SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
16S rRNA amplicons (V4 region) of bacteria living on and in roots and leaves of Boechera stricta from field experiments in the Rocky Mountains

Bacteria living on and in leaves and roots influence many aspects of their hosts’ health, so the extent of plant genetic control over their microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies may overestimate the influence of certain plant genes on the microbiome and fail to detect others, because they do a poor job simulating true environmental heterogeneity. We conducted a large-scale field experiment to disentangle the effects of genotype, environment, age, and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta, a wild perennial mustard.  Genetic control of the microbiome varied substantially among sites, and bacterial community composition shifted as plants aged. Furthermore, a large proportion of leaf bacteria were shared with roots, suggesting inoculation from soil. Our results highlight the complexity of microbiome formation in natural environments.

Biome: root:Host-associated:Plants
Infant Microbiota and Probiotic Intake Study (IMPRINT)

The purpose of this study is to determine if supplementing healthy term infants delivered by C-section or vaginal delivery who only consume breastmilk with a probiotic for 21 consecutive days increases levels of bacteria in infants'' stool.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human genetics shape the gut microbiome

Host genetics and the gut microbiome can both influence host metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we addressed this question by comparing microbiotas across more than 1,000 fecal samples obtained from members of the TwinsUK population, including 416 twin-pairs. We identified a variety of microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea, and was enriched in individuals with low BMI. Addition of Christensenella minuta to an obese donor???s fecal microbiome resulted in reduced weight gain and an altered fecal microbiota in recipient germfree mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Impact of conservative agricultural practices on soil microbial communities in South Africa

The study compares microbial communities from soil under contrasting agronomical practices in different locations of South Africa.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJEB34573 data set (Metagenomic analysis with long and short reads of 20 biogas reactors).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB34573, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Biogas plant.

Biome: root:Engineered:Biogas plant
Metagenomic analysis with long and short reads of 20 biogas reactors

The spread of antimicrobial resistance has been identified as one of the greatest threats to public health. Various factors, such as antibiotic consumption and antibiotic control in human and industrial use, as well as wastewater treatment and waste management play a cruicial role in the dissemination of antibiotic resistance. Mobile genetic elements, such as plasmids, gene cassettes and / or integrons on which most of the resistance genes are located, are readily transmissible resistance gene reservoirs, which also allow gene exchange between non-pathogenic and pathogenic bacterial species and vice versa. This has been increasingly observed in sewage treatment plants. The aim of this work is to investigate whether microbial diversity and density in biogas plants promote the transmission and distribution dynamics of resistance genes or whether the e. g. occasionally extreme fermentation conditions such as increased ammonium content, thermal pre-treatment, and elevated process temperatures prevents transfer or uptake of mobile DNA elements. For this purpose, the resistome of influence and effluence of various biogas processes will be analyzed using High-throughput and Long-Read Sequencing Technology.

Biome: root:Engineered:Biogas plant
Nasopharyngeal_microbiota_in_Maela_Thailand

A longitudinal study was undertaken for 21 infants living in the Maela refugee camp on the Thailand-Burma border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The 16S rRNA gene profiles of these 544 swabs were analysed to see how the microbiota changes with age, respiratory infection, and pneumococcal acquisition. 

This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science

Biome: root:Host-associated:Human:Respiratory system:Nasopharyngeal
EMG produced TPA metagenomics assembly of PRJNA466874 data set (Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States - LL-1505 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA466874, and was assembled with metaSPAdes v3.15.2. 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 PRJNA506221 data set (Microbial diversity and function in Antarctic paleomats).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA506221, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
EMG produced TPA metagenomics assembly of PRJNA593593 data set (Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 10).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA593593, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Wastewater.

Biome: root:Engineered:Wastewater
EMG produced TPA metagenomics assembly of PRJNA669352 data set (Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA669352, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Lab enrichment:Defined media.

Biome: root:Engineered:Lab enrichment:Defined media
EMG produced TPA metagenomics assembly of PRJNA673084 data set (Metagenomic analysis of microorganisms from Movile Cave - Romania).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA673084, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs
EMG produced TPA metagenomics assembly of PRJNA366267 data set (Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 B9 metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA366267, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Thermal springs:Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 11

Sewage-derived enrichment culture (anaerobic medium, 0.1% glucose), biofilm phase

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA593594 data set (Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 11).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA593594, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Engineered:Wastewater.

Biome: root:Engineered:Wastewater
EMG produced TPA metagenomics assembly of PRJNA650216 data set (PMC 728.11_cyano).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA650216, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater.

Biome: root:Environmental:Aquatic:Freshwater
EMG produced TPA metagenomics assembly of PRJNA605948 data set (Candidatus Udaeobacter sp. isolate:AEW3 Genome sequencing and assembly).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA605948, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Terrestrial:Soil:Forest soil.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
DDCA-metagenome

Evaluation of biodiversity and prediction of environmental changes by digital dna chip for establishment of core technology for the preservation and regeneration of marine biodiversity and ecosystems

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJNA563062 data set (Gut microbiome of Capybara (Hydrochoerus hydrochaeris) Metagenome).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA563062, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system.

Biome: root:Host-associated:Mammals:Digestive system
Correlations between shower hoses biofilm microbiome and its functions and the presence of Legionella spp.

Building plumbing systems are engineered environments in which some opportunistic pathogenic bacteria proliferate in complex biofilms, interacting and finding niches within resident microbial communities. Among these, Legionella spp. are the most reported waterborne pathogen associated with disease in industrialized countries. In this study, Shotgun sequencing has been performed on the DNA coming from shower hoses biofilms collected in different locations in Switzerland. The primary aim  of the work is to be able to correlate the microbiome compositions and specific functional annotation to the differential abundance of Legionella in the samples collected. This will help getting more insights about the ecology of Legionella and possibly identify conditions that can favour or not the growth of the opportunistic pathogen in plumbing systems.

Biome: root:Environmental:Aquatic:Freshwater:Storm water:Drainage pipe biofilm
Candidatus Udaeobacter sp. isolate:AEW3 Genome sequencing and assembly

A metagenome assembled genome was assembled from metagenomic DNA of cells which were prior to DNA extraction exposed to antibiotic pressure and separated from the soil matrix.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

Assembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments that are dominated by uncultured and/or under-studied groups. This study aimed to investigate the impact of incorporating long-read data into the process of reconstructing metagenome-assembled genomes (MAGs) from a complex groundwater aquifer. We generated shotgun metagenomes with traditional Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups. Groundwater was collected from the Hainich Critical Zone Exploratory, a near-surface aquifer transect that is established in NW Thuringia, Germany. This data set is part of the DFG-funded CRC AquaDiva (https://www.aquadiva.uni-jena.de/) of the Friedrich Schiller University Jena.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJEB35315 data set (Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB35315, and was assembled with metaSPAdes v3.15.2. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States - LL-1505 metagenome

Freshwater microbial communities from Lake Lanier, Atlanta, Georgia, United States

Biome: root:Environmental:Aquatic:Freshwater:Lake
Microbial diversity and function in Antarctic paleomats

Dessicated microbial mats that are thousands of years old found in the McMurdo Dry Valleys in Antarctica provide a unique opportunity to study the effects of prolonged desiccation on microbial composition and function. The goal of this work is to understand which microbes form these mats, whether they are transcriptionally active, and what mechanisms microbial cells use for long-term survival under extremely harsh conditions, with implications for our understanding of cell biology, Antarctic microbiology and biogeography, and the limits of life in cold, arid environments.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
Sewage microbial communities from Oakland, California, United States - Biofuel Metagenome 10

Sewage-derived enrichment culture (anaerobic medium, 0.1% glucose), planktonic phase

Biome: root:Engineered:Wastewater
Microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants

Using short- and long-read to reveal microbiome assembly for sulfonamide subsistence and the transfer of genetic determinants

Biome: root:Engineered:Lab enrichment:Defined media
Metagenomic analysis of microorganisms from Movile Cave - Romania

Samples were collected from Movile Cave (Romania) for metagenomic analysis to study microorganisms forming benthic or floating microbial mats. Emphasis was made to assemble the full genome of a Thiovulum sp. dominating veil-like structures close to the surface of a hypoxic air bell known as Air Bell 2.

Biome: root:Environmental:Aquatic:Thermal springs
marine metagenome Genome sequencing and assembly

The genome sequence of marine Synechococcus strain MITS9220 was obtained by Illumina and Oxford Nanopore MinIon sequencing. The MITS9220 culture used was non axenic and thus contained additional heterotrophic bacteria. The complete genome of one of the heterotrophic bacteria was also assembled; it belongs to the genus Thalassospira. In addition, assembly generated the complete genome of a cyanophage that also occurred in the MITS9220 culture.

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA623799 data set (marine metagenome Genome sequencing and assembly).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA623799, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
EMG produced TPA metagenomics assembly of the Gut microbial metabolism shifts towards a more toxic profile with supplementary iron in a kinetic model of the human large intestine (TIM2_iron_study) data set

The TIM2_iron_study Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB6542. This project includes samples from the following biomes : Human gut.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Sigmoid colon
Metagenomics of Diamante Hot Spring

Metagenomics of Diamante Hot Spring

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of PRJNA530103 data set (Viral metagenome groundwater aquifer).

TheThird Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set SRP189971, and was assembled with metSPAdes(v3.13.0).

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Viral metagenome groundwater aquifer

Viral DNA metagenome from three pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory

Biome: root:Environmental:Aquatic:Freshwater:Groundwater
Metagenomics of Carachipampa microbialite

Metagenomics of Carachipampa microbialite

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline
Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 bottle 8 metagenome


Biome: N/A
EMG produced TPA metagenomics assembly of the Hot spring thermophilic microbial communities from Obsidian Pool, Yellowstone National Park, USA - site 3 bottle 8 metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366343.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Active sludge microbial communities of municipal wastewater-treating anaerobic digesters from China - AD_SCU002_MetaG metagenome (activated sludge metagenome) data set.

The activated sludge metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA340752.  This project includes samples from the following biomes: Engineered, Wastewater, Activated Sludge.

Biome: root:Engineered:Wastewater:Industrial wastewater
Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - OCT_B metagenome


Biome: N/A
EMG produced TPA metagenomics assembly of the Hot spring and microbial mat streamer communities from Octopus Spring Streamers, Yellowstone National Park, USA - OCT_B metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA366312.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Elbow Spring sediment metaG metagenome

Sequencing as part of the Microbial Dark Matter project phase II project

Biome: N/A
EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Elbow Spring sediment metaG metagenome (sediment metagenome) data set.

The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364782.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 2m metaG metagenome

Microbial Dark Matter project phase II - Metagenome sequencing of Hot spring sediment microbial communities

Biome: N/A
EMG produced TPA metagenomics assembly of the Hot spring sediment microbial communities from Zodletone spring, Oklahoma to study Microbial Dark Matter (Phase II) - Zodletone Spring source 2m metaG metagenome (hot springs metagenome) data set.

The hot springs metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364990.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot (42-90C).

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Blank Spring sediment metaG metagenome

Sequencing as part of the Microbial Dark Matter project phase II project

Biome: N/A
EMG produced TPA metagenomics assembly of the Hot spring sediment bacterial and archeal communities from California, USA to study Microbial Dark Matter (Phase II) - Blank Spring sediment metaG metagenome (sediment metagenome) data set.

The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA364781.  This project includes samples from the following biomes: Environmental, Aquatic, Thermal springs, Hot.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
EMG produced TPA metagenomics assembly of the Marine microbial communities from oxygen minimum zone in mesopelagic equatorial Pacific - METZYME_3_550m metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA330041.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root
EMG produced TPA metagenomics assembly of the Estuarine microbial communities from the Columbia River estuary - Ebb tide non-ETM metaG S.743 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365277.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Intertidal zone, Estuary.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
EMG produced TPA metagenomics assembly of the Pelagic marine microbial communities from North Sea - COGITO_mtgs_110404 metagenome (marine metagenome) data set.

The marine metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA365007.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay16, Core 4569-2, 12-15 cm metagenome

Subseafloor sediment microbial communities from the background core at a depth of 12-15 cm, 2000m below sea level

Biome: N/A
EMG produced TPA metagenomics assembly of the Subseafloor sediment microbial communities from Guaymas Basin, Gulf of California, Mexico - Guay16, Core 4569-2, 12-15 cm metagenome (sediment metagenome) data set.

The sediment metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA406719.  This project includes samples from the following biomes: Environmental, Aquatic, Marine, Sediment.

Biome: root:Environmental:Aquatic:Marine:Sediment