SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Biomethanization of CO2 in anaerobic digestion plants

Anaerobic digestion uses a variety of organic wastes (domestic, industrial, agricultural) to produce biogas – a mixture of carbon dioxide and methane. Biogas is often used on the industrial application to generate heat and power but can also be upgraded to biomethane and injected directly into the National Grid as a substitute for natural gas. Currently, the upgrading step limits the wider use of biomethane as a gaseous biofuel. In order to increase the biomethane potential, biomethanization can be applied either by adding H2 to the reactor and converting it to methane in presence of endogenous (in-situ) or exogenous (ex-situ) CO2 by the resident microbiome.  Here, we upgraded biogas to biomethane using in-situ biomethanization. Using DNA sequencing approaches such as metagenomics and 16S amplicon sequencing the identity of microbial members of the enriched community and their functional potential was uncovered leading to better understanding on how the AD biomethanization process can be manipulated and improved.

Biome: root:Engineered:Biogas plant
Shotgun Metagenome Sequencing of Lake Soyang

The lakewater samples were collected from different depths and differnet seasons. The DNA was extracted after filtration through 0.2 um pore-size membrane.

Biome: root:Environmental:Aquatic:Freshwater:Lake
Bacterial communities collected on the surface of stainless steels samples exposed to seawater heated from 30°C to 40°C.

Stainless steels exposed to seawater undergo a several hundred millivolt increase of the open circuit potential called ennoblement.That phenomenon is caused by the bacteria present on the surface of the stainless steel.There is a critical temperature of 38°C above which the ennoblement is inhibited despite the presence of bacteria. We collected bacteria from samples exposed to a range of temperature: 30°C, 33°C, 36°C, 38°C and 40°C in order to compared the conditions leading to ennoblement (under 40°C).We find the presence of the electro-active bacteria Candidatus Tenderia electrophaga, an electro-autotrophic bacteria able to use an electrode as an electron donor to reduce oxygen. We propose a model for which electrotroph bacteria are responsible for the ennoblement.

Biome: root:Engineered:Lab enrichment:Defined media:Marine media
Association of metformin administration with gut microbiome dysbiosis in healthy volunteers

Metformin is a widely used first-line drug for treatment of type 2 diabetes. Despite its advantages metformin has variable therapeutic effects, contraindications, and side effects. Here, for the very first time, we investigate the short term effect of metformin on the composition of healthy human gut microbiota.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Actinobacterial endophytes of medicinal plant Melia toosendan

DNA was extracted from Melia toosendan plant bark, fruit, leaf, root and stem samples. Actinobacterial endophytes were analyzed using 16S rRNA targeted amplicon sequencing using actinobacteria specific primers.

Biome: root:Host-associated:Plants
Metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene of a mixed zooplankton assemblage was carried out using the 454 pyrosequencing platform.

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae.  However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings: Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta.  It also reveals rare species and parasites.  We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Biome: root:Environmental:Aquatic:Marine
Effect of size fractionation and DNA extraction on the diversity and composition of prokaryotic and eukaryotic plankton community

We determined the effect of sample size fractionation (5 size fractions) and DNA extraction (2 methods) on the composition of the prokaryotic (16s) and eukaryotic (18s) plankton community composition

Biome: root:Environmental:Aquatic:Marine
Pelagic Microbiome: viruses to protists. 16S and 18S data from oceanic samples collected at the chlorophyll maximum.

We collected environmental samples during the second cruise of the project “The Great Southern Coccolithophore Belt” collecting samples in the South Indian Ocean and Southern Ocean; during the RSS James Clark Ross Cruise JCR271 as part of the project on Arctic Ocean Acidification collecting samples in the Arctic; finally we collected two costal samples off the coast of South Africa during algal bloom events. Samples included 16S, 18S  amplicons and metagenomic data.

Biome: root:Environmental:Aquatic:Marine
16S and 18S sequences from the epiphytic biofilm on leaves of Enhalus acroides

Seagrass meadows are a crucial component of tropical marine reef ecosystems. The seagrass plants are colonized by a multitude of epiphytic organisms that contribute to determining the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared to the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased abundance of bacterial types associated with coral diseases at the CO2-impacted site (Fusobacteria, Thalassomonas) whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios.

Biome: root:Environmental:Aquatic:Marine:Coastal
Specific gut microbiome members are associated with distinct immune markers in allogeneic hematopoietic stem cell transplantation

Background:
Increasing evidence shows the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation, (HSCT), i.e. a replacement of the cellular part of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g. at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. 

Results:
In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) High concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state.

Conclusions: 
We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine.

Biome: root:Host-associated:Human:Circulatory system:Blood
COMPARE Food Ring Trial - wet

Due to the importance of foods in the transmission of zoonotic agents, within COMPARE Task 2.7 framework a food metagenomic proficiency test was organised between April and June, 2018. The aim of the proficiency test waa to compare microorganisms identity and corresponding abundances in a food matrix tested by shotgun metagenomic sequencing. The food matrix was smoked salmon spiked with a mock community containing bacteria, viruses and parasites. The food matrix was dispatched to each proficiency test participant frozen, including a thermo-logger to monitor the shipping temperature. It was expected that each Participant received the spiked smoked salmon shipped from DTU on April 24 2018, performed nucleic acid extraction and shotgun metagenomic sequencing and upload sequencing data.

Biome: root:Engineered:Food production
Microbial diversity in the Benguela coastal upwelling system as derived from 16S rRNA sequencing and RNA Stable Isotope Probing (SIP)

Sediment microbial diversity was assessed in samples retrieved from four sampled transects. 16S metagenomics was used to characterize microbial structure in the sediments of the different sampling stations. Furthermore, stable isotope probing was employed in samples from certain stations in an attempt to link the function and identity of the microorganisms of the sediment samples. Two microcosm experiments were conducted with one involving the addition of nitrate as substrate and the other one sulphate. In both experiments the provided electron donor was acetate.

Biome: root:Environmental:Aquatic:Marine:Sediment
Deep-amplicon sequencing as a powerful new tool to screen for sequence polymorphisms associated with anthelmintic resistance in parasitic nematode populations

Parasitic gastrointestinal nematodes contribute to significant human morbidity and cause billions of dollars per year in lost agricultural production. Control is dependent on the use of anthelmintic drugs, which in the case of livestock parasites, are severely compromised by the widespread development of drug resistance. More recently, there are concerns regarding the emergence of anthelmintic resistance in human parasitic nematodes in response to the selection pressure resulting from mass drug administration (MDA) programs. Consequently, there is an urgent need for sensitive, scalable and accurate diagnostic tools to detect the emergence of anthelmintic resistance.. Detecting and measuring the frequency of resistance-associated mutations in parasite populations has the potential to provide sensitive and quantitative assessment of resistance emergence from an early stage.  We describe the development and validation of deep-amplicon sequencing as a powerful new approach to detect and quantify the frequency of single nucleotide polymorphisms (SNPs) associated with benzimidazole resistance. We have used parasite communities in sheep, to undertake a proof-of-concept study of this approach. Sheep provide an excellent host system, as there are multiple co-infecting trichostrongylid nematode species, each with varying prevalence of benzimidazole resistance. We demonstrate that the approach provides an accurate measure of resistance allele frequencies, and can reliably detect resistance alleles down to a frequency of 0.1%, making it particularly valuable for screening mutations in the early stages of resistance. We illustrate the power of the technique by screening UK sheep flocks for benzimidazole resistance-associated SNPs at three different codons of the β-tubulin gene, in seven different parasite species from 164 populations (95 from ewes and 69 from lambs) in a single MiSeq sequencing run.  This approach provides a powerful new tool to screen for the emergence of anthelmintic resistance mutations in parasitic nematode populations of both animals and humans.

Biome: root:Host-associated:Animal
EMG produced TPA metagenomics assembly of the doi: 10.3389/fmicb.2016.00579 We employed shotgun metagenome and 16S rDNA gene amplicon sequencing of topsoil samples to robustly compare the taxonomic and functional gene content (Oklahoma and Alaska 1-Year Soil Warming Experiment) data set

The Oklahoma and Alaska 1-Year Soil Warming Experiment Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB10725. This project includes samples from the following biomes : Soil.

Biome: root:Environmental:Terrestrial:Soil:Permafrost
Abundance, diversity and distribution of Legionellales in wet environments in Sweden

In this study, 57 samples from water, soil and sediments were collected in different wet environments in Uppland, Sweden. 45 of them were taken from natural reserves, and 12 from a silver mine. The main objective was to study the abundance, diversity and distribution of members of the gammaproteobacterial order Legionellales.

Biome: root:Environmental
EMG produced TPA metagenomics assembly of the Characterization of the distal gut microbiota in obese patients following a weight-loss intervention using whole metagenome shotgun sequencing (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA290729.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
DEHP Alters Gut Microbiota in Human Neonates

Postnatal exposure to DEHP is associated the development of allergic diseases later in life. The objectives of this study is to investigate whether iatrogenic DEHP exposure affected the gut microbiota pattern in newborns and linked to allergic lung inflammation development as the child gets older.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the The fecal microbiota in L-DOPA naive PD patients (PD-GER) data set.

The PD-GER Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB17784.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Gut microbiome development along the colorectal adenoma-carcinoma sequence (AT_CRC) data set.

The AT_CRC Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB7774.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Prokaryotic microbiota associated to the digestive cavity of the jellyfish Cotylorhiza tuberculata

The microbiota associated to the gastric cavity of four exemplars of the jellyfish Cotylorhiza tuberculata has been studied by means of cultured-dependent and â€“independent methods. The pyrosequencing approach rendered a very reduced diversity of Bacteria in where four major groups were shared by the four exemplars and made up to 95% of the total diversity. The culturing approach recovered low abundant organisms but detected by the pyrosequencing approach. The major key organisms were related to the genera Spiroplasma, Thalassospira, Tenacibaculum (from the pyrosequencing data), and Vibrio (from the cultivable fraction). Altogether the results indicate that C. tuberculata contains an autochtonous microbiota of very reduced diversity that may have established a beneficious mutualist relation with the host. On the other hand, some of the major key players may be potential pathogens and the host may serve as dispersal mechanism.

Biome: root:Host-associated:Invertebrates:Cnidaria
EMG produced TPA metagenomics assembly of the Microbiome study of the RISK cohort (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA237362.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Durable coexistence of donor and recipient strains after fecal microbiota transplantation (Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients) data set.

The Impact of faecal microbiota transplantation on the intestinal microbiome in metabolic syndrome patients Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12357.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Reproducibility of associations between the human gut microbiome and colorectal cancer assessed in a patient population from Washington, DC, USA (Colorectal cancer and the human gut microbiome) data set.

The Colorectal cancer and the human gut microbiome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB12449.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
EMG produced TPA metagenomics assembly of the Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer (Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer) data set.

The Metagenomic analysis of fecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB10878.  This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine, Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Alginate oligosaccharide-induced shift in the intestinal microbiota of salmon.

Prebiotics are food/feed additives intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are potential prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harboured in the intestinal content and mucus of Atlantic salmon offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that AlgOS shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity showed a significant difference between control and AlgOS-fed groups. AlgOS supplementation facilitated the dominance of Proteobacteria and Spirochaetes, promoting the growth of presumed butyrate producers in the intestine. In addition, 0.5% AlgOS stimulated certain bacteria belonging to Proteobacteria, Spirochaetes and Actinobacteria. This indicates that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These results are expected to generate further interest in the potential of macroalgae-derived oligosaccharides as prebiotics for food and feed applications.  

Biome: root:Host-associated:Fish:Digestive system:Intestine
EMG produced TPA metagenomics assembly of the human gut Metagenome (human gut metagenome) data set.

The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJNA375935.  This project includes samples from the following biomes: Host-associated, Human, Digestive system.

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