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MGYS00000387
|
Lime was injected to acid sulfate soils with aim to balance the acidity. The indigenous microbial communities before and after injection were investigated.
|
Due to very low inflows from the Murray-Darling Basin from 2007-2009, water levels in the Lower Murray River dropped to -1m AHD in April 2009. The low water levels and restricted water allocations during this hydrological drought period caused the acid sulfate soils subsequently acidified and salinized. Given the acidic drainage water presents a potential risk to the water quality and environmental values of the Lower River Murray, a subsoil neutralisation using a limestone slurry and a modified mole drain technique was applied. The aim of this trial is to examine whether the introduction of alkalinity (limestone) at depth in the oxidised and rewet acid sulfate soils, will sufficiently raise the pH to begin the process of sulfate reduction. It is hoped by promoting sulfate reduction, via sulfate reducing bacteria, the soils will begin to remediate, producing less acidic drainage to the salt drains in the irrigation areas.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000388
|
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India
|
There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics, and compared that to a Swedish lake receiving no input of wastewater from industrial or municipal sources.
|
root:Environmental:Aquatic:Freshwater:Lake
|
MGYS00000389
|
Stable isotope probing/metagenomics of terrestrial dimethylsulfide degrading microorganisms
|
Dimethylsulfide (DMS), a volatile sulfur compound, plays an important role in the global sulfur cycle and atmospheric chemistry. Microorganisms can use DMS as sole carbon, sulfur or energy source, contributing to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, it has been recognised that a wide range of bacteria isolated from terrestrial ecosystems are able to degrade DMS, yet it remains unknown whether any of these play important roles in situ. In this study we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA.
|
root:Environmental:Aquatic:Freshwater:Lentic:Sediment
|
MGYS00000391
|
Sydney Harbour metagenomes
|
Spatial taxonomic and functional diversity in the Sydney Harbour
|
root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
|
MGYS00000392
|
Acid sulfate soil microbial profile - pre-investigation
|
A pre-investigation of the microbial composition of the acid sulfate soils were carried in Oct 2011 to obtain the microbial information before lime injection
|
root:Environmental:Terrestrial:Soil:Grasslands
|
MGYS00000393
|
Southampton Asthma metagenomics
|
55 subjects underwent detailed clinical and immunological phenotyping, sputum induction and bronchoscopy during periods of clinical stability. In addition to 15 healthy controls, 9 mild, 16 moderate and 15 severe ashthmatics (without bronchiectasis) were included. Protected bronchoalveolar lavage (BAL) and induced symptoms were analysed by WGS for RNA and DNA from bacterial, viral and fungal genomes. 88 samples were sequenced using 454 FLX Titanium. Single end library. Data were provided as fasta files following adapter trimming
|
root:Host-associated:Human
|
MGYS00000394
|
Metagenome fecal microbiota, Illumina seq reads of 12 individuals at 2 timepoints
|
Two diets, Korean and Western diet. Each 6 individuals, half of which lost a lot of weight and half of which lost little weight. Fecal samples taken before and after diet (3 months).
|
root:Host-associated:Human:Digestive system
|
MGYS00000395
|
Photoheterotrophy in a mesoscale anticyclonic eddy in the Eastern Mediterranean Sea
|
Mesoscale eddies are semi-closed rotating water bodies with distinct physico-chemical properties and are a widespread phenomenon in the world's oceans. Previous studies found that eddies can affect phytoplankton and bacterioplankton community structure, primary productivity and nitrogen fixation. A considerable fraction of the marine bacterioplankton consists of photoheterhophs. These bacteria can use light to generate biochemical energy for transport and metabolic needs. Unlike photoautotrophs they depend on organic carbon for growth and biomass production. Photoheterotrophy can potentially enhance bacterial growth and/or survival in oligotrophic oceanic conditions. A common group of photoheterotrophs consists of proteorhodopsin (pr) bearing bacteria. The pr gene occurs in diverse microbial taxa including SAR11, a dominant Alphaproteobacteria clade. We hypothesize that anticyclonic eddies, which facilitate nutrient poor conditions by downwelling surface water, favor photoheterhophy. In November 2013 we conducted an oceanographic survey aboard R/V Mediterranean Explorer with the goal to assess the abundance, diversity and expression of photoheterophic genes in an anticyclonic eddy in the ultra-oligotrophic Eastern Mediterranean Sea. The results of this study will shed light on the potential role of physical and chemical gradients created by mesoscale eddies on changes in photoheterotrophic communities, which can have global effects on ocean biogeochemistry and energy flow.
|
root:Environmental:Aquatic:Marine:Oceanic:Photic zone
|
MGYS00000399
|
Transcriptomic analysis of microbial communities isolated from the rhizospheres of wheat, oat and pea, compared to unplanted soil
|
Rhizosphere microbes are key players in biogeochemical cycles and maintainance of plant health and productivity. Here we used metatranscriptomic analysis of rRNA depleted RNA from the rhizospheres of wheat, oat, pea, and unplanted soil to compare the metabolic functions of microbes in these environments. Using biological replication (n=5) we were able to give statisistical significance to the differences found. Microbes responsed to the rhizosphere environment by increasing metabolic activity in general, and particularly in metabolic pathways involved in sugar, organic acid and aromatics metabolism, oxidative stress, and motility. While general rhizosphere effects on the microbial communities were observed, many specific effects were plant species dependent.
|
root:Host-associated:Plants:Rhizosphere:Soil
|
MGYS00000400
|
Transcriptome of Lecane inermis for phylogenomic studies of sppiralian relationships
|
Transcriptome data of Lecane inermis were used alongside other transcriptomic data of spiralian taxa to investigate spiralian relationships in a phylogenomic approach
|
root:Host-associated:Spiralia
|
MGYS00000401
|
Metagenomic sequencing of a Bison priscus bone sample from the Trois-Freres cave (Ariege, France)
|
The steppe bison (Bison priscus) is an extinct species that was widely distributed in Europe, Central Asia, Beringia and North America during the Pleistocene. It is known from abundant remains, including complete animals found in the permafrost, and from Palaeolithic rock-art pictures. However, the molecular information available for this species is limited to a fragment of the mitochondrial genome control region. In order to obtain a thorough genetic characterization of the steppe bison, we performed high-throughput shotgun sequencing of DNA extracted from a specimen of the Trois-Freres cave (Ariege, France). Analysis of several bone samples from the Salle du Grand Eboulis of this cave enabled identifying a rib from which bison DNA could be reproductively recovered and amplified by PCR. One DNA extract obtained from this rib was converted into an Illumina library, and about 1 billion DNA reads were analysed. Using these sequence data we reconstructed a complete mitochondrial genome of 16,318 bp with an average unique read depth of 10x
|
root:Host-associated:Animal
|
MGYS00000406
|
Metagenomic analysis of sediments along a uranium gradient
|
Surface sediment from a billabong in the Northern Territory of Australia was collected and spiked with uranyl sulfate at 6 different concentrations (0 - 4,000 mg/ kg). The sediments were then re-deployed at the site and left in these natural environmental conditions for 5 months. DNA was extracted from the sediments and submitted for metagenomic sequencing on the Illumina HiSeq 2500 instrument.
|
root:Environmental:Aquatic:Freshwater:Sediment
|
MGYS00000410
|
Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for prokaryotes.
|
Seawater was filtered from different depths to retain small cell sizes (Bacteria Organisms). The DNA was extracted and submitted to high throughput sequencing.
|
root:Environmental:Aquatic:Marine
|
MGYS00000412
|
metagenomic analysis of human gut microbiome
|
metagenomic analysis of human gut microbiome
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000414
|
Analysis of sample SRA022105 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)
|
The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00000415
|
Analysis of sample SRA022106 from Southern Ocean Marine Metagenome ( J. Craig Venter Institute, submitted to NCBI on 28-JUL-2010)
|
The comparative study of metagenomes arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude. This project's main objectives are: (i) to perform a comparative study between two metagenomes from different environments (cold and warm waters), in order to establish the influence caused by abiotic factors on microbial community present at the collection site, (II) assess the diversity present in each data set (III) Linking genomic each set containing the respective biological pathways, (iv) Undertake comparisons between different sets and identify their commonalities and their differences (V) Expand the information obtained in this study with the literature data.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00000416
|
Analysis of sample GS112 take in the Indian Ocean
|
The comparative study of metagenomas arising from oceanic surface waters has attracted great interest in the scientific community. Recent studies have shown the association of microbial communities to environmental factors such as temperature, salinity and latitude.
|
root:Environmental:Aquatic:Marine:Oceanic
|
MGYS00000418
|
non corroding sheet piles in the soil.
|
We have investigated the community composition and their metabolic potential of samples from sheet piles in soil. Samples were taken from the soil and soil attached to the sheet piles. The sheet piles were not corroded and showed a mineral coating. The metagenomes were sequenced by the Illumina Miseq technique.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000419
|
cattle and buffalo based on roughage based diet
|
Analysis of rumen microbiome from cattle and buffaloes which were fed with same roughage diet using metatranscriptomics approache
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000421
|
Sao Paulo Zoo Lake Study
|
Sao Paulo Zoo Lake Study
|
root:Environmental:Aquatic:Freshwater:Lake
|
MGYS00000422
|
Microbial diversity and isolation of novel hydrolases from the Kudu Rumen
|
Rumen of various angulates contain a variety of microbes that aid with the digestion of consumed plant material. These microbes have proved to be an important source of hydrolytic enzymes such as cellulases that are of immense importance in the emerging biofuels industry. This study seeks to understand the diversity and function of the Kudu rumen microflora and isolate its novel hydrolases.
|
root:Host-associated:Mammals
|
MGYS00000424
|
Metagenomic analysis of the Binga Hot Springs in Zimbabwe for Microbial Diversity and Hydrolytic Enzymes
|
Hot springs are an important source novel thermostable industrial enzymes. This study is seeks to use bioinformatics to analyze the metagenome derived from the Binga Hotsprings in Zimbabwe. The analysis will focus on microbial diversity and function prediction of genes encoding Novel hydrolases of industrial importance
|
root:Environmental:Aquatic:Thermal springs
|
MGYS00000427
|
Gut and Oral Microbiome Dysbiosis in Rheumatoid Arthritis
|
Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier, and assemble a pathogen?s draft genome using SOAPMeta.
|
root:Host-associated:Human:Digestive system
|
MGYS00000429
|
Metagenomics of Spartina anglica phyllosphere
|
Spartina anglica phyllosphere was investigated using metagenomics and metaproteomics in order to investigate bacterial Dimethylsulphide degradation associated with Spartina anglica in more detail. DNA from Spartina anglica phyllosphere was extracted and used for metagenomics using the Nextera XT Kit (Illumina). Sequencing was carried out on the Illumina MiSeq. (2 x 301 bp paired end reads)
|
root:Host-associated:Plants:Phylloplane
|
MGYS00000432
|
Evidence for salt tolerance in the human gut mobilome and potential mechanisms.
|
The human gut microbiome and its associated mobilome is critical to health and wellbeing. It hosts a complex ecosystem comprising a multitude of bacterial species, which contributes functionality that would otherwise be absent from the host. Transient and commensal bacteria in the gut must withstand many stresses. The influence of mobile genetic elements, such as plasmids, in stress adaptation within the ecosystem is relatively unknown. We found evidence for plasmid mediated osmotolerance as a phenotype amongst the Proteobacteria in healthy faecal slurries. A transconjugant carrying multiple plasmids acquired from healthy faecal slurry demonstrated increased osmotolerance in the presence of metal salts, particularly potassium chloride, which was not evident in the recipient. Sequencing and analysis of the total plasmid DNA demonstrated the presence of plasmid-borne osmotolerance systems (including KdpD and H-NS) which may be linked to the observed phenotype. This is the first report of a transferable osmotolerance phenotype in gut commensals and may have implications for the transfer of osmotolerance in other niches.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000434
|
BASE - Biomes of Australian Soil Environments
|
The samples in this study were collected as part of the BASE (Biomes of Australian Soil Environments) project, which is developing a database of Australian soil microbial diversity. The soil ecosystem is critical for ecosystem functioning, affecting human health and food supply, animal and plant health, edaphic factors and climate. The Base project has sampled soils from across a wide range of ecosystem types on the Australian continent and collected both contextual and DNA based data that are publically available and form a base line database of Australian soil microbial biodiversity. More information about BASE can be found at http://www.bioplatforms.com.au/special-initiatives/environment/soil-biodiversity. Collected here is Illumina shotgun sequencing data from these soils.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000436
|
Synthetic community metagenomes study
|
Sequencing was carried out using Illumina MiSeq 2 x250bp sequencing.
|
root:Engineered:Modeled
|
MGYS00000447
|
Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries looking at the ecological communities.
|
Metagenomic sequence data was obtained for multiple sites on three SE Queensland river estuaries (Logan, Maroochydoore and Noosa). The study is looking at the ecological communities in each of these systems, and how they are impacted by pollution and environmental conditions.
|
root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
|
MGYS00000448
|
Elixir marine metagenomics pilot - towards user centric service
|
Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research. The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting. Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms. The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a "user community" for marine metagenomics analysis in ELIXIR
|
root:Environmental:Aquatic:Marine
|
MGYS00000449
|
Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories
|
Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories
|
root:Environmental:Terrestrial:Soil:Forest soil
|
MGYS00000450
|
Enriched Hetertrophic-Methantrophic Cultures from Different Soils (amplicon)
|
The project aimed to develop a robust consortia for oxidizing methane from possible emission sources e.g. coal mine and landfills. Different soil/sediments were collected and enriched under 20% methane atmosphere for more than 100 days and DNA were extracted for metagenomic studies. Methane oxidation potentials of each enrichments were analysed and byproducts were screened. Further testings were on-going using the enriched cultures for biofilter applications to treat continuous emissions of methane from point sources.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000452
|
Metagenomics of a freshwater pond in Sheffield, UK.
|
The microbial community used in the microcosm study was obtained from this pond. The inoculums were subjected to nutrient enrichment studies.
|
root:Environmental:Aquatic:Freshwater:Lentic
|
MGYS00000453
|
Hydrocarbon Metagenomics Project
|
Metagenomics for Greener Production and Extraction of Hydrocarbon Energy:
Creating Opportunities for Enhanced Recovery with Reduced Environmental Impact
|
root:Environmental:Aquatic:Freshwater
|
MGYS00000454
|
Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris
|
Secondary metabolites like pyrrolizidine alkaloids (PAs) act as defense compounds against aboveground and belowground attackers. We studied to get a better understanding of relevance of microbial diversity in the rhizosphere for plant growth and behavior, specifically related to secondary metabolites production. We made soil dilution to compare the composition of soil microbial communities of soil suspension, incubation and rhizosphere soil by 16s rRNA high throughput pyrosequencing, as a consequence, to determine the effects on plant behaviors. The dilution procedure leads to reduction of the diversity of bacteria at the phylum level. After regrown, the structure of microbial community in the rhizosphere changed significantly as compared to the composition in the incubated soil. Jacobeae vulgaris as model plants growing in the soil where microbial diversity were decreased, had a higher biomass and higher amount of free base form of PAs? production, which indicates the reduction of soil microbial community in the rhizosphere shows significant feedback. Our study adds evidence that soil microbes may play a role in the evolution of plant secondary metabolites in plants.
|
root:Host-associated:Plants:Rhizosphere:Soil
|
MGYS00000455
|
Benchmark of metagenome analysis tools
|
A set of complex, realistic data sets were simulated based on real Illumina HiSeq 2000 data (100 bp PE reads). Two "conditions" consisting of 3 replicates each were used to evaluate the performance of a number of metagenome analysis tools.
|
root:Engineered:Modeled:Simulated communities (sequence read mixture)
|
MGYS00000456
|
Comparison of distal gut microbiota structure and function in US and Egyptian children
|
Cultural traditions, diet, and lifestyles of ethnic groups living in different geographic locations can serve as a source of variability in human gut microbiota. To examine the differences in gut microbiome of geographically distinct populations, we have carried out phylogenetic, functional, and metabolite analyses of the distal gut microbiota of healthy adolescents from United States and Egypt using next generation high-throughput sequencing.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000464
|
Denovo test of eDNA sample
|
In this study we are going to establish the analyses of eDNA from sea water to identify macrofauna species from the North Sea.Instead of targeting single genes of taxa, we aim to sequence total DNA extracts. As a consequence, we expect to catch more diversity and to reduce the loss of information caused by unregularly binding of group specific primers.
|
root:Environmental:Aquatic:Marine
|
MGYS00000465
|
The fecal microbiome was studied in a group of IBD suffers and compared to a control group's fecal microbiome
|
Ten IBD and 10 healthy individual's fecal microbiomes were determined by NGS sequencing, to identify features that are unique to each group. This was done using shot-gun metagenomics of DNA extracted from fecal samples and run on a HiSeq 2500.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000466
|
Metagenomic exploration of Lasundra hot spring
|
Geothermal areas are the main permanent hot places of the world, and these areas are the major habitats of thermophilic bacteria. In culture independent method, metagenome was isolated using manual and kit based methods. The short gun sequencing of metagenome was performed using Ion torrent PGM platform. The analysis of sequencing data revealed that this spring is dominated by bacterial taxa. MG-RAST based community analysis showed that bacteria were found in dominancy with 99.2% in domain hit distribution. Firmicutes were found to be dominant in domain hit classification followed by proteobacteria. Moreover, unclassified sequences also found in this metagenome indicate there are possibilities of getting novel organisms.
|
root:Environmental:Aquatic:Thermal springs
|
MGYS00000467
|
A human gut microbial gene catalog established by deep metagenomic sequencing (MetaHIT)
|
A human gut microbial gene catalog established by deep metagenomic sequencing
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000468
|
Reseq_Jan15 - Eukaryotic mRNA from 1 year old litter in beech forest of the German Exploratories
|
Reseq_Jan15 - Metatranscriptommic study of eukyryotic microbial activity in 1 year old litter in beech forest of the German Exploratories
|
root:Environmental:Terrestrial:Soil:Forest soil
|
MGYS00000470
|
Metagenomes of hydrogen producing, xylan fed termites
|
Metagenome study with samples from the guts of termites (Nasutitermes exitiosus sp). The termites had xylan as their only carbon source and were raised at temperatures of 33, 40 and 45 degrees respectively while producing highly concentrated hydrogen.
|
root:Host-associated:Arthropoda:Digestive system:Gut
|
MGYS00000476
|
Lacto broiler1d
|
To study the effect of feed additives on caecum microbiome
|
root:Host-associated:Birds:Digestive system:Ceca
|
MGYS00000477
|
Microbial life in geothermal and volcanic areas
|
Extreme environments, such as volcanic/geothermal areas, are sites of complex interactions between geosphere and biosphere. Although biotic and abiotic components are strictly related, they were separately studied for long time. , Nowadays, innovative and interdisciplinary approaches are available to explore microbial life thriving in these environments. Pantelleria island (Italy) hosts a high enthalpy geothermal system characterized by high CH4 and low H2S fluxes. Two selected sites, FAV1 and FAV2, located at the main exhalative area of the island Favara Grande, show similar physical conditions with a surface temperature close to 60?C and a soil gas composition enriched in CH4, H2 and CO2. FAV1 soil is characterized by harsher conditions (pH 3.4 and 12% of H2O content); conversely, milder conditions were recorded at site FAV2 (pH 5.8 and 4% of H2O content). High methanotrophic activity (59.2 nmol g?1 h?1) and wide diversity of methanotrophic bacteria were preliminary detected at FAV2, while no activity could be detected at FAV1(1). Our aim was to investigate how the soil microbial communities of these two close geothermal sites at Pantelleria respond to different geochemical conditions. Bacterial and Archaeal communities of the sites were investigated by MiSeq Illumina sequencing of hypervariable regions of the 16S rRNA gene. More than 33,000 reads were obtained for Bacteria and Archaea from soil samples of the two sites. At FAV1 99% of the bacterial sequences were assigned to four main phyla (Proteobacteria, Firmicutes, Actinobacteria and Chloroflexi). FAV2 sequences were distributed in the same phyla with the exception of Chloroflexi that were represented below 1%. Results indicate a high abundance of thermo-acidophilic chemolithotrophs in site FAV1 dominated by Acidithiobacillus ferrooxidans (25%), Nitrosococcus halophilus (10%), Alicyclobacillus spp. (7%) and the rare species Ktedonobacter racemifer (11%). The bacterial community at FAV2 soil is dominated by the methanotrophs (~40% of the reads) Methylocaldum gracile, Beijerinckia sp. and Methylobacterium sp.. The Archaea assemblages are similar in both sites and dominated by the moderately thermophilic chemolithotrophic ammonia-oxidating candidate species Nitrososphaera gargensis, in the phylum Thaumarchaeota. Volcanic/geothermal activities represent a complex phenomenon, thuis shapeing different and peculiar microbial niches even at adjacent sites. Lower pH, higher water, NH4+ and H2 content are probably the discriminating factors that prevent methanotrophy at FAV1 and favor chemolithotrophy. Site FAV2 hosts an extraordinary diversity of methanotrophs due to large supply of CH4, scarce presence of inhibitors of methanotrophy (H2S and NH3) and slightly acidic soil pH. This study integrates geochemical and biological information to move a step ahead in the still scarce knowledge on the complex ecology of microbes living in geothermal sites and their interactions with the geosphere. (Oppure: This study integrates geochemical and biological information to move a step forward a more complete knowledge on the complex ecology of microbes living in geothermal sites and their interactions with the geosphere)
|
root:Environmental:Terrestrial:Volcanic
|
MGYS00000479
|
Synthetic community metagenomes
|
Library methods comparison across illumina GAII, HiSeq, MiSeq using a synthetic community.
Four libraries methodology Nextera, NexteraXT, TruSeq, Low input have been used in this study
|
root:Engineered:Modeled:Simulated communities (microbial mixture)
|
MGYS00000480
|
Understanding the carriage dynamics of nasopharyngeal microbiota in Malawian children and adults: a metagenomic analysis.
|
This study was part of a project investigating the nasopharyngeal carriage of streptococcus pneumoniae in Malawian children and adults by microarray. Because the nasopharynx is colonised by several other microorganisms, we decided to investigate whether pneumococcal carriage dynamics was associated with carriage of particular microbial species. We collected nasopharyngeal swabs from children (n=51) aged 0-15 years and adults (n=55), all carriers of Streptococcus pnumoniae. DNA was extracted directly from the samples, followed by a PCR amplification of the 16S rRNA gene. The 16S amplicons were sequenced by 454 pyrosequencing.
|
root:Host-associated:Human
|
MGYS00000482
|
Elixir marine metagenomics pilot - towards user centric service - Gut samples
|
Marine genomics and metagenomics (the study of genetic material recovered directly from marine environmental samples) are still in its infancy, but it is rapidly expanding. To prevent the large-scale implementation of such studies from being disruptive (where the data production is faster than the speed users are able to analyze and interpret it) there is an urgent need to establish dedicated data management e-infrastructure and bioinformatics pipelines specialized for marine research. The EBI metagenomics portal has for the last year analyzed 3 trillion nucleotides and an increase of 98% over the previous year. To address some of these challenges the Norwegian node suggests establishing a pilot towards marine metagenomics together with EBI and potentially other collaboration partners as a start for marine services. While EBI has developed the EBI-metagenomics portal, a generic pipeline, which aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of the samples, the Norwegian node has developed Meta-pipe in the direction coupled with marine bioprospecting. Both approaches have their own strengths and weakness, and while there is some overlap in the respective approaches, it is clear that the optimal solution for the community would be harmonization and interoperability between the analysis platforms. The Norwegian node together with EBI and potentially other partners will harmonize existing pipelines and develop new or improve established components in the pipelines in order to establish long-term sustainable service platforms and not least to start building a "user community" for marine metagenomics analysis in ELIXIR
|
root:Host-associated
|
MGYS00000484
|
Marine metagenomes from 3 sediment samples along a pH gradient in Papua New Guinea
|
Sediment microbial communities are key players in biogeochemical cycling and the remineralization of organic matter on tropical reefs. To better understand the long-term effects of low pH conditions on sediment microbial communities, microbial diversity and community composition were investigated at naturally CO2-rich tropical coral reefs in Papua New Guinea. Metagenomic and metatranscriptomic analyses will reveal insights into the response of sediment microbial communities and their functions to low pH environments.
|
root:Environmental:Aquatic:Marine:Sediment
|
MGYS00000486
|
Controlling enteric pathogens of poultry
|
There is rich genetic diversity in India?s native poultry breeds, and the hybrid exotic lines often used in Indian commercial production are distinct from the majority of poultry reared in the UK. The prevalence and dynamics of gastrointestinal infection at farm-level has a direct bearing on economic risk to individual farmers and contributes to overall global concerns of food security and food safety.Changes to diet, use of vaccines or antimicrobials, and flock-level interventions such as ?thinning?, can have profound effects on intestinal health and the evolution and spread of disease-causing microbes and may be amplified by genetic variation in host and microbe populations. Whilst major advances in genomics and genotyping of commercial poultry lines is facilitating the identification of loci linked to susceptibility or resistance, the impact of host and pathogen diversity on disease and production outcomes remains largely unexplored.
|
root:Host-associated:Birds:Digestive system:Ceca
|
MGYS00000488
|
metageomics 16S analysis
|
A metagenomics analysis and taxonomy 16S RNA
|
root:Environmental
|
MGYS00000494
|
Anopheles_Genome_Variation_Project
|
For information on this project, contributing investigators and studies, sample details, and data sharing policies please visit http://www.malariagen.net/node/287
|
root:Host-associated:Insecta
|
MGYS00000499
|
The comparison of gut microbiota obtained from centenarian, elderly, and adults living in southwestern longevity belt in Korea
|
Centenarians have lived for long ages and survived from various death causing factors. Several studies were analyzed the factors of health maintaining in centenarians, while the longevity factors are not completely understood. Recent analyses of gut microbiota have been reported the association of microbiota with health, and some studies were reported the alteration of gut microbiota with aging. In this study, we analyzed the gut microbiota of centenarians in particular regions of Korea to understand their longevity factors. The gut microbiota of centenarians (n=30) was compared with elderly (n=17) and adults (n=9) using pyrosequencing based on 16S rRNA gene. The relative abundance of Bacteroidetes was decreased, while those of Firmicutes and Proteobacteria were increased with aging. However, the proportion of Bacteroidetes was higher in centenarians than elderly subjects. The difference of gut microbiota composition between centenarians and elderly could be generated by diet patterns. Although additional studies such as functional analyses of microbiota between groups were need to understand, this study can provide the information of longevity factors of centenarians.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000500
|
Changes imposed by Clostridium difficile infection on the human gut microbiome
|
Clostridium difficile-associated diarrhoea (CDAD) is caused by C. difficile toxins A and B and represents a serious health problem. In this study, we analyzed the metabolic changes associated to C. difficile infection in the human gut microbiota and its relation with the production or not of toxins A and B. In addition, we sequenced the amplicons of the 16SrDNA gene of the fecal samples to explore the effect of Clostridium difficile infection and toxin production on the intestinal microbial composition.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000502
|
Gut microbial succession follows acute secretory diarrhea in humans
|
Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these communities respond to diarrheal disease and its treatment. Here, we report that after V. cholerae infection, human gut microbiota undergo an orderly and reproducible succession featuring transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest multiple mechanisms driving microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure, but driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.
|
root:Host-associated:Human:Digestive system
|
MGYS00000503
|
Axial Seamount Marker 113 RNA-SIP metatranscriptomes from 2013
|
Hydrothermal vent systems provide access points to the extensive microbial communities of the rocky subseafloor. These subseafloor communities have the potential to influence ocean biogeochemistry and, in particular, the chemolithoautotrophic populations could potentially provide a large amount of new production to the deep sea. In this study, we used RNA-based stable isotope probing (RNA-SIP) metatranscriptomics to identify the active autotrophic players and genomic pathways present in venting fluids from Axial Seamount, a submarine volcano off the coast of Oregon, USA. Vent fluids for RNA-SIP were collected from a singular vent, Marker 113, and used in shipboard incubations with 13C labeled sodium bicarbonate at 30, 55, and 80?C. Results from RNA-SIP incubations show enrichment of RNA at all three temperatures after 18-36 hours, indicating the presence and activity of subseafloor chemolithoautotrophic microbes in vent fluids. In RNA-SIP experiments across a range of temperatures, both taxonomic and functional diversity was reduced compared to un-manipulated diffuse fluids. At 30?C and 55?C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55?C, and were the only autotrophs present at 80?C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive TCA cycle to the reductive acetyl-CoA pathway with increasing temperature. This study demonstrates the presence of an active autotrophic subseafloor community across geothermal gradients, lending insight into chemolithoautotrophic communities in the subseafloor at deep-sea hydrothermal vents
|
root:Environmental:Aquatic:Marine:Hydrothermal vents
|
MGYS00000504
|
Metagenome analysis of Amlakhadi canal
|
Gauging the innate microbial community prevailing in Amlakhadi Canal, Ankleshwar
|
root:Environmental:Aquatic:Freshwater
|
MGYS00000505
|
Defining the core Arabidopsis thaliana root microbiome
|
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root), and the endophytic compartment (within the root), contribute to plant growth, productivity, carbon sequestration, and phytoremediation1,2,3. Colonization of the root occurs despite a sophisticated plant immune system4,5, suggesting finely-tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. We pyrosequenced the bacterial 16S rRNA gene of >600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophyte compartment microbiota of plants grown under controlled conditions in natural soils are (i) sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and (ii) sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils, and in rhizosphere and endophyte compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophyte compartments from either soil feature overlapping low-complexity communities that are markedly enriched for Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stages and genotypes. Our work provides unprecedented rigor to define an endophyte compartment microbiome, facilitating controlled dissection of plant-microbe interactions derived from complex soil communities.
|
root:Host-associated:Plants
|
MGYS00000506
|
Pooled sample of human tongue scrapes from 9 healthy adults.
|
Human tongue scrapes were taken from 9 healthy adults at University College London, metagenomic DNA extracted and sequenced using 454 technology.
|
root:Host-associated:Human:Digestive system:Oral:tongue dorsum
|
MGYS00000507
|
Tongue metagenome from 9 healthy individuals.
|
Tongue scrapes were collected from 9 healthy individuals over a period of 3 or 4 weeks, total DNA was extracted, pooled and sequenced.
|
root:Host-associated:Human:Digestive system:Oral
|
MGYS00000508
|
Drain metagenome.
|
Hair blocking drain was removed from a bathroom shower cubicle. Liquid surrounding the hair and hair were used for the total dna extraction.
|
root:Environmental:Aquatic:Freshwater:Storm water:Drainage pipe biofilm
|
MGYS00000509
|
Soil sample taken from wild flower meadow for metagenome study.
|
Soil sample taken from wild flower meadow in Danesbury Park, Hertfordshire.
|
root:Environmental:Terrestrial:Soil:Grasslands
|
MGYS00000510
|
Study of the bacterial and fungal diversity in soil habitats with increased ligninocellulolytic activity
|
This study aims at the metagenomic analysis of ligninocellulose-degrading microbial communities of Mediterranean forest soils. For this purpose, two soil ecosystems with distinct ecophysiological characteristics were selected, and thorough spatio-seasonal sampling was undertaken. Total DNA was extracted from 48 soil samples, and PCR amplification was performed with both 16S (V3-V4) region- and ITS2-specific universal primers for the analysis of bacterial and fungal diversity, respectively. High-throughput amplicon sequencing was performed with the Illumina MiSeq technology.
|
root:Environmental:Terrestrial:Soil:Forest soil
|
MGYS00000511
|
Coupled metagenomic and metatransciptomic study of the Columbia River coastal margin salinity gradient
|
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel shift in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 ?m filters and collected on 0.2 ?m filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, were an average of only 31% similar. We observed shifts from river to ocean in the abundance of genes encoding specific functions, such as catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were highly abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community shifted strongly with salinity, 2) metabolic potential was highly similar across samples, with only small differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.
|
root:Environmental:Aquatic:Marine:Coastal
|
MGYS00000512
|
Rumen Virome metagenome sequencing
|
The present study was carried out to explore the ruminal viruses and phages from buffalo
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000513
|
Use of plant growth promoting rhizobacteria on the production of lettuce
|
Analysis of the effect of different plant growth promoting rhizobacteria on the production of lettuce plants.
|
root:Host-associated:Plants:Rhizosphere:Soil
|
MGYS00000514
|
Metagenomic approach to Analyze Rumen Microbiome from Gir Cows
|
Gir cows were fed with different diet and investigated rumen microbiome using shotgun sequencing on Ion-torrent platform
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000515
|
Metagenomic profiling through 16S rRNA deep sequencing of mice strains
|
Comparative analysis of microbiomes from stools obtained from WT and genetically engineered mice, subjected to normal or high-fat content diet
|
root:Host-associated:Mammals:Gastrointestinal tract:Intestine:Fecal
|
MGYS00000516
|
The role of biogeography in shaping diversity of the intestinal microbiota in house mice
|
The microbial communities inhabiting the mammalian intestinal tract play an important role in diverse aspects of host biology. However, little is known regarding the forces shaping variation in these communities and their influence on host fitness. To shed light on the contributions of host genetics, transmission and geography to diversity in microbial communities between individuals, we performed a survey of intestinal microbial communities in a panel of 121 house mice derived from eight locations across western Europe using pyrosequencing of the bacterial 16S rRNA gene. The host factors studied included population structure estimated by microsatellite loci and mitochondrial DNA, genetic distance and geography. To determine whether host tissue (mucosa)-associated communities display properties distinct from those of the lumen, both the cecal mucosa and contents were examined. We identified Bacteroides, Robinsoniella and Helicobacter as the most abundant genera in both the cecal content and mucosa-associated communities of wild house mice. Overall we found geography to be the most significant factor explaining patterns of diversity in the intestinal microbiota, with a comparatively weaker influence of host population structure and genetic distance. Furthermore, the influence of host genetic distance was limited to the mucosa communities, consistent with this environment being more intimately coupled to the host.
|
root:Host-associated:Mammals:Digestive system:Large intestine:Cecum
|
MGYS00000517
|
Gene-targeted metagenomic analysis of 1-4-?-glucan branching enzyme gene profiles among human and animal fecal microbiota
|
Organismal and functional aspects of the gut microbiota are of great interest in human microbiome studies. Although 16S rRNA gene sequence-based phylogenetic and whole-genome shotgun (WGS) data analysis are frequently used for assessment of genetic diversity, these techniques pose biological challenges for in-depth understanding of metabolic genes related to the gut microbiota. Phylogenetic analyses of 16S rRNA gene sequences provide limited information on their involvement in metabolic pathways. WGS data provide useful information on metabolic functions; however, this technique generates a large amount of data unrelated to the gene of interest at a high cost. In this study, we employed a metagenomic approach targeting the 1-4-?-glucan branching enzyme (gBE) gene of four host species (chicken, cow, pig, and human). Glycoside hydrolases (GHs) are key enzymes associated with the gut microbiota and its metabolic functions. The gBE gene, belonging to GH family 13, is responsible for glycogen branching and determines its solubility and subsequent catabolic metabolism. In addition to 16S rRNA gene-based phylogenetic analyses, an average of 1,200 reads of gBE were generated from fecal microbiota samples from human (n = 16), chicken (n = 18), cow (n = 15) and pig (n = 20). Each of the hosts showed distinct 16S rRNA and gBE sequence profiles. Human and pig exhibited both unique and common characteristics of operational taxonomic units (OTUs) and gBE profiles. Interestingly, the OTUs identified from the 16S rRNA and gBE gene sequences differed among the host species, suggesting the presence of different gBE genes in the same OTU in 16S rRNA sequences of different vertebrate hosts. Our data suggest that gene-targeted metagenomic analysis is useful for an in-depth understanding of the diversity of a particular gene of interest. Moreover, specific OTUs in the gut may contain metabolic genes the characteristics of which differ according to host genetic background and/or diet.
|
root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
|
MGYS00000518
|
These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015
|
These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015
|
root:Host-associated:Human:Skin
|
MGYS00000519
|
Study of microbial consortia of withered berries of cv. Corvina using whole metagenome sequencing approach
|
A whole metagenome sequencing approach was carried out, aiming at the taxonomic identification of the microbial components of berry ecosystem and to unveil whether the variations of environmental withering conditions could lead to significant modifications of microbial consortia and metabolic pathways on grape berries.
|
root:Host-associated:Plants
|
MGYS00000521
|
The Effect of Propidium Monoazide Treatment on Identification of Bacterial Communities of Very Low Birth Weight Preterm Infant Faeces Analysed by 16s rRNA Gene Sequencing
|
Next-gen sequencing technology had provided a platform for rapid advancement in the field of microbial ecology. The 11 original bacterial phyla, identified by Woese, have been expanded to over 50 following widespread use of NGS techniques. However, NGS is not without it?s flaws. This study will attempt to improve the validity of the NGS protocol by validating the use of propidium monoazide: a dsDNA chelating agent; for non-viable cell exclusion from clinical samples. This will enable researchers and clinicians to identify bacterial phyla actively affecting the biotopes of the preterm infant gut and tailor targeted therapy accordingly.
|
root:Host-associated:Human:Digestive system:Large intestine:Fecal
|
MGYS00000523
|
Metagenomics of TB-associated sputum
|
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instru- ment, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of ?modern? M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence- based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplifica- tion steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
|
root:Host-associated:Human:Respiratory system:Pulmonary system:Lung
|
MGYS00000525
|
Influence of soil properties on Archaeal diversity and distribution in the McMurdo Dry Valleys, Antarctica
|
Archaea are the least studied members of the microbial community in Antarctic soils. Their occurrence in coastal mineral soils has been documented, however, less is known about their distribution in soils across the McMurdo Dry Valleys, Victoria Land. In this study, terminal-restriction fragment length polymorphism (T?RFLP) analysis and 454 pyrosequencing were coupled with a detailed analysis of physicochemical properties to characterize archaeal diversity and identify the environmental factors that might shape and maintain these archaeal communities in soils of the three most southern McMurdo Dry Valleys (Garwood, Marshall, Miers). Archaea were present, although at a low diversity (< 6 operational taxonomic units (OTUs) per sample site) in all mineral soils tested. In total, eighteen archaeal OTUs were detected which showed a predominance of Crenarchaeota belonging to Marine Group 1.1b (>?80% of all archaeal sequences recovered). Less abundant OTUs (2% of all archaeal sequences) were restricted to glacial moraines, including three OTUs (<?0.02% of all archaeal sequences) closely related to members of the phylum Euryarchaeota. Multivariate statistical analysis, ordination of T?RFLP and physicochemical data indicated that differences in moisture, carbon and nitrogen content in the soils have the greatest influence on archaeal community structure. This is the first comprehensive study showing a widespread distribution of Archaea in soils of the McMurdo Dry Valleys and verifies the worldwide distribution of Marine Group 1.1b Crenarchaeota.
|
root:Environmental:Terrestrial:Soil:Wetlands:Permafrost
|
MGYS00000528
|
Soil metagenome.
|
SoilB soil sample was collected on a rough grass terrain with the trees nearby in Danesbury Park in Hertforshire, UK.
|
root:Environmental:Terrestrial:Soil:Grasslands
|
MGYS00000529
|
Permafrost 454 amplicons
|
Study of microbial communities in permafrost, active layer and thermokarst bog in Alaska
|
root:Environmental:Terrestrial:Soil:Permafrost
|
MGYS00000531
|
different diet treatments
|
Mice of 2 genotypes followed 2 different diets.
|
root:Host-associated:Mammals:Digestive system:Fecal
|
MGYS00000532
|
Does dietary mitigation of enteric methane production affect rumen function and animal productivity in dairy cows?
|
It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000533
|
Trans-kingdom control of microbiota diurnal oscillations promotes metabolic homeostasis
|
All domains of life feature diverse molecular clock machineries that synchronize physiological processes to diurnal environmental fluctuations. However, no mechanisms are known to cross-regulate prokaryotic and eukaryotic circadian rhythms in multi-kingdom ecosystems. Here, we show that the intestinal microbiota, in both mice and humans, exhibits diurnal oscillations that are influenced by feeding rhythms, leading to time-specific compositional and functional profiles over the course of a day. Ablation of host molecular clock components or induction of jet lag leads to aberrant microbiota diurnal fluctuations and dysbiosis, driven by impaired feeding rhythmicity. Consequently, jet lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation. Together, these findings provide the first evidence of coordinated meta-organism diurnal rhythmicity, and offer a microbiome-dependent mechanism for common metabolic disturbances in humans with aberrant circadian rhythms, such as those documented in shift workers and frequent flyers.
|
root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
|
MGYS00000535
|
Study on the microbial community of a bioleaching column test
|
Study on the microbial community related to de bioleaching processes of copper sulfide ore.
|
root:Engineered:Biotransformation
|
MGYS00000536
|
The 2014 and 2015 International Geobiology Courses took place at Little Hot Creek (LHC), California. The data shown here represents an attempt to gather information from a number of sources at LHC.
|
Samples were collected from a series of hot springs at the headwaters of Little Hot Creek located in the Long Valley Caldera near Mammoth Lake, CA. The springs are supersaturated for carbonate, circumneutral in pH, and range from a temperature of 50? to 80? C. Genomic DNA was isolated from biofilms and water filtered through a PES 0.22?m 13mm filter using the Zymo Xpedition Soil/Fecal kit (Zymo Research Corp., Irvine, CA). Sequencing was conducted using either MiSeq PE250, PE300, or HiSeq Rapid PE250. MiSeq runs were prepared using the Agilent SureSelect kit (Agilent Technologies, Irvine, CA) with an approximate insert size of 400bp, and HiSeq PE250 samples were prepared using the Nextera XT library preparation kit (Illumina, San Diego, CA).
|
root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
|
MGYS00000537
|
In this study we describe some of the challenges of clinical metagenomics through benchtop sequencing of two distinct sample types, designed to highlight current application and opportunities in this field.
|
Availability of fast, high throughput and low cost whole genome sequencing (WGS) holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events, to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. In this study we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological mode using benchtop technology, highlighting the current challenges and opportunities in this field.
|
root:Engineered:Modeled:Simulated communities (microbial mixture)
|
MGYS00000538
|
Analysis of the goat rumen microbial community following inhibition of methane formation by bromochloromethane (a halogenated methane analogue)
|
Japanese goats fed a diet of 50% Timothy grass and 50% concentrate with increasing levels of the anti-methanogenic compound, bromochloromethane (BCM) were investigated with respect to the microbial population shifts in the rumen. Microbial ecology methods identified species that exhibited positive and negative responses to the increasing levels of BCM. The methane-inhibited rumen appeared to adapt to the higher H2 levels by shifting fermentation to propionate which was mediated by an increase in the population of hydrogen-consuming Prevotella and Selenomonas spp.
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000539
|
Diesel contamination of Antarctic soils and sediments
|
Hydrocarbon contamination is a threat resulting from human activity in Antarctica because of the low degradation rate due to the cold climate conditions and the seasonal freezing and thawing of soil in summer ice-free areas like the Antarctic Peninsula. Hydrocarbons can accidentally reach soil and sediments and distribute underground, likely affecting the biota and causing changes in bacterial communities. Monitoring and study of the distribution of hydrocarbons and the consequent response of the microbiota helps in the design of bioremediation strategies and elaboration of contingency plans, both required by the Antarcic Treaty.
|
root:Environmental:Terrestrial:Soil:Contaminated
|
MGYS00000540
|
The RNA metagenomes of Argentine ants (Linepithema humile) collected in New Zealand.
|
Argentine ants were collected from two nests located in Wellington, New Zealand. RNA was extracted from a pool of 30 ants collected from each of these nests. All RNA was then combined and subjected to de novo metagenomic analysis, using an Illumina MiSeq instrument. Multiple displacement amplification was used to increase the yield of transcribed DNA to meet the minimum input requirements of the Illumina MiSeq. The Illumina TruSeq DNA library preparation was used to prepare libraries, and produce 250 bp paired end reads.
|
root:Host-associated:Arthropoda
|
MGYS00000542
|
Assimilation of C by microbial populations in glacial forefields
|
Microbial communities and soil carbon (C) have been shown to vary in response to increasing vegetation cover during soil development after deglaciation. However, little is known about the ability of microorganisms to utilize various C sources in glacier forefield soils. We supplied ecologically relevant 13C-labelled C sources (Chlorella, Penicillium and Festuca) to three distinct environments (supraglacial sediments, barren soils and vegetated soils) of the Damma glacier area to monitor 13CO2 production. We identified prokaryotic and fungal populations able to utilize these sources by using DNA-stable isotope probing coupled with Illumina MiSeq sequencing of ribosomal markers. A high initial 13CO2 pulse indicated that 13C-labelled microbial and plant material were consumed. The 13C-enriched DNA results indicated that betaproteobacterial taxa affiliated to the families Oxalobacteraceae and Comamonadaceae were important players in C utilization from different sources and present in all environments. In contrast, different fungal taxa played different roles in C degradation depending on the soil environment. Overall, our findings reveal that C utilization is driven by similar prokaryotic populations along a glacier forefield, while the distribution of active fungal populations are more influenced by environmental factors.
|
root:Environmental:Terrestrial:Soil
|
MGYS00000544
|
Does dietary mitigation of enteric methane production affect rumen function and animal productivity in dairy cows?
|
It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000566
|
Effect and mode of action of chitosan and ivy fruit saponins on the microbiota, fermentation and methanogenesis in the rumen simulation technique
|
Manipulation of the rumen microbial ecosystem to increase the efficiency of nutrient use by the animal, or to decrease its environmental impact, has long been a goal for nutritionists and gut microbiologist. This paper investigates the effect and mode of action of chitosan (CHI) and ivy fruit saponins (IVY) when used as novel feed additives for ruminants. These compounds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation technique. Both, CHI and IVY had a strong and similar ability to decrease methane emissions in comparison to CON (-42% and -40%, respectively). The mode of action of these feed avidities was however remarkably different: CHI promoted a shift in the fermentation pattern towards more energetically favourable pathways (propionate) which explained about two thirds of the decrease in rumen methanogenesis. This shift was achieved by a simplification and modification of the structure in the bacterial community consisting on an increment of Bacteroidetes and Proteobacteria in detriment of Firmicutes and Fibrobacteres. This substitution of fibrolytic bacteria by amylolitic bacteria induced by CHI resulted on a 2.5-fold increase in the amylase enzymatic activity, lactate concentration (+53%) and microbial protein yield (+14%) with no detrimental effect on feed digestibility. Additionally, CHI decreased the relative abundance of methanogens respect to total bacteria which could also contribute to lower rumen methanogenesis. On the contrary, IVY promoted only minor changes on the fermentation pattern and on the structure of the bacterial community which explained only one third of the observed decrease in rumen methanogenesis. Instead, IVY had a specific effect on the methanogens population. This effect consisted on a change in the structure of the methanogens community and a decrease in its diversity. This specific effect, together with the anti-protozoal activity, can be thus considered the main anti-methanogenic property for IVY. Moreover IVY showed to have some beneficial effect to buffer the post-prandial drop in rumen pH and to decrease rumen ammonia levels (-61%), but its anti-microbial properties had a negative impact on microbial protein synthesis (-10%). Therefore, both CHI and IVY should be further investigated in vivo in order to determine the optimum doses which maintain low rumen methanogenesis but prevent negative effects on the rumen microbial ecosystem.
|
root:Host-associated:Mammals:Digestive system:Stomach:Rumen
|
MGYS00000567
|
Effect and mode of action of chitosan and ivy fruit saponins on the microbiota, fermentation and methanogenesis in the rumen simulation technique
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Manipulation of the rumen microbial ecosystem to increase the efficiency of nutrient use by the animal, or to decrease its environmental impact, has long been a goal for nutritionists and gut microbiologist. This paper investigates the effect and mode of action of chitosan (CHI) and ivy fruit saponins (IVY) when used as novel feed additives for ruminants. These compounds were supplemented at 5% inclusion rate into a control diet (CON) in a rumen simulation technique. Both, CHI and IVY had a strong and similar ability to decrease methane emissions in comparison to CON (-42% and -40%, respectively). The mode of action of these feed avidities was however remarkably different: CHI promoted a shift in the fermentation pattern towards more energetically favourable pathways (propionate) which explained about two thirds of the decrease in rumen methanogenesis. This shift was achieved by a simplification and modification of the structure in the bacterial community consisting on an increment of Bacteroidetes and Proteobacteria in detriment of Firmicutes and Fibrobacteres. This substitution of fibrolytic bacteria by amylolitic bacteria induced by CHI resulted on a 2.5-fold increase in the amylase enzymatic activity, lactate concentration (+53%) and microbial protein yield (+14%) with no detrimental effect on feed digestibility. Additionally, CHI decreased the relative abundance of methanogens respect to total bacteria which could also contribute to lower rumen methanogenesis. On the contrary, IVY promoted only minor changes on the fermentation pattern and on the structure of the bacterial community which explained only one third of the observed decrease in rumen methanogenesis. Instead, IVY had a specific effect on the methanogens population. This effect consisted on a change in the structure of the methanogens community and a decrease in its diversity. This specific effect, together with the anti-protozoal activity, can be thus considered the main anti-methanogenic property for IVY. Moreover IVY showed to have some beneficial effect to buffer the post-prandial drop in rumen pH and to decrease rumen ammonia levels (-61%), but its anti-microbial properties had a negative impact on microbial protein synthesis (-10%). Therefore, both CHI and IVY should be further investigated in vivo in order to determine the optimum doses which maintain low rumen methanogenesis but prevent negative effects on the rumen microbial ecosystem.
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root:Host-associated:Mammals:Digestive system:Stomach:Rumen
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MGYS00000579
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Brain meta-transcriptomics from harbor seals to infer the role of the microbiome and virome in a stranding event
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Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have?applied this technique in marine systems.?In 2009 seven harbor seals,?Phoca vitulina,?stranded along the California coast from a similar brain disease of?unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified?Burkholderia?and?Coxiella burnetii?as important pathogens associated with this stranding event.?Burkholderia?were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while?C. burnetii?was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, C. burnetii?showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that?Burkholderia?taxa and?C. burnetii?are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.
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root:Host-associated:Mammals:Nervous system:Brain
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MGYS00000583
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The oral microbiome in HIV infected individuals
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The aim of this project was to compare the oral microbiome of HIV-infected individuals to that of age- and gender-matched HIV-negative individuals. A 16S rRNA gene sequencing approach by means of a Roche GS-FLX+ sequencer was used to characterise the bacterial communities of plaque and saliva from each of the study participants.The oral microbiomes of HIV-positive and -negative individuals were found to be similar overall, although there were minor but significant differences in the composition of the salivary microbiota of the two groups. In addition, the results confirmed that plaque and saliva have a differing bacterial composition.
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root:Host-associated:Human:Digestive system:Oral
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