SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Arctic microbiome along Svalbard Cross Shelf transects

Global worming and climate change has been manifested in the decrease of the Arctic Ocean see ice extent and thickness. The thinner sea-ice regime that the Arctic has been facing changed Arctics primary productivity and biogeochemistry. Understand the dynamics of the microbial communities that feed Arctic phytoplankton and biologically derived carbon export will be worthwhile in order to draw future trends. In this study we present a comprehensive analysis of the biogeographic patters of Arctic microbiome diversity and distribution along two oceanographic transects in the Marginal Ice Zone around Svalbard, within strong environmental gradients (Ripfjorden, Kongsfjorden). A total of 11 stations were sample at three depths (surface, chlorophyll maximum and bottom) during the Norwegian Polar Institute MOSJ-ICE 2016 plankton-monitoring program. Samples were concentrated on board through Sterivex 0.2 mm filtration and preserved at -80oC for later DNA extraction. Amplification of 16S rRNA and 18S rRNA genes were performed and sequenced in Illumina MiSeq with a sequence depth of about 100 thousand readpairs. The prokaryotic and eukaryotic MOSJ-ICE16 data sets collection comprises highly complex and diverse microbial communities with a marked biogeographic pattern of distribution. Strong links were identified between bacterioplanckton and phytoplankton/picophytoplankton distribution driven by environmental and biogeochemical forces, most relevant to unravel the role of microbial pathways in supporting Arctic Ocean Primary productivity and system integrity.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Metagenomic sequencing of preterm infant gut microbiota raw sequence reads

Dysbiotic colonization of the preterm infant gut microbiota may have lifelong effects on host health. The normal progression of colonization of preterm infants is a patterned, yet chaotic, process, and thought to be chiefly driven by host factors. While preterm infants almost universally receive early and often repeated and/or prolonged intravenous antibiotic therapy, it remains unclear if and how specific antibiotics alter the developmental progression of the gut microbiota in this population. By analyzing 401 fecal samples from 84 longitudinally-sampled preterm infants, we demonstrate that meropenem, cefotaxime, and ticarcillin-clavulanate significantly reduce species richness during their administration, and significantly enrich or deplete specific bacterial species and antibiotic resistance (AR) genes. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness. We show this response is predictable with 85% accuracy based on the relative abundance of only two bacterial species and two AR genes before treatment. To more fully investigate the role of the gut-associated resistome in response to specific antibiotics, we performed functional metagenomic selections for resistance to 16 clinically relevant antibiotics from a set of 21 preterm infants' gut microbiota. Of the 794 AR genes identified, 79% had not previously been classified as providing any resistance phenotype. Combined with deep shotgun sequencing of all 401 fecal samples, we find that multidrug resistant Escherichia, Klebsiella, and Enterobacter species, which are commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. We show that AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and highly correlated (p<0.001) with the abundance of a single species. The most notable exception includes ticarcillin-clavulanate and ampicillin, both of which enrich a large number of overlapping AR genes, and are highly correlated with Klebsiella pneumoniae species in the preterm infant gut microbiota. In addition to AR genes relevant to specific antibiotics likely providing a protective function, we show that all antibiotic treatments also result in widespread collateral microbiome impact through enrichment of AR genes with no known direct activity against the specific antibiotic treatment.

Biome: root:Host-associated:Human:Digestive system:Large intestine
EMG produced TPA metagenomics assembly of PRJNA430179 data set (glacier metagenome Genome sequencing).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA430179, and was assembled with metaSPAdes v3.14.1, SPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
glacier metagenome Genome sequencing

research of englacial ecosystem

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
Shotgun Sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for  small DNA viruses.

Analysis of the genes and genomes present in Tara Oceans Polar Circle virus size fractions through shotgun DNA sequencing.
Seawater from different depths was precipitaded  then filtered to retain small particle sizes (Virus particles). The DNA was extracted and submitted to high throughput sequencing.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJNA698063 data set (High throughput sequencing of Tea microbial communities).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA698063, and was assembled with metaSPAdes v3.14.1, megahit v1.2.9. This project includes samples from the following biomes: root:Host-associated:Plants:Rhizosphere:Soil.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
High throughput sequencing of Tea microbial communities

This dataset contains the microbial communities associated with organically grown tea cultivation in Assam, India

Biome: root:Host-associated:Plants:Rhizosphere:Soil
EMG produced TPA metagenomics assembly of PRJEB37860 data set (Metagenomics and metatranscriptomics data of Blattella germanica's hindgut microbiota.).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB37860, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Arthropoda:Digestive system:Hindgut.

Biome: root:Host-associated:Arthropoda:Digestive system:Hindgut
Metagenomics and metatranscriptomics data of Blattella germanica's hindgut microbiota.

Pair-end metagenomics and metatranscriptomics data of the german cockroach hindgut to validate a meta-omics data integration pipeline, called gNOMO.

Biome: root:Host-associated:Arthropoda:Digestive system:Hindgut
Ecological Genomics of a Seasonally Anoxic Fjord; Saanich Inlet

Saanich Inlet is a seasonally anoxic fjord opening to the Strait of Georgia on the southeast coast of Vancouver Island, British Columbia. It is approximately 24 kilometers long with a maximal basin depth of 234 meters and receives limited freshwater input from the surrounding watershed. A shallow glacial entrance sill 75 meters deep restricts circulation within interior and basin waters for most of the year. During spring and summer months, restricted circulation combined with high levels of primary productivity in surface waters lead to oxygen loss with concomitant water column stratification indicated by accumulation of methane (CH4), Ammonia (NH3) and Hydrogen Sulfide (H2S). In late summer and fall, oxygenated nutrient-rich ocean waters upwelling through the Strait cascade into Saanich Inlet shoaling anoxic bottom waters upward and transforming the redox chemistry of the water column. This process is stable on decadal time scales exhibiting a relatively narrow deviation in the depth distribution of the oxycline at different times of year. The recurring seasonal development of water column anoxia followed by deep-water renewal enables spatiotemporal profiling of microbial community structure and function across a wide range of water column redox states.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Shotgun metagenome sequences of Anthelia biocrust samples.

Samples of biocrust (~200 mg from uppermost 3 mm) dominated by the liverwort Anthelia jurkatzkana from various locations in Iceland. DNA extracted with DNeasy Power Soil kit. Illumina Nextera XT shotgun libraries prepared and sequenced 2x75b on MiSeq.

Biome: root:Environmental:Terrestrial:Soil
EMG produced TPA metagenomics assembly of PRJEB27054 data set (Global surveillance of antimicrobial resistance).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB27054, and was assembled with metaSPAdes v3.12.0. This project includes samples from the following biomes: root:Engineered:Wastewater:Water and sludge.

Biome: root:Engineered:Wastewater:Water and sludge
Global surveillance of antimicrobial resistance

Antimicrobial resistance (AMR) is one of the most serious global public health threats, however, obtaining representative data on AMR for healthy human populations is difficult. We characterized the bacterial resistome from untreated sewage from 79 sites in 60 countries. We found systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data only explained a minor part of the AMR variation and no evidence for cross-selection between antimicrobial classes nor effect of travel by flight between sites were found. However, AMR abundance was strongly correlated with socio-economic, health and environmental factors, which we used to predict AMR abundances in all countries in the world. Our findings suggest that the global AMR gene diversity and abundance varies by region and are caused by national circumstances. Improving sanitation and health could potentially limit the global burden of AMR. We propose to use sewage for an ethically acceptable and economically feasible continuous global surveillance and prediction of AMR.

Biome: root:Engineered:Wastewater:Water and sludge
Herbal rhizosphere metagenomics

Herbal rhizosphere culture mix

Biome: root:Host-associated:Plants:Rhizosphere
metatranscriptomic approaches to unravel taxonomic and functional diversities of a coastal aquatic ecosystem and their reaction to hypoxia

Two previous integrative research programs: PREDHYPO (AMIDEX Foundation 2015-2016) and PREDHYP-O2 (EC2CO 2016-2017, CNRS-INSU) have enabled the coupling between physics and biogeochemical processes of the Berre lagoon sediment during laboratory experiments under controlled oxygenation conditions. These programs have also initiated regular in situ measurements during a three-year period, leading to the first-step development of a 1D predictive benthic-pelagic biogeochemical model of the lagoon. We set up a laboratory experiment to follow the biological and chemical dynamics at the sediment-water interface on the short-term period (i.e. one month incubation of sediment core samples), while we conducted an in situ approach to characterize seasonal and yearly dynamics (i.e. from may 2015 to august 2016) of biogeochemical processes at the sediment-water interface for three sites showing contrasted oxygenation conditions. Because microorganisms are key actors of biogeochemical processes and organic matter turnover, we dedicated an important part of these research programs to the characterization of taxonomic and functional responses of the sediment microbiome to hypoxia events. Based on Next Generation Sequencing (NGS) technologies (i.e. ILLUMINA), we developed a metabarcoding approach that aims at exploring taxonomic diversity of Bacteria and Archaea living in the sediment, and we developed a metatranscriptomic approach that aims at identifying metabolic activities and pathways involved in the ecosystem functions. The laboratory experiment considered triplicate samples of sediment at various depth layers and according to oxygenation conditions of the water column ranging from 0% to 100%.

Biome: root:Environmental:Aquatic:Marine:Sediment
Multi-omics of the nitrate-reducing iron(II)-oxidizing culture KS

Nitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment contribute to nitrate removal and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and poorly understood. The most prominent model system for this type of studies is enrichment culture KS, which originates from a freshwater sediment in Bremen, Germany. To gain insights in the metabolism of nitrate reduction coupled to iron(II) oxidation under in the absence of organic carbon and oxygen limited conditions, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS.This dataset contains: (1) Raw sequencing data of 16S (V4 region, primers 515f and 806r) rRNA amplicon sequencing of the microbial community composition of the autotrophic NRFeOx enrichment culture KS. Illumina MiSeq sequencing (Illumina, San Diego, CA, USA) using PE 250 bp MiSeq Reagent Kit v2 (500 cycles kit) were performed at Microsynth AG (Balgach, Switzerland). (2) Raw sequencing data of shotgun metagenomics. For short reads, library was prepared with TruSeq DNA PCR-Free Kit (Illumina) and sequenced with PE 150 bp on a NovaSeq 6000 totalling 55 and 48 Gbp by CeGaT, Tuebingen, Germany. For long read sequencing, library preparation with ONT Native Ligation Kit was followed by sequencing with PromethION (Oxford Nanopore Technologies) flow cell (version 9.4.1) for 72h with standard settings (basecalling with HAC mode, bias voltage -180 mV) yielding 53 Gbp in 5 million reads by the NGS Competence Center Tuebingen (NCCT) of the University of Tuebingen, Germany. (3) Short and long reads were assembled with metaSPAdes v3.13.1 using https://github.com/nf-core/mag v1.0.0. (4) Raw sequencing data of shotgun metatranscriptomes (2 conditions, triplicates). Library preparation including bacterial ribodepletion (NuGen Universal Prokaryotic RNA-Seq kit incl. bacterial ribodepletion) and Illumina NextSeq v2.5 sequencing with PE 75 bp and 21 to 62 Mio clusters per sample were performed by Microsynth AG (Balgach, Switzerland).

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Reeindeer lichens as potential natural products source

Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.

Biome: root:Host-associated:Fungi
Gut microbiome of Capybara (Hydrochoerus hydrochaeris) Metagenome

The aim of this project is to investigate the gut microbiome of Capybara (Hydrochoerus hydrochaeris), a monogastric herbivore, also known as master of the grasses, which feeds on a recalcitrant diet that has digestive efficiency comparable to that of ruminants to recover enzymatic strategies of lignocelulose degradation.

Biome: root:Host-associated:Mammals:Digestive system
EMG produced TPA metagenomics assembly of the PRJNA46333 data set (Gene-Environment Interactions at the Skin Surface).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA46333.  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 Arctic Ocean metagenomes from HLY1502 (Arctic Ocean metagenomes) data set

The Arctic Ocean metagenomes Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB14154. This project includes samples from the following biomes : Marine.

Biome: root:Environmental:Aquatic:Marine:Oceanic
The microbiome associated with the carrageenophyte Chondracanthus chamissoi from the Central Coast of Peru

Chondracanthus chamissoi belongs to the family Gigartinaceae and is considered an endemic carrageenophyte alga of the temperate coast of the South Pacific. Microbes are ubiquitously distributed, and they are also present in algae natural systems. Additionally, the algal microbiome is a pivotal part of the algae holobiont and has a key role in modulating its polysaccharide quality. Recently, unique microbiote has been isolated from polysaccharide-producers algae conferring specific  chemical properties to these compounds (e.g. agar, carrageenan). This study aims to identify specific microbiote associated to the carrageenophyte Chondracanthus chamissoi from the Central Coast of Peru including its biological, cellular, and molecular metabolism.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone
sediment metagenome Metagenome

River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we, therefore, analyzed such river sediments by a functional metagenomics approach

Biome: root:Environmental:Aquatic:Freshwater:Lotic:Sediment
EMG produced TPA metagenomics assembly of PRJNA655119 data set (Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx)).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA655119, and was assembled with SPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Intestine.

Biome: root:Host-associated:Human:Digestive system:Intestine
Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx)

Metatranscriptome sequencing of the extended simplified human intestinal microbiota (SIHUMIx), consisting of eight bacterial species, namely Anaerostipes caccae (DSMZ 14662), Bacteroides thetaiotaomicron (DSMZ 2079), Bifidobacterium longum (NCC 2705), Blautia producta (DSMZ 2950), Clostridium butyricum (DSMZ 10702), Clostridium ramosum (DSMZ 1402), Escherichia coli K-12 (MG1655) and Lactobacillus plantarum (DSMZ 20174) cultivated in bioreactors under anaerobic conditions. The metatranscriptome provides information on the functional interaction of the bacterial community and also supports the identification of novel small proteins.

Biome: root:Host-associated:Human:Digestive system:Intestine
Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics

In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes "rep1_" and "rep2_" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Lenisia limosa and epibiotic Arcobacter

Identifying potential metabolic interactions between Lenisia limosa and it's epibiotic Arcobacter

Biome: N/A
EMG produced TPA metagenomics assembly of PRJNA277740 data set (Lenisia limosa and epibiotic Arcobacter).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA277740, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum:Wadden Sea-Germany.

Biome: root:Engineered:Bioreactor:Continuous culture:Marine intertidal flat sediment inoculum:Wadden Sea-Germany
EMG produced TPA metagenomics assembly of PRJNA301235 data set (Moose metagenomic assembly).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA301235, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Midgut.

Biome: root:Host-associated:Mammals:Digestive system:Midgut
EMG produced TPA metagenomics assembly of PRJNA244670 data set (Microbial consortium enriched at the cathode of a solar microbial fuel cell).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJNA244670, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm.

Biome: root:Environmental:Aquatic:Freshwater:Groundwater:Biofilm
EMG produced TPA metagenomics assembly of PRJEB25540 data set (Metatranscriptomics of Kentrophoros ciliate-bacteria symbiosis).

The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB25540, and was assembled with metaSPAdes v3.14.1. This project includes samples from the following biomes: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Metatranscriptomics of Kentrophoros ciliate-bacteria symbiosis

Metatranscriptomics of Kentrophoros spp., a ciliate from marine sediments with symbiotic bacteria, to complement metagenomic study of the symbiosis (PRJEB25374).

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