SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Marine bacteria Targeted Locus (Loci)

This study examines the composition of bacterial communities associated with four species of crustose coralline algae.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
marine sediment metagenome Metagenome

Bacteria in marine sediments (High Arctic)

Biome: root:Environmental:Aquatic:Marine:Sediment
SB Marine Metagenome

The study of bacterial diversity.  Marine metagenome from Malaysian coastal water.

Biome: root:Environmental:Aquatic:Marine:Coastal
Temporal dynamics of bacterioplankton community in response to excessive nitrate loading in the oligotrophic coastal water

Coastal ecosystems are receiving elevated inputs of nitrogen (N), primarily as nitrate, from anthropogenic sources. Bacterioplankton play important roles in marine N-cycle. Understanding how excessive N-loading affects marine bacterioplankton communities is critical for the insight into the biodiversity of marine ecosystems under the condition of eutrophic disturbance. In this study, the oligotrophic coastal water microcosms were perturbed with a certain nitrate level of 1.0 mg L-1 in two loading modes: 1) one-off loading (OL) with the level of 1.0 mg L-1 at the beginning; 2) periodic loading (PL) with the level of 0.125 mg L-1 every two days during 16 days.

Biome: root:Environmental:Aquatic:Marine:Coastal
Characterization of Growing Bacterial Populations in McMurdo Dry Valley (Antarctica) Soils through Stable Isotope Probing with 18O-water

Stable isotope probing of soil bacterial DNA with 18O labeled water was performed to identify which bacterial populations are active by sequencing 16S rRNA gene sequences from heavy and light fractions of soil DNA.

Biome: root:Environmental:Terrestrial:Soil
Evidence  of  bacterioplankton community adaption in responses to  long-term mariculture disturbance

Mariculture activity acts as a disturbance to bacterioplankton community because it results in coastal eutrophication known to alter the bacterial composition. However, to what extent that such disturbance affects turnover of bacterioplankton community composition (BCC) and network interactions among bacterial assemblages are largely unknown. To this end, using 454  pyrosequencing of bacterial 16S rRNA gene, we evaluated the effects of mariculture disturbance on the temporal dynamics of BCC in Xiangshan Bay, the East China Sea. Clearly seasonal succession and sites (fish farm and control sites) separation of BCC were observed, which follow the time-decay for similarity  relationship.  Sampling  time  and mariculture  disturbance  respectively contributed 19.3% (P = 0.001) and 4.3% (P = 0.008) variations of the BCC. However, seasonal dynamics of bacterial alpha-diversity had no obvious trend, but were tightly associated with the relative abundances of potential bacterial predators. The temporal succession of the  BCC was significantly correlated with seawater temperature, chemical oxygen demand, N/P  ratio, dissolved inorganic nitrogen and chlorophyll a. We observed over the three seasons the  same change pattern for a few dominant bacterial families under mariculture disturbance. Additionally, mariculture disturbance considerably decelerated the temporal turnover rate, but  intensified the network interactions of bacterial community. These results demonstrate that BCC is sensitive to mariculture disturbance in this study region, while the consistency with which sensitive bacterial assemblages could characterize such disturbance. Low temporal turnover rate and complex network interactions, thus enabling bacterial communities were adaptive to long-term mariculture disturbance.

Biome: root:Environmental:Aquatic:Marine:Coastal
Bacterial communitiesl in first and subsequent rounds in Korean ginseng field soil

Investigation of bacterial diversities and communities in the soil of ginseng fields at the first round and subsequent round

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Foraminifera Metagenome

Spatial patchiness is a natural feature that strongly influences the level of species richness we perceive in surface sediments sampled in the deep-sea. Recent environmental DNA (eDNA) surveys of benthic micro- and meiofauna confirmed this exceptional richness. However, it is unknown to which extent the results of these studies, based usually on few grams of sediment, are affected by spatial patchiness of deep-sea benthos. Here, we analyse the eDNA diversity of Foraminifera in 42 deep-sea sediment samples collected across different scales in the Southern Ocean.

Biome: root:Environmental:Aquatic:Marine:Sediment
Spatial Variation of Coastal Bacterioplankton Community along a Nitrogen and Phosphorus Co-pollution Gradient

Anthropogenic discharges of nitrogen (N) and phosphorus (P) have caused widespread threats to coastal ecosystems. Bacterioplankton are known to play crucial roles in N/P cycling in marine environments, but little is known about how bacterioplankton community responds to N-P co-pollution. Here, we collected surface seawater samples along a transect in East China Sea. We applied 16S rRNA gene amplicon pyrosequencing to investigate the spatial variation of bacterioplankton communities under a N-P co-pollution gradient. The bacterioplankton communities were dominated by Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes and Betaproteobacteria, which were distinct from those of sediment bacterial assemblages at the same transect. The bacterioplankton community compositions (BCCs) did not vary consistently along the pollution gradient, but clustered into nearshore and offshore groups. The combined environmental factors and spatial distances contributed 30.4% and 12.2% to the variation of the BCC, respectivelys, with a high auto-correlated effect that constrained 25.8% variation. In addition, a series of sensitive bacterial OTUs were identified, whose abundances were significantly associated with the N and/or P levels. This study demonstrates that coastal N-P co-pollution dramatically alter the BCCs, while these changes could be characterized by a few sensitive bacterioplanktonic OTUs.

Biome: root:Environmental:Aquatic:Marine
Peruvian eddy shotgun metagenomes

Shotgun metagenomes sampled from a mesoscale water eddy during strong upwelling conditions in Eastern tropical South Pacific waters off the Peruvian coast, February to March 2013.

Biome: root:Environmental:Aquatic:Marine:Pelagic
EMG produced TPA metagenomics assembly of PRJNA748214 data set (saliva samples Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA748214, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJNA408025 data set (Global studies of microbial diversity in pig gut).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA408025, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA737271 data set (Piglet gut and in-barn manure from farms on Raised Without Antibiotics program display a reduced antimicrobial resistance but an increased prevalence of pathogens).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA737271, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Mixed.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of PRJNA645191 data set (Parity is associated with maternal gut microbiome composition during pregnancy and offspring microbiome composition in pigs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA645191, and was assembled with megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA575543 data set (Metagenomic characterization of intestinal regions in pigs with contrasting feed efficiency).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA575543, and was assembled with metaSPAdes v3.15.3. 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 PRJNA547717 data set (human oral metagenome Raw sequence reads).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA547717, and was assembled with metaSPAdes v3.14.1. 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 PRJEB21574 data set (We studied the effect of different zinc sources on the intestinal microbiome in weaned pigs).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB21574, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJDB5315 data set (Metgenomic analysis of human saliva microbiome from healthy subjects).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJDB5315, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
EMG produced TPA metagenomics assembly of PRJEB36291 data set (Defining the oral microbiome by Whole Genome Sequencing and resistome analysis: the complexity of the healthy picture).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB36291, and was assembled with megahit v1.2.9. 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 PRJNA678453 data set (Species-specific gene expression of the oral microbiota in health and diesease).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA678453, 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 PRJNA741688 data set (saliva metagenomic analysis of Crohn`s disease-related periodontitis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA741688, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Early life nasopharyngeal bacteriome in a low-income community in South Africa

Public description:Imbalances in early life nasopharyngeal (NP) bacterial profiles have been associated with lower respiratory tract infection (LRTI) but are understudied in low-income communities where risk factors for LRTI are prevalent. We intensively investigated longitudinal NP bacterial profiles, and associated exposures, among infants born in low-income households in South Africa

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
Eukaryotic diversity in Central Park

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of aboveground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here we present an assessment of soil biodiversity and biogeographical patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system can harbor large amounts of undescribed soil biodiversity. Despite high variability across the Park, belowground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographical patterns. Further, Central Park soils harbored nearly as many distinct soil microbial taxa and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents. Our data therefore suggest that the dominant factors controlling soil biodiversity differ markedly to those controlling aboveground plant and animal diversity.

Biome: root:Mixed
Comprehensive amplicon-based metagenome analyses reveal long-term impacts of timber harvesting on soil microbial communities at reforested sites across North America.

Soil management is necessary to ensure the fertility of reforested land, yet the long-term impact of harvesting on the soil microbial communities which mediate fertility remains largely a matter of conjecture. In 1989, the North American-wide ‘long-term soil productivity’ (LTSP) study was initiated to assess the impacts of organic matter removal on forest soils on a decadal timeframe. We sampled comprehensively within the LTSP framework in six biogeographic zones throughout British Columbia, California, Ontario and Texas, producing ITS and 16S pyrotag libraries. We observed major expansions in populations of desiccation, radiation and heat-resistant organisms from a broad diversity of fungal and bacterial groups. By identifying specific taxa, genes and processes altered post-harvesting, we contribute to refining long-term monitoring efforts and reveal important phenomenon impacting long-term forest regeneration.

Biome: root:Host-associated:Plants:Rhizosphere:Forest soil
Marine Water Column Samples Targeted loci environmental

Surface water samples collected from locations within Mobile Bay out into the northern Gulf of Mexico shelf region off the coast of Alabama for examination of microbial eukaryotes. 20-24 L water samples were collected bi-monthly from July 2009- Dec 2011, prefiltered through a 150um mesh and eukaryotic fraction was collected on a 0.7um glass fiber filter. This data was used to explore spatial and temporal variation as well as impact of the Deepwater Horizon Oil Spill on this community.

Biome: root:Environmental:Aquatic:Marine
Ecozone dependent impact of forest harvesting on soil microbial community structure

Here we examined the microbial communities in soils from both the organic and mineral layer from 18 sites in six ecozones across North America. This is 16S rRNA gene data

Biome: root:Environmental:Terrestrial:Soil:Loam:Forest soil
Metagenomes of marine macroalgae, surrounding seawater and surrounding sediments

Here we analysed the microbial ecology of marine macroalgae, surrounding seawater, and surrounding sediment at Weihai, China (122.12 N, 37.56 E). Metagenomic sequencing of marine macroalgae, surrounding seawater, and surrounding sediment samples collected on 4 sampling dates in the year 2018-2019. For macroalgae, loosely attached microorganisms were removed by washing whole macroalgae thrice in flasks about 80% filled with sterile seawater on a shaker and collecting the washing suspensions in sterile bottles. Algae were then put in sterile seawater and remaining bacteria were removed by ultrasonication (2x 60s, 50-60 kHz). Suspensions with removed bacteria of each sample were subsequently pooled with the previously obtained washing suspensions. Then the washing suspension of each sample was filtered on 0.2 μm pore size polycarbonate membrane filters. Seawater samples were filtered on a 0.2 μm pore size polycarbonate membrane filters. For sediments, DNA was extracted from 300 mg sub-samples. Sequencing was done on the Illumina novaseq 6000 platform and 2x 150 base pair chemistry.

Biome: root:Environmental:Aquatic:Marine
American Gut Project

The American Gut project is the largest crowdsourced citizen science project to date. Fecal, oral, skin, and other body site samples collected from thousands of participants represent the largest human microbiome cohort in existence. Detailed health and lifestyle and diet data associated with each sample is enabling us to deeply examine associations between the human microbiome and factors such as diet (from vegan to near carnivore and everything in between), season, amount of sleep, and disease states such as IBD, diabetes, or autism spectrum disorder-as well as many other factors not listed here. The American Gut project also encompasses the British Gut and Australian Gut projects, widening the cohort beyond North America. As the project continues to grow, we will be able to identify significant associations that would not be possible with smaller, geographically and health/disease status-limited cohorts.

Biome: root:Host-associated:Human
EMG produced TPA metagenomics assembly of PRJNA932553 data set (Oral microbiome in periodontitis).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA932553, 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 PRJNA548383 data set (Subgingival Microbiome of Tobacco Cigarette Smokers with and without Periodontal Disease).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA548383, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque.

Biome: root:Host-associated:Human:Digestive system:Oral:Subgingival plaque
EMG produced TPA metagenomics assembly of PRJNA373834 data set (Metagenomic analysis of gut microbiota in sows and piglets).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA373834, and was assembled with metaSPAdes v3.15.3. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Fecal.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
EMG produced TPA metagenomics assembly of PRJNA752888 data set (Longitudinal saliva bacteriome and early childhood caries).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA752888, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Oral:Saliva.

Biome: root:Host-associated:Human:Digestive system:Oral:Saliva
Microbial indicators of anthropogenic marine pollution identified by 16S and 18S metagenomic library analysis

Microbial indicators of anthropogenic marine pollution identified by 16S and 18S metagenomic library analysis. Research supported by FP7 European Project “Winning Applications of nanoTEchnology for Resolutive hydropurification – WATER” (Grant Agreement n° 316082).

Biome: root:Environmental:Aquatic:Marine
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease

The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in adult animals, suggesting that postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ-free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of αSyn-overexpressing mice with microbiota from PD-affected patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice and suggest that alterations in the human microbiome represent a risk factor for PD.

Biome: root:Host-associated
Metabarcoding surveys of the Arctic marine environment

This is a collection of samples taken for metabarcoding of environmental samples following the Earth Microbiome Project protocol.For bacteria and archaea, we used the following primer set published by Apprill et al. (doi:10.3354/ame01753)515F GTGCCAGCMGCCGCGGTAA806RB GGACTACNVGGGTWTCTAATFor Eukaryotes, we used the following primer set published by Stoeck et al. (doi:10.1111/j.1365-294X.2009.04480.x)TAReuk454FWD1 CCAGCASCYGCGGTAATTCCTAReukREV3_modified ACTTTCGTTCTTGATYRATGA

Biome: root:Mixed
Different agricultural practices amended with bean residues Metagenome

To investigate how different management practices affected the bacterial community structure in soil, ii) to investigate how the application of bean residue affected the bacterial community structure in soil with different agricultural practices and iii) compare the bacterial populations involved in the mineralization of bean residue with those when maize residue was applied to soil.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Community structure of Archaea in the western North Pacific and the Arctic Ocean

we report archaeal community structure in the western North Pacific and the Arctic Ocean based on the deep sequencing of 16S rRNA genes directly amplified from seawater filtrates.

Biome: root:Environmental:Aquatic:Marine