SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Diagnostic Metagenomics: A Culture-Independent Approach to the Investigation of Bacterial Infections

Design, Setting and Patients Forty-five samples were selected from a set of fecal specimens obtained from patients with diarrhea during the 2011 outbreak of STEC O104:H4 in Germany. Samples were chosen to represent STEC-positive patients with a range of clinical conditions and colony counts together with a small number of patients with other infections (Campylobacter jejnuni, Clostridium difficile and Salmonella enterica). Samples were subjected to high-throughput sequencing on the Illumina MiSeq and HiSeq 2500, followed by bioinformatics analysis.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Gut microbiota in chronic kidney disease

gut microbiota in chronic kidney disease

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Human gut microbiota associated to Clostridium difficile infection

We performed a follow-up study of the gut microbiota in patients treated with antibiotic therapy, whom developed Clostridium difficile infection as a consequence. We used the 16s rRNA and metagenomic approaches to gain insights in the effect of the pathogen infection in the structure and functions of the human gut microbiota.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Danube river water sampling at 4 different sites

Goal is to compare the metagenomes (composition and functional annotation) of the four different sites (clean, town, agricultural area and industrial area) in order to generate specific markers (genes, species ) characteristic for the three different "pollution phenotypes"

Biome: root:Environmental:Aquatic:Freshwater:Lotic
Meta-transcriptomic analysis of rumen microbiome of Mehsani buffalo

Mehsani buffaloes were fed with different proportion of roughages to concentrate ration and investigated for effects of different diet regimes on the meta-transcriptome profile of the rumen microbiome by shotgun sequencing

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Southern Ocean Marine Metagenome

Microbial communities from a marine environment.
Sequences deposited into the Sequence Read Archive can be found using the Project data link.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Metagenomic sequencing of coprolites

No abstract provided. See http://rspb.royalsocietypublishing.org/content/279/1739/2825.full.pdf

Biome: root:Host-associated:Animal:Digestive system
Eukaryotic metatranscriptome from beech litter

Eukaryotic metatranscriptome extracted from Oe litter layer of beech forest Steigerwald.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Coprolithes_Chauvet

No abstract provided. 

Biome: root:Host-associated:Animal:Digestive system
Metagenomes and metatranscriptomes from the diffuse hydrothermal vents of Axial Seamount, 2011-2012

This projects explores the functional diversity and activity of rocky subseafloor microbial communities in hydrothermal vent systems. Samples were collected in 2011 and 2012 from a number of low temperature diffuse fluid vents at Axial seamount, located in the northeast Pacific Ocean. Shotgun metagenomics and metatranscriptomics were performed on four diffuse vent samples.  Previous work at this site determined the taxonomic structure and distribution of microbial communities in venting fluids, but the contribution and mechanisms of the different redox driven metabolisms and the impact these reactions have on vent chemical signatures have not been fully characterized. This study helps to determine the genetic potential and expression patterns of the largely uncharacterized subseafloor microbial community and shows how these patterns change across the complicated biogeochemical gradients of hydrothermal vent systems. 

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents:Sediment
Bacterial community composition of banded-winged whitefly

Facultative bacterial endosymbionts are common, influential associates of arthropods, yet their movement among host species has not been well documented. Plant-mediated transmission of Rickettsia was shown for the whitefly Bemisia tabaci. Bemisia tabaci in USA cotton fields harbors the secondary symbionts Rickettsia, and Hamiltonella, and co-occurs with Trialeurodes sp. nr. abutiloneus whiteflies. To determine whether symbionts may be shared, the microbial diversity of these whiteflies on cotton across the USA was analyzed. Trialeurodes sp. nr. abutiloneus bore Portiera, Pseudomonas, Serratia, Arsenophonus and Wolbachia. No Rickettsia or Hamiltonella were detected. These results provide no evidence for horizontal transmission of symbionts between these whitefly genera.

Biome: root:Host-associated:Insecta
Comprehensive characterization of plant cell wall degrading enzymes in Cerambycid beetles

Wood-boring beetles from the family Cerambycidae feed exclusively on woody tissues, and to efficiently access the nutrients present in this sub-optimal environment, they depend heavily on the secretion of a range of enzymes, known as plant cell wall degrading enzymes (PCWDEs), to efficiently digest both hemicellulose and cellulose networks.  Here we sequenced the larval gut transcriptome of the Mulberry longhorn beetle, Apriona japonica (Cerambycidae, Lamiinae), in order to investigate the arsenal of putative PCWDEs secreted by this species.  We combined our transcriptome with all available sequencing data derived from other cerambycid beetles in order to analyze and get insight into the evolutionary history of the corresponding gene families.  Finally, we heterologously expressed and functionally characterized the A. japonica PCWDEs we identified from the transcriptome.  Our analyses greatly contribute to a better understanding of the digestion physiology of this important group of insects, many of which are major pests of forestry worldwide.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Soil metagenomes profiling for forensic purposes

Forensic soil analysis has the potential to play a crucial role in criminal investigations. This is particularly the case when a crime occurs outdoors such that soil is transferred to shoes, clothing, vehicles and tools. Owing to the large microbial diversity of soil, DNA profiling of soil microbial communities can serve as a powerful tool for forensic soil examination. This project uses metagenomic approaches to analyse the entire genetic composition of soil samples and use these sequence data for comparison purposes.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Metagenome sequencing of biogas plant operating wet fermentation

Metagenome sequencing of biogas plant operating wet fermentation

Biome: root:Engineered:Biogas plant:Wet fermentation
Functional metagenomic profiling of Tibetan Plateau soils affected by permafrost or seasonal freezing

Approximately two thirds of the Tibetan Plateau is affected by permafrost and this area reacts particularly sensitively to possible effects of climate change. However, little is known about the functional potential of the microbial communities inhabiting this environment, which is of key importance to predict potential feedback effects, such as increased emissions of greenhouse gas. A metagenomic analysis was performed on soil profiles from two meadow sites on the Tibetan Plateau, either affected by permafrost (site Huashixia [HUA]) or seasonal freezing (Site Haibei Station [HAI]). The goal was to determine how respiratory and fermentative pathways varied with soil depth and across sites.

Biome: root:Environmental:Terrestrial:Soil
Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system

The recycling of fixed nitrogen from marine systems proceeds via two different nitrogen removal pathways, namely denitrification or anaerobic ammonium oxidation (anammox). Both processes require oxidized N (i.e. nitrate or nitrite) as electron acceptor to ultimately release dinitrogen gas (N2). For a supply with its substrates (ammonium and nitrite) anammox activity depends on the tight coupling with other nitrogen transformations.  The aerobic oxidation of ammonium is one of the routes that have been described recently as a source of nitrite. Another possibility is the linkage of the aforementioned N2-releasing processes, a scenario in which denitrification might be providing substrates for anammox. We were especially interested in coupling sulfide-dependent denitrification to anammox, as sulfide is, besides oxygen, the most important reductant at the chemocline of marine anoxic basins and also abundant within sediments. Although sulfide is toxic at ?M concentrations and has been shown to have a negative effect on anammox activity, we hypothesize that denitrification converts sulfide and nitrate, thereby allowing anammox to stay active despite an influx of sulfide and supply them with nitrite from partial denitrification.

Biome: root:Engineered:Bioreactor
Illumina and 454-based metatranscriptomic analyses of a diatom-induced bacterioplankton bloom in the North Sea

Planktonic bacteria from marine pelagic coastal zones are much more diverse than in the open ocean and consist of members with distinct ecological niches. In this study we investigated bacterioplankton communities that were sampled during a diatom-dominated spring phytoplankton bloom near the North Sea island Helgoland (about 40?km off the German coast). Sequencing of total community RNA allowed simultaneous detection of the community composition via 16S ribosomal RNA analyses, and the expressed functional genes via messenger RNA analyses. As most prominent community members, Flavobacteria (Ulvibacter, Formosa, Polaribacter), Alphaproteobacteria (SAR11 clade and Rhodobacteraceae) and Gammaproteobacteria (Reinekea spp. and SAR92 clade) could be identified down to genus level, which was confirmed by 16S rRNA gene amplicon ('pyrotag') sequencing of the same samples. These samples were also sequenced in a metagenome approach, assembled and taxonomically classified. Mapping of the transcripts on the metagenomes allowed investigation of the expression profiles of the prominent taxa. Members of the Flavobacteria, Alphaproteobacteria and Gammaproteobacteria exhibited distinct expression profiles of uptake transporters and carbohydrate-active enzymes, indicating a specialization on different nutrients. Members of the flavobacterial genera Formosa and Polaribacter acted as major polymer degraders, whereas members of the alphaproteobacterial Rhodobacteraceae and the gammaproteobacterial Reinekea exhibited a less specialized behavior, enabling them to rapidly adapt to changing nutrient conditions. Complementary sequencing effort using 454 pyrosequencing and Illumina enabled a comprehensive picture of the dominant metabolic processes down to genus level. This helped to identify the strategies of how members of the bacterioplankton evade extinction in a seemingly homogenous habitat.

Biome: root:Environmental:Aquatic:Marine
ASS lime injection - injection site

Due to very low inflows from the Murray-Darling Basin from 2007-2009, water levels in the Lower Murray River dropped to -1m AHD in April 2009. The low water levels and restricted water allocations during this hydrological drought period caused the acid sulfate soils subsequently acidified and salinized. Given the acidic drainage water presents a potential risk to the water quality and environmental values of the Lower River Murray, a subsoil neutralisation using a limestone slurry and a modified mole drain technique was applied. The aim of this trial is to examine whether the introduction of alkalinity (limestone) at depth in the oxidised and rewet acid sulfate soils, will sufficiently raise the pH to begin the process of sulfate reduction. It is hoped by promoting sulfate reduction, via sulfate reducing bacteria, the soils will begin to remediate, producing less acidic drainage to the salt drains in the irrigation areas.

Biome: root:Environmental:Terrestrial:Soil:Clay
Saline desert Metagenome

Saline desert Metagenome

Biome: root:Environmental:Terrestrial:Soil
Xenomicrobiota transplanted into germfree mice

Xenomicrobiota from a variety of different environments were transplanted into germfree mice. Assembly and composition of the gut-selected communities were analyzed by amplicon-sequencing. In a follow-up experiment, mice that harbored gut-selected communities were cohoused with each other.

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
Vitamin Supplementation by Gut Symbionts Ensures Metabolic Homeostasis in an Insect Host

Many animals are dependent on intestinal microbes for nutrition. However, our understanding of how the host regulates its metabolism in response to beneficial symbionts remains limited. Here we elucidate the functional importance of the African cotton stainer?s (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect?s transcriptional response following symbiont elimination. Genomic analyses and bioassays demonstrate the symbionts? contribution towards host fitness through the supplementation of B vitamins. Concordantly, comparative transcriptomic analyses reveal a differential up-regulation of genes involved in import and processing of B vitamins in aposymbiotic bugs; an expression pattern that is indicative of vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect?s diet or reinfection with actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 (THTR2) through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. Taken together, our findings demonstrate that ? despite an extracellular localization ? beneficial gut microbes can be integral to an insect?s metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.

Biome: root:Host-associated:Arthropoda:Digestive system:Gut
Metagenome of grass carp intestinal contents and mucosa

Intestinal microbiota is a complex ecosystem and plays an important role in host biology. More and more researches focus on the bacterial community of the host intestine. However, there is still limited information on a better understanding of fish intestinal microbiota. Due to the importance of grass carp in aquaculture of China, it is necessary to pay attention to its intestinal microbiota. In this study, the composition of bacterial communities in intestinal contents and mucosa of grass carp was analyzed by 454 pyrosequencing.

Biome: root:Host-associated:Fish:Digestive system:Intestine
Amazon Continuum Metagenomes

This project focuses on the Amazon River-to-tropical Atlantic Ocean continuum because of both its immense scale and its apparent sensitivity to climate variability and anthropogenic forcing. The river's effect on the ocean depends not only on the river hydrology, but what the river carries and how those components are modified during transit from their terrestrial or aquatic origins. We brought together limnologists and oceanographers in an integrated project to improve our understanding of carbon exchange between the atmosphere and this tropical river continuum, focusing on the lower reach, nearshore, and offshore tropical Atlantic, with the goal of improving predictive capabilities under differing climate change scenarios.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Lime was injected to acid sulfate soils with aim to balance the acidity. The indigenous microbial communities before and after injection were investigated.

Due to very low inflows from the Murray-Darling Basin from 2007-2009, water levels in the Lower Murray River dropped to -1m AHD in April 2009. The low water levels and restricted water allocations during this hydrological drought period caused the acid sulfate soils subsequently acidified and salinized. Given the acidic drainage water presents a potential risk to the water quality and environmental values of the Lower River Murray, a subsoil neutralisation using a limestone slurry and a modified mole drain technique was applied. The aim of this trial is to examine whether the introduction of alkalinity (limestone) at depth in the oxidised and rewet acid sulfate soils, will sufficiently raise the pH to begin the process of sulfate reduction. It is hoped by promoting sulfate reduction, via sulfate reducing bacteria, the soils will begin to remediate, producing less acidic drainage to the salt drains in the irrigation areas.

Biome: root:Environmental:Terrestrial:Soil
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India

There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics, and compared that to a Swedish lake receiving no input of wastewater from industrial or municipal sources.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Stable isotope probing/metagenomics of terrestrial dimethylsulfide degrading microorganisms

Dimethylsulfide (DMS), a volatile sulfur compound, plays an important role in the global sulfur cycle and atmospheric chemistry. Microorganisms can use DMS as sole carbon, sulfur or energy source, contributing to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, it has been recognised that a wide range of bacteria isolated from terrestrial ecosystems are able to degrade DMS, yet it remains unknown whether any of these play important roles in situ. In this study we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA.

Biome: root:Environmental:Aquatic:Freshwater:Lentic:Sediment
Sydney Harbour metagenomes

Spatial taxonomic and functional diversity in the Sydney Harbour

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Acid sulfate soil microbial profile - pre-investigation

A pre-investigation of the microbial composition of the acid sulfate soils were carried in Oct 2011 to obtain the microbial information before lime injection

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Southampton Asthma metagenomics

55 subjects underwent detailed clinical and immunological phenotyping,  sputum induction and bronchoscopy during periods of clinical stability. In  addition to 15 healthy controls, 9 mild, 16 moderate and 15 severe ashthmatics  (without bronchiectasis) were included. Protected bronchoalveolar lavage (BAL)  and induced symptoms were analysed by WGS for RNA and DNA from bacterial, viral  and fungal genomes. 88 samples were sequenced using 454 FLX Titanium. Single end  library. Data were provided as fasta files following adapter trimming

Biome: root:Host-associated:Human
Metagenome fecal microbiota, Illumina seq reads of 12 individuals at 2 timepoints

Two diets, Korean and Western diet. Each 6 individuals, half of which lost a lot of weight and half of which lost little weight. Fecal samples taken before and after diet (3 months).

Biome: root:Host-associated:Human:Digestive system
Photoheterotrophy in a mesoscale anticyclonic eddy in the Eastern Mediterranean Sea

Mesoscale eddies are semi-closed rotating water bodies with distinct physico-chemical properties and are a widespread phenomenon in the world's oceans. Previous studies found that eddies can affect phytoplankton and bacterioplankton community structure, primary productivity and nitrogen fixation. A considerable fraction of the marine bacterioplankton consists of photoheterhophs. These bacteria can use light to generate biochemical energy for transport and metabolic needs. Unlike photoautotrophs they depend on organic carbon for growth and biomass production. Photoheterotrophy can potentially enhance bacterial growth and/or survival in oligotrophic oceanic conditions. A common group of photoheterotrophs consists of proteorhodopsin (pr) bearing bacteria. The pr gene occurs in diverse microbial taxa including SAR11, a dominant Alphaproteobacteria clade. We hypothesize that anticyclonic eddies, which facilitate nutrient poor conditions by downwelling surface water, favor photoheterhophy. In November 2013 we conducted an oceanographic survey aboard R/V Mediterranean Explorer with the goal to assess the abundance, diversity and expression of photoheterophic genes in an anticyclonic eddy in the ultra-oligotrophic Eastern Mediterranean Sea. The results of this study will shed light on the potential role of physical and chemical gradients created by mesoscale eddies on changes in photoheterotrophic communities, which can have global effects on ocean biogeochemistry and energy flow.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Photic zone
Transcriptomic analysis of microbial communities isolated from the rhizospheres of wheat, oat and pea, compared to unplanted soil

Rhizosphere microbes are key players in biogeochemical cycles and maintainance of plant health and productivity. Here we used metatranscriptomic analysis of rRNA depleted RNA from the rhizospheres of wheat, oat, pea, and unplanted soil to compare the metabolic functions of microbes in these environments. Using biological replication (n=5) we were able to give statisistical significance to the differences found. Microbes responsed to the rhizosphere environment by increasing metabolic activity in general, and particularly in metabolic pathways involved in sugar, organic acid and aromatics metabolism, oxidative stress, and motility. While general rhizosphere effects on the microbial communities were observed, many specific effects were plant species dependent.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Transcriptome of Lecane inermis for phylogenomic studies of sppiralian relationships

Transcriptome data of Lecane inermis were used alongside other transcriptomic data of spiralian taxa to investigate spiralian relationships in a phylogenomic approach

Biome: root:Host-associated:Spiralia
Metagenomic sequencing of a Bison priscus bone sample from the Trois-Freres cave (Ariege, France)

The steppe bison (Bison priscus) is an extinct species that was widely distributed in Europe, Central Asia, Beringia and North America during the Pleistocene. It is known from abundant remains, including complete animals found in the permafrost, and from Palaeolithic rock-art pictures. However, the molecular information available for this species is limited to a fragment of the mitochondrial genome control region. In order to obtain a thorough genetic characterization of the steppe bison, we performed high-throughput shotgun sequencing of DNA extracted from a specimen of the Trois-Freres cave (Ariege, France). Analysis of several bone samples from the Salle du Grand Eboulis of this cave enabled identifying a rib from which bison DNA could be reproductively recovered and amplified by PCR. One DNA extract obtained from this rib was converted into an Illumina library, and about 1 billion DNA reads were analysed. Using these sequence data we reconstructed a complete mitochondrial genome of 16,318 bp with an average unique read depth of 10x

Biome: root:Host-associated:Animal