{"links":{"first":"https://www.ebi.ac.uk/metagenomics/api/v1/studies?ordering=study_id&page=1","last":"https://www.ebi.ac.uk/metagenomics/api/v1/studies?ordering=study_id&page=208","next":"https://www.ebi.ac.uk/metagenomics/api/v1/studies?ordering=study_id&page=2","prev":null},"data":[{"type":"studies","id":"MGYS00000256","attributes":{"bioproject":"PRJNA169357","accession":"MGYS00000256","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP001743","centre-name":"Joint Genome Institute, U.S. Department of Energy","public-release-date":null,"study-abstract":"Many natural ecosystems are efficiently degrading lignocellulose and harbor enzymes that could potentially be harnessed for the production of next generation biofuels from plant biomass. We have used shotgun metagenome sequencing to provide a survey of the microbial community and potential metabolic pathways present in the tropical rain forest soil of Puerto Rico. Wet tropical forest soils are some of the most productive and diverse terrestrial ecosystems on earth. These soils are characterized by high iron concentrations and regular fluctuations between oxic and anoxic conditions on a scale of days to weeks. These dynamic conditions suggest that bacterial and archaeal processes are more important in this type of environment than in other ecosystems.","study-name":"Rainforest Soil","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Terrestrial:Soil:Tropical rainforest","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil:Tropical%20rainforest"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000256"}},{"type":"studies","id":"MGYS00000257","attributes":{"bioproject":"PRJEB2064","accession":"MGYS00000257","samples-count":10,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP000118","centre-name":"Plymouth Marine Laboratory","public-release-date":null,"study-abstract":"Here we present a multi-omic study of the Bacterial and Archaeal diversity found at the L4 long-term marine observatory.  We have previously generated a six year time series from L4 that showed that the bacterial community shows strong seasonal structuring and diversity peaks every year on the winter solstice.  Here we further confirm this pattern by extending this study to include genes and transcripts generated for eight additional time points in 2008.  This data includes further 16S datasets as well as eight metagenomes (1.2 GB) and eight metatranscriptomes (157MB).  These time points cover three seasons (Jan, April and August) and include day and night (diel) publicSamples.  In addition, the August publicSamples (4) include 4 consecutive samplings within 24 hours at six hour intervals.  Using these data we test whether Archaea also show the same observed seasonal patterns and whether these patterns hold true at the gene (functional) level. Analysis of this combined data set allows five main conclusions to be drawn.  First, Archaea show evidence of following the same seasonal patterns as Bacteria, but have ~6% the richness.  Second, for both Bacteria and Archaea, we confirm that higher 16S diversity reflects higher diversity at the gene-level (including expressed genes) and this diversity also peaks at the winter solstice. Third, interestingly, detectable diversity appears to be higher at night, and this is of special potential relevance as there is more diversity in winter when nights are longer.  Fourth, despite the diversity of these communities, night and day publicSamples taken using Lagrangian (drift) sampling were successful in isolating the same community suggesting communities are more structured than is commonly believed. Finally, this data, as expected, contains a large proportion of orphan genes without known homologues.  When compared to the housekeeping genes identified through SEED subsystem classification, these unknown genes appear to be driving the differences between publicSamples across seasons.  This underscores the importance of determining the functions of more of these sequences in the future. In summary, this study further confirms the strong seasonal patterns characterizing both the bacterial and archaeal communities at this important marine site.  The finding that, despite the huge diversity of these communities, there are evident signs of predictable patterns and detectable stability over time provides compelling evidence that renewed efforts should be focused on finding deterministic patterns in even the most complex microbial communities. The Western Channel Observatory maintains more than 100 years of continual environmental monitoring, including oceanographic and biological measures. At PML we are committed to developing this outstanding time series to include the most up to date techniques available. Our aim is to provide an holistic ecologically relevant dataset that can be used to inform environmental models and help with prediction of the impact that climate change will have on the coastal seas of the United Kingdom. With further development and comparative publicStudies this information can help to inform on global marine environments. To this end we have been employing the latest in high-throughput sequencing technology to investigate the microbial diversity and community function in this ecosystem. The technologies applied include 16S rDNA tag-pyrosequencing to deep sequence microbial diversity, as well as total community metagenomics and metatranscriptomics. This initial study includes 16S rDNA tag sequencing data for bacteria and archaeal groups as well as metagenomics and metatranscriptomics all performed on the GS-flx titanium platform using techniques outlined in Gilbert et al (2009 – Environmental Microbiology) and Gilbert et al (2008 – PloS One.) We will continue to add to this repository to maintain the temporal analysis of this community.","study-name":"Western English Channel diurnal study","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine:Oceanic","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000257"}},{"type":"studies","id":"MGYS00000258","attributes":{"bioproject":"PRJNA32089","accession":"MGYS00000258","samples-count":16,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP000319","centre-name":"CGS-GL","public-release-date":null,"study-abstract":"We have characterized the fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. The results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiologic states (obese versus lean)","study-name":"A core gut microbiome in obese and lean twins","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Human:Digestive system:Large intestine:Fecal","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000258"}},{"type":"studies","id":"MGYS00000259","attributes":{"bioproject":"PRJNA30701","accession":"MGYS00000259","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP000240","centre-name":"G2L (Goettingen Genomics Lab)","public-release-date":null,"study-abstract":"The largest part of the Earth's microbial biomass is stored in cold environments, which represent almost untapped reservoirs of novel species, processes, and genes. In this study, the first metagenomic survey of the metabolic potential and phylogenetic diversity of a microbial assemblage present in glacial ice is presented. DNA was isolated from glacial ice of the Northern Schneeferner, Germany. Pyrosequencing of this DNA yielded 1,076,539 reads (239.7 Mbp). The phylogenetic composition of the prokaryotic community was assessed by evaluation of a pyrosequencing-derived data set and sequencing of 16S rRNA genes. The Proteobacteria (mainly Betaproteobacteria), Bacteroidetes, and Actinobacteria  were the predominant phylogenetic groups. In addition, isolation  of psychrophilic microorganisms was performed, and 13 different  bacterial isolates were recovered. Analysis of the 16S rRNA gene sequences of the isolates revealed that all were affiliated to the predominant groups. As expected for microorganisms residing in a low-nutrient environment, a high metabolic versatility with respect to degradation of organic substrates was detected by analysis of the pyrosequencing-derived data set. The presence of autotrophic microorganisms was indicated by identification of genes typical for different ways of carbon fixation. In accordance  with the results of the phylogenetic samples, in which mainly  aerobic and facultative aerobic bacteria were detected, genes  typical for central metabolism of aerobes were found. Nevertheless, the capability of growth under anaerobic conditions was indicated by genes involved in dissimilatory nitrate/nitrite reduction. Numerous characteristics for metabolic adaptations associated with a psychrophilic lifestyle, such as formation of cryoprotectants and maintenance of membrane fluidity by the incorporation of unsaturated fatty acids, were detected. Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments.","study-name":"Glacier Metagenome","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Freshwater:Ice:Glacier","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Freshwater:Ice:Glacier"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000259"}},{"type":"studies","id":"MGYS00000260","attributes":{"bioproject":"PRJEB2451","accession":"MGYS00000260","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP000554","centre-name":"JIC","public-release-date":null,"study-abstract":"The interaction between microbes and plants in the region around plant roots (rhizosphere) is a key determinant of plant productivity. Here we use meta-transcriptomic sequences of mRNA extracted from 4 pooled 1g wheat rhizosphere soil samples to map metabolic interactions in the rhizosphere.","study-name":"Wheat Rhizosphere, John Innes Centre","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Terrestrial:Soil","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000260"}},{"type":"studies","id":"MGYS00000274","attributes":{"bioproject":null,"accession":"MGYS00000274","samples-count":2,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP000664","centre-name":"THE PENNSYLVANIA STATE UNIVERSITY","public-release-date":null,"study-abstract":"How many species inhabit our immediate surrounding? A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds. The windshield of a moving vehicle is subjected to numerous insect strikes and can be used as a collection device for representative sampling. Combined with next-generation sequencing this approach allows for species identification. Here we describe an application of this methodology to two geographic locations within the Northeastern United States. We identified 61 arthropod and 39 plant species, seven of which showed significant difference in the relative abundance between the two localities. Importantly, we developed a novel robust computational framework for the comparison of relative species abundances between geographic locations, which can be used in other read-count-based applications of next-generation sequencing, such as comparison of expression levels. \r\nThe main aim of our study was to contrast eukaryotic species differences between two distinct geographical location in northeastern United States. DNA, isolated from the material stuck to the tapped front bumper of a car driven in these locations, was sequenced using 454 (Roche) FLX pyrosequencing technology.","study-name":"Windshield splatter","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Air","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Air"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000274"}},{"type":"studies","id":"MGYS00000275","attributes":{"bioproject":null,"accession":"MGYS00000275","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP002017","centre-name":"DIVISIÓN DE MICROBIO, Evolutionary Genomics Group, Universidad Miguel Hernández, Alicante, Spain.","public-release-date":null,"study-abstract":"The Deep Chlorophyll Maximum (DCM) is a zone of maximal photosynthetic activity, generally located towards the base of the photic zone in lakes and oceans. The DCM in the Mediterranean is a seasonal phenomenon. The metagenome from a single sample of a mature Mediterranean DCM community has been 454 pyrosequenced both directly and after cloning in fosmids. The comparison between the two approaches revealed a bias in the fosmid libraries against low GC DNA and specifically against the two most dominant members of the community, Candidatus Pelagibacter and Prochlorococcus marinus subsp. pastoris, thus unexpectedly providing a feasible method to obtain large genomic fragments from other less prevalent members of this community. This study is the first to be carried out at this sequencing depth (ca. 600 Mbp combining direct and fosmid sequencing) at any DCM. Our results indicate a microbial community massively dominated by the high-light adapted P. marinus subsp. pastoris, Synechococcus sp. and the heterotroph Candidatus Pelagibacter. The sequences retrieved were remarkably similar to the existing genome of P. marinus subsp. pastoris with a nucleotide identity over 98%. Besides, we found a large number of cyanophages that could prey on this microbe although sequence conservation was much lower. The high abundance of phage sequences in the cellular size fraction indicated a remarkably high proportion of cells suffering phage lytic attack. In addition, several fosmids clearly belonging to Group II Euryarchaeota were retrieved and recruited many fragments from the total DNA sequencing suggesting that this group might be quite abundant in this habitat.\r\nWe have extracted metagenomic DNA from the pico-planktonic 5-0.2 μm size fraction (mostly prokaryotic cells) from a single sample obtained in mid October at 50 m depth and analyzed the DNA from this sample (without cloning or amplification) by 454 pyrosequencing (hereafter referred to as Direct Sequencing, DS). We also used 454 to sequence ca. 1152 randomly selected fosmid clones from a metagenomic fosmid library constructed from the same DNA sample. Here we compare the output from both methods and the picture of the microbial community that they provide.","study-name":"The Metagenome of the deep chlorophyll maximum in the Mediterranean studied by direct and fosmid library 454 pyrosequencing","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine:Oceanic","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000275"}},{"type":"studies","id":"MGYS00000276","attributes":{"bioproject":"PRJNA50815","accession":"MGYS00000276","samples-count":10,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP003198","centre-name":"Department of Life Science, Chung-ang university","public-release-date":null,"study-abstract":"Kimchi, the Korean culture's traditional food, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation. Metagenomic DNA was extracted from kimchi samples obtained periodically and followed by sequencing using a 454 GS-FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera; Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of MG-RAST revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophage during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.\r\nWe have extracted metagenomic DNA from fermented food kimchi and sequenced the DNA from this sample by 454 GS-FLX titanium without cloning or amplification. Here we analyze changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation using metagenomic approaches.","study-name":"Kimchi metagenome","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/biomes"},"data":[{"type":"biomes","id":"root:Engineered:Food production:Fermented vegetables","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Food%20production:Fermented%20vegetables"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000276"}},{"type":"studies","id":"MGYS00000277","attributes":{"bioproject":"PRJNA46321","accession":"MGYS00000277","samples-count":19,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP002423","centre-name":"NIDDK","public-release-date":null,"study-abstract":"Inflammatory bowel diseases (IBD), such as Crohn’s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. \r\nIn this application, we propose to develop and demonstrate the ability to profile Crohn’s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will employ a multidisciplinary approach based on metagenomic and metaproteomic molecular tools to elucidate the composition of the commensal microbiota in monozygotic twins that are either healthy or exhibit Crohn’s disease (for concordant, both are diseased; for discordant, one is healthy and one is diseased). \r\nThe central hypotheses of this proposal are (1) that specific members and/or functional activities of the gastrointestinal (GI) microbiota differ in patients with Crohn’s disease as compared to healthy individuals, and (2) that it will be possible to elucidate microbial signatures which correlate with the occurrence and progression of this disease by integration of data obtained from 16S rRNA-based molecular fingerprinting, metagenomics, and metaproteomics approaches. To address these hypotheses, three specific aims are proposed: 1) Obtain data on community gene content (metagenome) in a subset of healthy twins and twins with Crohn’s Disease to assess potential differences in the metabolic capabilities of the gut microbiota associated with CD, 2) Obtain data on community protein content (metaproteome) in a subset of healthy twins and twins with Crohn’s Disease to assess the state of expressed proteins associated with CD, 3) Apply various statistical clustering and classification methods to correlate/associate microbial community composition, gene and protein content with patient metadata, including metabolite profiles and clinical phenotype. \r\nThe ultimate goal of these efforts is to identify novel biomarkers for non-invasive diagnostics of CD and to eventually identify drug targets (i.e. bacterial strains) for cure or suppression of disease symptoms. \r\nPUBLIC HEALTH RELEVANCE: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn’s disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn’s disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression.","study-name":"Human Gut Microbiome in Crohn's Disease","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Human:Digestive system:Large intestine:Fecal","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000277"}},{"type":"studies","id":"MGYS00000278","attributes":{"bioproject":null,"accession":"MGYS00000278","samples-count":17,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP002437","centre-name":"Cornell University","public-release-date":null,"study-abstract":"The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-year case study of the assembly of the human infant gut microbiome to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ~500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present prior to the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome could be attributed to life events.","study-name":"Developing infant gut microbiome","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Human:Digestive system:Large intestine:Fecal","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000278"}},{"type":"studies","id":"MGYS00000282","attributes":{"bioproject":"PRJNA33179","accession":"MGYS00000282","samples-count":18,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP001803","centre-name":"J. Craig Venter Institute","public-release-date":null,"study-abstract":"Microbial metagenome from a lake in Antarctica.\r\nMicrobial community isolated from an aquatic lake in Antarctica. ","study-name":"Antarctica Aquatic Microbial Metagenome","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000282"}},{"type":"studies","id":"MGYS00000283","attributes":{"bioproject":null,"accession":"MGYS00000283","samples-count":13,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"MetaSoil","centre-name":"MetaSoil","public-release-date":null,"study-abstract":"The soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. Soil has more unknown biodiversity than any other ecosystem. We have applied diverse DNA extraction methods coupled with high throughput pyrosequencing to explore 4.88 x 10^9 bp of metagenomic sequence data from the longest continually studied soil environment (Park Grass experiment at Rothamsted Research in the UK). Results emphasize important DNA extraction biases and unexpectedly low seasonal and vertical soil metagenomic functional class variations. Clustering-based subsystems and carbohydrate metabolism had the largest quantity of annotated reads assigned although o50% of reads were assigned at an E value cutoff of 10^-5. In addition, with the more detailed subsystems, cAMP signaling in bacteria (3.24±0.27% of the annotated reads) and the Ton and Tol transport systems (1.69±0.11%) were relatively highly represented. The most highly represented genome from the database was that for a Bradyrhizobium species. The metagenomic variance created by integrating natural and methodological fluctuations represents a global picture of the Rothamsted soil metagenome that can be used for specific questions and future inter-environmental metagenomic comparisons. However, only 1% of annotated sequences correspond to already sequenced genomes at 96% similarity and E values of 10^-5, thus, considerable genomic reconstructions efforts still have to be performed. See http://www.genomenviron.org/Projects/METASOIL.html for additional details.","study-name":"MetaSoil","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Terrestrial:Soil:Grasslands","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil:Grasslands"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000283"}},{"type":"studies","id":"MGYS00000288","attributes":{"bioproject":null,"accession":"MGYS00000288","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP001095","centre-name":"CCME","public-release-date":null,"study-abstract":"This project describes a population genomic study focused on determining the evolutionary rates in natural populations, and to correlate human disturbance to major evolutionary divergence events. Biofilm samples from acid mine drainage were taken in the period 2006-2010 at four locations in the Richmond Mine (Iron Mt., CA). Community genomic DNA was extracted and sequenced by either 454 or Illumina sequencing.","study-name":"Brazos-Trinity Basin Sediment Metagenome: IODP Site 1320","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine:Oceanic:Sediment","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic:Sediment"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000288"}},{"type":"studies","id":"MGYS00000289","attributes":{"bioproject":null,"accession":"MGYS00000289","samples-count":5,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP000183","centre-name":"CCGB","public-release-date":null,"study-abstract":"The subseafloor marine biosphere may be one of the largest reserviors of microbial biomass on Earth and has recently been the subject of debate in terms of the composition of its microbial inhabitants, particularly on sediments from the Peru Margin. A metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment. A total of 61.9 Megabases of genetic material was sequenced from sediments at horizons 1, 16, 32 and 50 meters below seafloor. These depths include sediments from both primarily sulfate-reducing and also methane-generating regions of the sediment column. Many genes of the annotated genes, including those encoding ribosomal proteins, corresponded to those from the Chloroflexi and Euryarchaeota. However, analysis of the 16S small subunit ribosomal genes suggests that Crenarchaeota are the abundant microbial member. Quantitative PCR confirms that uncultivated Crenarchaeota are indeed a major microbial group in these subsurface samples. These findings show that the marine subsurface is a distinct microbial habitat and is different than environments previously studied by metagenomics, especially due to the predominance of uncultivated archaeal groups.\n\nA metagenomic analysis was made using whole genome amplification and pyrosequencing of sediments from Ocean Drilling Program Site 1229 on the Peru Margin to further explore the microbial diversity and overall community composition within this environment.","study-name":"Peru Margin Subseafloor Biosphere","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine:Oceanic:Sediment","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic:Sediment"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000289"}},{"type":"studies","id":"MGYS00000291","attributes":{"bioproject":"PRJEB2280","accession":"MGYS00000291","samples-count":2,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP000339","centre-name":"UBP-CNRS","public-release-date":null,"study-abstract":"Viruses are known to be the most abundant biological entities in\n    aquatic environment, where they are (i) important top-down regulation factors for\n    microbial communities, (ii) known to interfere in major biogeochemical cycles, and\n    (iii) thought to be an important source of genetic diversity. Yet, diversity and\n    distribution of these viruses is still far from being understood, especially in\n    freshwater ecosystems. Metagenomic analysis of two different temperate freshwater\n    viral communities showed that most of the viral sequences were not similar to those\n    in the current databases. A deep sequencing (1.5 billion sequences) associated to a\n    large read size (400 bp) allowed us to assess, for the first time, the diversity in\n    the main viral families through direct phylogenetic analysis of specific marker\n    genes. The analysis of the major viral groups found in the two lakes shed light on a\n    great diversity, and retrieved previously unknown clades among single-stranded DNA\n    viruses (Microviridae, Circoviridae, Nanoviridae) and among Caudovirales. The\n    absence of lake-specific clade indicated that the new viruses identified were\n    ubiquitous, at least on a regional freshwater lake scale. Compared to the previously\n    published viromes, a significant genetic similarity between viral communities of\n    related environments was highlighted for the first time, despite the great\n    geographical distances separating these different communities. Thus, viruses appear\n    to be distributed worldwide, and are likely selected by the presence or absence of\n    their hosts. Gene richness analysis assessed through rarefaction curves showed an\n    extraordinary genetic diversity of viruses in each of the two lakes under study.\n    Such diversity was never retrieved previously, even in the last generation of\n    published viromes. The global virome is thereby a fantastic pool of unknown genes,\n    which remains partially sampled and understood.","study-name":"Viral metagenomic study of two freshwater Lakes","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Freshwater:Lake","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Freshwater:Lake"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000291"}},{"type":"studies","id":"MGYS00000293","attributes":{"bioproject":"PRJEB2763","accession":"MGYS00000293","samples-count":2,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001021","centre-name":"UH/IB","public-release-date":null,"study-abstract":"We investigated the effect of marination on microbiota in modified athmosphere packaged broiler meat using metagenomics. To be able to see the differences in lactic acid bacteria communities on a strain level and to evaluate congruence between the methods, we characterized the lactic acid bacteria communities also by identification of isolates. Most raw poultry sold in Finland at the retail level is mixed with marinades containing oil, sugar, spices and acetic acid and packaged under modified atmosphere. Growth of Leuconostoc spp. has been observed to cause premature spoilage  of marinated broiler meat packages. In this study we investigated whether marinating enriched Leuconostoc spp. in meat microbiota. To obtain a complete view of the microbiota, we sequenced total DNA and 16S rRNA gene amplicons from the microbial communities. In addition, the lactic acid bacterial communities were characterized by identification of colonies. The results showed that marinade increased the proportions of the spoilage-associated Leuconostoc gasicomitatum in the communities as well as the proportions of L. gelidum and Lactobacillus spp.. The proportions of Carnobacterium, Vagococcus, Brochothrix thrermosphacta, Clostridium, Enterobacteriaceae and Vibrio were diminished. Analysis of 16S rRNA gene amplicons resulted in 312 and 284 operational taxonomical units (dissimilarity 0.03) in unmarinated and marinated meat, respectively, indicating that the meat communities were more diverse than hitherto shown. A number of bacterial taxa that have not been associated with late shelf-life meat before were detected, including Vagococcus and Vibrio that belonged to the predominating part of the microbial community in unmarinated meat. According to the functional analysis of the metagenomes, both communities were characterized by high proportions (15.6% or 17.9%) of genes involved in carbohydrate metabolism.","study-name":"Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/biomes"},"data":[{"type":"biomes","id":"root:Engineered:Food production","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Food%20production"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000293"}},{"type":"studies","id":"MGYS00000294","attributes":{"bioproject":"PRJEB2778","accession":"MGYS00000294","samples-count":12,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001038","centre-name":"Texas A&M University","public-release-date":null,"study-abstract":"Ongoing efforts are directed at understanding the mutualism between the\n                gut microbiota and the host in breast-fed versus formula-fed infants. Due to the\n                lack of tissue biopsies, no investigators have performed a global transcriptional\n                analysis of the developing intestine in healthy infants. As a result, the crosstalk\n                between the microbiome and the host transcriptome in the developing\n                mucosal-commensal environment has not been determined. In this study, we examined\n                the host intestinal mRNA gene expression and microbial DNA profiles in full term 3\n                month-old infants exclusively formula fed (FF; n=6) or breast fed (BF; n=6) from\n                birth to 3 months. Host mRNA microarray measurements were performed on intact\n                sloughed epithelial cells in stool samples collected at 3 months. Microbial\n                composition from the same stool samples was assessed by metagenomic pyrosequencing.\n                Both host mRNA expression and bacterial microbiome phylogenetic profiles provided\n                strong feature sets that classified the two groups of babies (FF and BF). To\n                determine the relationship between epithelial cell gene expression and the bacterial\n                colony profiles, the host transcriptome and functionally profiled microbiome data\n                were analyzed in a multivariate manner. From a functional perspective, analysis of\n                the gut microbiota's metagenome revealed that virulence characteristics differed\n                between the FF and BF babies. Using canonical correlation analysis, evidence of\n                multivariate structure relating eleven host immunity/mucosal defense-related genes\n                and microbiome virulence characteristics was observed. These results, for the first\n                time, provide insight into the integrated responses of the host and microbiome to\n                dietary substrates in the early neonatal period.In this study, we examined the host intestinal mRNA gene expression\n                and microbial DNA profiles in full term 3 month-old infants exclusively formula fed\n                (FF; n=6) or breast fed (BF; n=6) from birth to 3 months. Host mRNA microarray\n                measurements were performed on intact sloughed epithelial cells in stool samples\n                collected at 3 months. Microbial composition from the same stool samples was\n                assessed by metagenomic pyrosequencing. Both host mRNA expression and bacterial\n                microbiome phylogenetic profiles provided strong feature sets that classified the\n                two groups of babies (FF and BF). To determine the relationship between epithelial\n                cell gene expression and the bacterial colony profiles, the host transcriptome and\n                functionally profiled microbiome data were analyzed in a multivariate manner. From a\n                functional perspective, analysis of the gut microbiota's metagenome revealed that\n                virulence characteristics differed between the FF and BF babies. Using canonical\n                correlation analysis, evidence of multivariate structure relating eleven host\n                immunity/mucosal defense-related genes and microbiome virulence characteristics was\n                observed. These results, for the first time, provide insight into the integrated\n                responses of the host and microbiome to dietary substrates in the early neonatal\n                period.","study-name":"Mutualism between gut microbiota and the host as revealed in a comparative study of breast-fed versus formula-fed infants","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Human:Digestive system:Large intestine:Fecal","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000294"}},{"type":"studies","id":"MGYS00000295","attributes":{"bioproject":"PRJEB2790","accession":"MGYS00000295","samples-count":8,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001068","centre-name":"CEH","public-release-date":null,"study-abstract":"Numerous globally distributed 16S rRNA surveys of soil bacterial communities are\n    now revealing consistent trends in the main environmental drivers of\n    biodiversity. Soil pH is consistently revealed as the predominant correlate of\n    taxonomic diversity, with low pH soils comprising less diversity and being\n    dominated by a few broad taxonomic groups such as the oligotrophic acidobacteria\n    phylum. What is less clear is what these broad differences in patterns of\n    taxonomic diversity mean for the functional genetic potential of soils. The low\n    culturability of many taxa from low pH soils means that they are significantly\n    underrepresented in genome sequence databases. Therefore, this study aims to\n    provide a metagenomic comparison of geographically isolated soils of low pH with\n    neutral pH soils to identify any broad functional differences between soils of\n    similar taxonomic composition.","study-name":"Functional diversity of soil microbes across environmental gradients","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Terrestrial:Soil","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Terrestrial:Soil"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000295"}},{"type":"studies","id":"MGYS00000296","attributes":{"bioproject":"PRJNA13694","accession":"MGYS00000296","samples-count":26,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP003580","centre-name":"JCVI","public-release-date":null,"study-abstract":"Collection of metagenomes obtained during the Global Ocean Sampling Expedition","study-name":"Global Ocean Sampling Expedition","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000296"}},{"type":"studies","id":"MGYS00000297","attributes":{"bioproject":"PRJEB2859","accession":"MGYS00000297","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001178","centre-name":"EMBL","public-release-date":null,"study-abstract":"Polar winter waters are one of the least studied marine ecosystems with regard to microbial life and Thaumarchaeota are key microorganisms in this environment. We collected data on abundance and metabolic activity of Thaumarchaeota in Arctic and Antarctic waters in different seasons, including the wintertime. As previously observed, Arctic Thaumarchaeota grew throughout the winter, increasing their abundances one order of magnitude from January to March 2008. Yet, paradoxically, in situ single-cell measurements revealed an unexpected low metabolic activity for this group in both polar systems, i.e., less than 5% of archaeal cells taking up leucine or bicarbonate, inconsistent with known heterotrophic or autotrophic archaeal lifestyles. To resolve how archaea obtain energy and carbon for growth, we analyzed a metagenome collected during the Arctic winter, when the Thaumarchaeota population was at its maximum of abundance (18% of cell counts). Metagenomics and quantitative PCR showed that archaeal amoA genes were abundant in Arctic and Antarctic waters, indicating that polar Thaumarchaeota have the potential for ammonia oxidation.  The presence of a large number of archaeal genes involved in urea transport and degradation together with detectable uptake of 14C-labeled urea by the prokaryotic assemblage, suggest that the products of urea hydrolysis (NH3 and CO2) may be sources of both energy and carbon for polar ammonia oxidizing archaea. This hypothesis, consistent with the idea of polar archaea growing as nitrifiers but with apparent low incorporation of bicarbonate, would provide the molecular basis for the recurrent archaeal growth in polar winter waters.","study-name":"Arctic Winter marine ecosystem","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000297"}},{"type":"studies","id":"MGYS00000298","attributes":{"bioproject":"PRJEB2888","accession":"MGYS00000298","samples-count":8,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001227","centre-name":"MPI-BREMEN","public-release-date":null,"study-abstract":"Phytoplankton blooms characterize temperate ocean margin zones in spring and contribute substantially to their high productivity. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed an as yet unseen dynamic succession of thriving populations at genus level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes, transporters (in particular TonB-dependent transporters) and phosphate acquisition systems were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria and Alphaproteobacteria acted like guilds specialized for successive algal-derived organic matter decomposition. Our results suggest that algal substrate availability and bacterial ecological niches determined the succession. A better understanding of such couplings between bacterioplankton and phytoplankton is needed to pave the way for predictive models of bacterioplankton bloom dynamics and thus more accurate global carbon turnover balances.","study-name":"Substrate-controlled succession of distinct marine bacterioplankton populations induced by a spring phytoplankton bloom","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/biomes"},"data":[{"type":"biomes","id":"root:Environmental:Aquatic:Marine","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000298"}},{"type":"studies","id":"MGYS00000299","attributes":{"bioproject":"PRJEB2885","accession":"MGYS00000299","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001224","centre-name":"UNIVIE-GENECO","public-release-date":null,"study-abstract":"Geodia barretti is a marine cold-water sponge harbouring high numbers of microorganisms. Significant rates of nitrification have been observed in this sponge, indicating a substantial contribution to nitrogen turnover in marine environments with high sponge cover. In order to get closer insights into the phylogeny and function of the active microbial community and the interaction with its host G. barretti, a metatranscriptomic approach was employed, using the simultaneous analysis of rRNA and mRNA. Of the 262,298 RNA-tags obtained by pyrosequencing, 92% were assigned to ribosomal RNA (ribo-tags). A total of 109 325 SSU rRNA ribo-tags revealed a detailed picture of the community, dominated by group SAR202 of Chloroflexi, candidate phylum Poribacteria and Acidobacteria, which was different in its composition from that obtained in clone libraries prepared form the same samples. Optimized assembly strategies allowed the reconstruction of full-length rRNA sequences from the short ribo-tags for more detailed phylogenetic studies of the dominant taxa. Cells of several phyla were visualized by FISH analyses for confirmation. Of the remaining 21,325 RNA-tags, 10,023 were assigned to mRNA-tags, based on similarities to genes in the databases. A wide range of putative functional gene transcripts from over 10 different phyla were identified among the bacterial mRNA-tags. The most abundant mRNAs were those encoding key metabolic enzymes of nitrification from ammonia-oxidizing archaea as well as candidate genes involved in related processes. Our analysis demonstrates the potential and limits of using a combined rRNA and mRNAapproach to explore the microbial community profile, phylogenetic assignments and metabolic activities of a complex, but little explored microbial community.","study-name":"Metatranscriptomics of the marine sponge Geodia barretti: Tackling phylogeny and function of its microbial community.","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Porifera","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Porifera"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000299"}},{"type":"studies","id":"MGYS00000300","attributes":{"bioproject":"PRJNA48475","accession":"MGYS00000300","samples-count":2,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"SRP004311","centre-name":"HMP","public-release-date":null,"study-abstract":"The HMP metagenomes mock pilot represents the shotgun sequencing of HMP even and staggered Mock communities, distributed to each of the four HMP sequencing centers. The goal of the pilot was to test the sequencing protocol and to evaluate accuracy and consistency between centers.","study-name":"HMP Mock Community samples","data-origination":"HARVESTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/biomes"},"data":[{"type":"biomes","id":"root:Engineered:Modeled:Simulated communities (DNA mixture)","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Engineered:Modeled:Simulated%20communities%20(DNA%20mixture)"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000300"}},{"type":"studies","id":"MGYS00000303","attributes":{"bioproject":"PRJEB3061","accession":"MGYS00000303","samples-count":1,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001477","centre-name":"MPI-BREMEN","public-release-date":null,"study-abstract":"The shrimp Rimicaris exoculata flourishes on deep-sea hydrothermal chimneys along the Mid-Atlantic Ridge (MAR). This species harbors dense community of chemoautotrophic epibiotic bacteria associated with mineral oxide deposits in its enlarged gill chamber. We used metagenomics on specimens from the Rainbow hydrothermal vent site, to investigate the metabolism of the two main sulfur-oxidizing epibionts affiliated to the Epsilonproteobacteria and Gammaproteobacteria. Both epibionts had genes of the Sox pathway for sulfur oxidation and hydrogenases. In the epsilonproteobacterial epibiont, two distinct denitrification systems (Nas/Nir and Nap/Nrf) as well as a complete rTCA cycle for carbon dioxide fixation were found, while the gammaproteobacterial epibiont was found to fix carbon dioxide via the CBB cycle with RuBisCo form II. The shrimp gill chamber metagenome provided information on host-epibiont interactions, like on virulence gene homologues and genes for surface attachment. Likewise, genes were found that might play a role in host nutritional and detoxification processes, and thus are of major importance for the survival of the shrimp and its adaptation to the hydrothermal vent environment. Interestingly, analysis of the metagenome revealed sequences affiliated to the iron-oxidizing class Zetaproteobacteria, which would explain gill chamber iron oxyhydroxide deposits. Presence of Zetaproteobacteria was confirmed by fluorescence in situ hybridizations and thereby provided first evidence for a Zetaproteobacteria-invertebrate.","study-name":"Metagenomics of the gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata and discovery of zetaproteobacterial epibionts","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Arthropoda:Respiratory system:Gills","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Arthropoda:Respiratory%20system:Gills"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000303"}},{"type":"studies","id":"MGYS00000304","attributes":{"bioproject":"PRJEB3085","accession":"MGYS00000304","samples-count":12,"is-private":false,"last-update":"2016-01-20T14:12:06","secondary-accession":"ERP001506","centre-name":"CSISP","public-release-date":null,"study-abstract":"Recent research has disclosed a tight connection between beta-lactam antibiotics, microbial gut metabolism and health but obtaining a complete understanding of this process remains a major goal. Here, we conducted, to the best of our knowledge, the first global comparative OMIC investigation of gut microbial communities in samples of an individual subjected to β-lactam antibiotic therapy at different time frames. Results indicated a drastic change of the total community at response to AB at the day 11thwhich correlated with changes at the level of metabolites, mRNA transcripts and production of proteins. By contrast, AB-resistant active microbiota remains constant, showing a relevant decrease three days later, which indicate an AB time-delay between total and active bacteria. Forty days after AB therapy, the total community is restored but, surprisingly, the low abundant bacteria (Proteobacteria) become the most active members. This is in agreement with unique metabolomic signatures which indicate that human-gut microbe interactions seem to be restored (or improved) as a consequence of AB therapy. It is worth to mention that as a consequence of AB a drastic under-expression of protein production and an attenuation of the metabolic status occurred irreversibly, in agreement with the biodiversity and richness decreased of the total microbiota. Most likely, at the initial stages, AB-resistant bacteria may become, albeit at lower numbers, the most active bacterial members, but their consequent instability as response to AB therapy produced a re-establishment of the overall community containing new active members that has a connection with the host. A complete reprogramming of the bacterial structure and metabolic status seems to occur most likely at day 11th. Taken together, this study suggests a tighter, more coordinated and complex evolutionary and AB ecology scenario of human gut microbial communities than has been previously assumed.","study-name":"Beta Lactam Antibiotics and Human Gut Microbiota","data-origination":"SUBMITTED"},"relationships":{"geocoordinates":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/geocoordinates"}},"biomes":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/biomes"},"data":[{"type":"biomes","id":"root:Host-associated:Human:Digestive system:Large intestine:Fecal","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Host-associated:Human:Digestive%20system:Large%20intestine:Fecal"}}]},"publications":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/publications"}},"analyses":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/analyses"}},"downloads":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/downloads"}},"samples":{"links":{"related":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304/samples"}}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000304"}}],"meta":{"pagination":{"page":1,"pages":208,"count":5197}}}