.

Biome: root:Environmental:Aquatic:Marine:Oceanic
mouse gut metagenome Raw sequence reads

Mice intestine metagenome

Biome: root:Host-associated:Mammals:Digestive system:Large intestine
Investigating the viral ecology of global bee communities with high-throughput metagenomics

The ecology of bee viruses is complex, as viruses are readily shared among bee species and plants. However, our understanding of bee viral communities is primarily derived from studies of North America and European Apis mellifera honey bee populations. Here, we develop a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and screening through a series of filters to identify contigs specifically corresponding to viral sequences. We evaluated samples of honey bees and co-foraging non-Apis bee species (12 bee species in total) from 9 countries and 5 continents. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, 127 contigs corresponding to novel viruses (previously not observed in bees), with 29 represented by >0.1% of the reads in a given sample. These 29 contigs corresponded to 9 viral families, including 6 viral families that have not been previously observed in bees. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for analysis of insect viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.

Biome: root:Host-associated:Insecta
Evaluation of methods to purify virus-like particles for the sequencing of intestinal viromes

In this study we used an in vitro assembled microbiota sample to evaluate the efficiency and biases of purification methods used to purify virus-like particles from gut content for metagenome sequencing. The artificial microbiome sample contained six bacteriophages (P22, phiVPE25, phi6, T3, T7 and M13)two bacterial strains (gr+: Listeria monocytogenes EGD-e and gr-: Bacteroides thetaiotaomicron VPI5482), which were mixed into feces from germ-free mice.  Three purification methods were tested: (1) Filtration + DNase (FD), (2) DTT treatment + filtration + DNase (DTT), (3) filtration + DNase + CsCl density gradient (CsCl). Additionally, metagenomes of the complete microbiome sample were sequenced (MG). Each treatment was done in duplicate.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Viral Metagenomics of fecal samples of fruit bats

The characterisation of virome of Cameroonian fruit bats to identify novel viruses of zoonotic potential

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use

Metagenomics has provided insights into the species composition and function of microbial communities and revealed that many species even in highly competitive environments seem to share the same sets of genes for acquiring and utilising nutrients. This questions whether niche differentiation between microbes under competitive stress exists and if so, how it is maintained. Rumen microbes exist in a highly competitive, anaerobic environment, and compete for access to the limited nutrients available in the biomass consumed by the host. The rumen microbiome affects the efficiency and health of the host, and has been mined for novel enzymes and anti microbial peptides and is known as a potent contributor to greenhouse gas emissions. A better understanding of the structure and function of this community has large potential benefits. We generated separate metagenomic libraries from 14 Limousin cows. Following assembly, gene prediction and taxonomic assignment, SNPs were identified and functional isoform diversity (pN/pS) was calculated for each gene. The independent calculations from each sample were used to calculate confidence intervals for testing for diversity of function between microbes, a signature of niche differentiation. We identified significant differences in functional diversity between competing organisms in genes involved in carbon, amino-sugar and nucleotide sugar metabolism, suggesting adaptation to utilizing different routes for nutrient acquisition in the rumen. This suggests that a greater understanding of the rumen microbiome and considering macro-ecological concepts, such as successional change and adaptation, are likely to improve strategies for increasing the efficiency and health of the host and reducing greenhouse gas emissions.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Thermophilic microbial communities from the Joint Bioenergy Institute, California, USA of rice/straw/compost enrichment - eDNA_2 metagenome


Biome: root:Engineered:Bioreactor
Freshwater Viruses Metagenomic assembly

To identify viruses, freshwater samples were collected from six different locations of Lake Ontario and Lake Erie

Biome: root:Environmental:Aquatic:Freshwater:Lentic
viral metagenome Metagenome

Viral metagenomes

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Taxonomic and gene content analysis of the bacterial viral metagenomes from the oral cavity from healthy youngsters in Valencia

Samples were collected from 72 healthy young Spanish people from Valencia (Spain) in November 2012. Samples consisted of mouthwash using sterile saline serum (NaCl 0.9%) from 72 volunteers (38 females and 34 males).Sampling was anonymized and only sex was recorded.For all samples, the metagenomic analysis of the bacterial DNA viral communities was carried out, using the Illumina MiSeq with 300 bp x2 chemistry.

Biome: root:Host-associated:Human:Digestive system:Oral
Baboon feces Metagenome

Raw metagenomic sequencing reads collected from samples from 48 adult baboons in two social groups during July - August 2012.

Biome: root:Host-associated:Mammals:Digestive system
Metagenome analysis of the trench microbiome project on Northwest Pacific Ocean

The trench microbiome project analyzed planktonic microbiomes associated with sea surface to hadal waters along the water columns on Mariana, Ogasawara (Izu-Bonin), Japan and Chishima (Kuril) Trenches.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Aphotic zone
Using salinity to select for progressive onset denitrifiers

To gain an understanding of the bacteria capable of performing nitrite accumulation from nitrate (denitratation) in such system a study of a nitrite accumulation bioreactor has been undertaken. Our goal was to assess how the salinity parameter affected the nitrogen removal performance of this bioreactor, and which microorganisms were responsible for the nitrite accumulation needed to sustain the denitration process in this bioreactor. The reactor used in this study was a mixed, unsealed, electron donor-limited continuous reactor with acetate and nitrate as substrates operated under diverse salinity regimes.

Biome: root:Engineered:Bioreactor
Reclaimed water Metagenome

Zero valent iron filtered and unfiltered reclaimed water collected from a tertiary wastewater treatment plant in the Mid-Atlantic United States.

Biome: root:Engineered:Wastewater:Water and sludge
EMG produced TPA metagenomics assembly of the PRJEB22104 data set (Unusual ecophysiology of Candidate phylum Acetothermia bacteria associated with anaerobic digesters revealed by complete genome sequencing and advanced in situ microscopy).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB22104.  This project includes samples from the following biomes: root:Engineered:Wastewater.

Biome: root:Engineered:Wastewater
EMG produced TPA metagenomics assembly of the PRJNA319556 data set (A mock community containing 9 viruses and four bacterial species Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA319556.  This project includes samples from the following biomes: root:Engineered.

Biome: root:Engineered
EMG produced TPA metagenomics assembly of the PRJDB4437 data set (Osaka Bay Virome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB4437.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal.

Biome: root:Environmental:Aquatic:Marine:Coastal
Metagenome of biofouled reverse osmosis membranes

This project aims to understand the microbial community and its functional potential of biofouled reverse osmosis membranes used in water purification.

Biome: root:Engineered:Bioreactor
Unusual ecophysiology of Candidate phylum Acetothermia bacteria associated with anaerobic digesters revealed by complete genome sequencing and advanced in situ microscopy

Members of the candidate phylum Acetothermia are globally distributed and have been detected in diverse natural habitats as well as engineered systems. However, little is known about their physiology and ecological importance. In this study, an OTU belonging to Acetothermia was identified as one of the most abundant genus-level bacterial taxa in full-scale mesophilic anaerobic digesters at two Danish wastewater treatment plants. A closed genome was obtained by differential coverage binning of metagenomes and long Nanopore reads. Genome annotation and metabolic reconstruction revealed an anaerobic chemoheterotrophic lifestyle in which the bacterium obtain energy and carbon from the fermentation of peptides, amino acids, and simple sugars to acetate, formate and hydrogen. In contrast to previously studied Acetothermia, the genome did not encode a functional acetyl-CoA pathway required for acetogenesis. Fluorescent in situ hybridization probes targeting Acetothermia were designed and used in combination with confocal laser scanning microscopy and atomic force microscopy. This revealed an unusual morphology composed of a central rod cell with bipolar prosthecae similar to those observed in Caulobacter and Asticcacaulis. These prosthecae greatly expand the cell surface to volume ratio and allow for increased nutrient uptake, providing the bacteria with a competitive advantage under nutrient limited conditions.

Biome: root:Engineered:Wastewater
A mock community containing 9 viruses and four bacterial species Raw sequence reads

We optimised and validated a method that allows for high throughput virome analysis. For that we evaluated the quantitative effect of homogenisation, centrifugation, filtration, chloroform treatment and random amplification on a mock-virome and a bacterial mock-community using quantitative PCR and next-generation sequencing.

Biome: root:Engineered
EMG produced TPA metagenomics assembly of the PRJDB5708 data set (Metagenomic sequences of the Ofunato Bay 2015).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB5708.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Coastal.

Biome: root:Environmental:Aquatic:Marine:Coastal
EMG produced TPA metagenomics assembly of the PRJEB14899 data set (Oil spill dispersant strategies and bioremediation efficientcy).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB14899.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Oil-contaminated
Denitrification-dependent anaerobic methane oxidizers in a marine oxygen minimum zone

To show presence and activity of bacteria associated with denitrification-dependent anaerobic oxidation of methane in the a permanent marine oxygen minimum zone

Biome: N/A
EMG produced TPA metagenomics assembly of the PRJNA277357 data set (Denitrification-dependent anaerobic methane oxidizers in a marine oxygen minimum zone).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA277357.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
Seasonal Cycling in the Gut Microbiome of the Hadza Hunter-Gatherers of Tanzania


Biome: root:Host-associated:Human:Digestive system:Large intestine
MTR skin microbiome

A metagenomic study on the skin microbiome after contact with MTR trains

Biome: root:Host-associated:Human:Skin
NRC/UOttawa - Peace Athabasca Delta Raw sequence reads

Metagenomic analysis of the hydrocarbon degradation potential of microbial communities in lakes of the Peace-Athabasca Delta, AB, Canada in relation to petroleum hydrocarbons

Biome: root:Environmental:Aquatic:Freshwater:Lake
Metagenomic sequences of the Ofunato Bay 2015

The Ofunato Bay in Iwate Prefecture, Japan, is a deep coastal bay located at the center of the Sanriku Rias coast and considered an economically and environmentally important asset. Here we present the first whole genome sequencing (WGS) study on the microbial communities of the Bay where surface water samples were collected in 2015 from three stations along its length to cover the entire bay. We sequenced 0.2-??m filter fraction, targeting the free-living fraction only, among the sequentially size-fractionated samples of 20.0-, 5.0-, 0.8- and 0.2-??m filters,. As expected, Proteobacteria (Alpha, Beta and Gamma) were the most abundant phyla in the Ofunato Bay followed by Bacteroidetes, Firmicutes, Actinobacteria, Cyanobacteria and Tenericutes. We detected a wide range of heterotrophic bacteria, Archaea and eukaryotic algae. The majority of these bacteria are considered significant in oceans and marine ecology.

Biome: root:Environmental:Aquatic:Marine:Coastal
Osaka Bay Virome

Metagenome sequencing project for Osaka Bay sea water samples by 0.22 micrometer filtrate containing viruses.

Biome: root:Environmental:Aquatic:Marine:Coastal
Metagenome and viral metagenome fraction isolated from Blanes (Mediterranean Sea)

Surface seawater samples were collected form the Blanes Bay Microbial Observatory (BBMO) in the north-western Mediterranean Sea, and they was used for metaviromics and metagenomics analyses.

Biome: N/A
EMG produced TPA metagenomics assembly of the PRJEB12379 data set (Metagenome and viral metagenome fraction isolated from Blanes (Mediterranean Sea)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12379.  This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of the PRJEB7772 data set (An analysis of the composition of viruses and bacteria in stool samples from IBD patients and healthy controls.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB7772.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the PRJEB8249 data set (Bariatric surgery induces long-term changes on the gut metagenome contributing to fat mass regulation).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8249.  This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine.

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