AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceHealth CareGeographicals
MetagenomicsMetagenomePhylogenySequence Analysis, DNAEnvironmental MicrobiologyBacteriaBiodiversityGenetic VariationGenomicsBiotaGastrointestinal TractChenopodium ambrosioidesMicrobial ConsortiaRNA, Ribosomal, 16SOceans and SeasSeawaterGenome, BacterialMicrobiotaEcosystemMolecular Sequence DataCluster AnalysisArchaeaComputational BiologyDNA VirusesSoftwareProteobacteriaEcologyVirusesCircoviridaeSoil MicrobiologyFusobacteriaLakesMarine BiologyAquatic OrganismsDatabases, GeneticMethylophilaceaeAlgorithmsGene LibraryHeterotrophic ProcessesGenetics, MicrobialBiotechnologyHigh-Throughput Nucleotide SequencingGenome, ViralWater MicrobiologyDNA, BacterialBase SequenceActinobacteriaGenomeSequence AlignmentRNA, ArchaealEvolution, MolecularGeologic SedimentsHot SpringsGenome, ArchaealEnvironmentGenes, ArchaealCultural DiversityDNA, RibosomalGenes, BacterialEukaryotaPolymerase Chain ReactionInternetGenes, rRNAGeographyEnzymesBacteriophagesSequence Homology, Nucleic AcidMolecular Sequence AnnotationPrincipal Component Analysis
GenomicsMicrobiomeDevelop a metagenomicsGenetic diversityAmplicon basedHigh-throughputMolecularGenomeGenomesBacteriaGeneticsShotgun2021GenomicBenthicMicrobesAbundanceBacterial diversityEnvironmentsPathogensDetectionTaxonomicAnalysisVirusesApproachesInfectiousEnables2020RhizosphereMechanismsSequencesSoilAnalysesHttpsHabitatsNewlyAssessDataSamplesStudyComplexityPublicCommunitiesStrainDiverseProcessIdentify
Genomics3
  • I employ a range of meta-omics approaches including: meta-barcoding of microbiomes to assess microbial diversity coupled with the use of comparative meta-genomics and meta-transcriptomics in the frame of interdisciplinary and integrated research projects to link structural and functional diversity of microbes with diversity and community composition of plant communities. (ufz.de)
  • Our main projects revolve around population, medical, and evolutionary genomics, as well as metagenomics. (lu.se)
  • As part of the Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium of over 100 cities worldwide, we collaborate with experts across many fields, including genomics, data analysis, engineering, public health, and architecture. (lu.se)
Microbiome6
  • According to the authors, this provides a more comprehensive view of skin microbiome diversity (at least, for samples obtained in North America). (cosmeticsandtoiletries.com)
  • In fact, the booming field of metagenomics - the study of genomic sequences - is using big data to help scientists better understand new and vast unexplored regions of the natural world: the microbiome. (stamen.com)
  • In the short term, we'll see pay-off from studies of the human gut microbiome - from a broader understanding of the total diversity of microbes in our gastrointestineal (GI) tract. (ubc.ca)
  • This research is the first non-culture-based study to analyse the similarities and dissimilarities of the faecal microbiome by using 16S amplicon based metagenomics coupled with NGS (next generation sequencing) in different Swedish breeds of sheep and goat (outgroup). (slu.se)
  • We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. (cdc.gov)
  • The colonic microbiome view is controversial, some people Metagenomics of the Human Intes- is the most diverse and also the best consider the gut microbiota to be tinal Tract (MetaHIT) consortium re- characterized microbial community. (who.int)
Develop a metagenomics2
  • In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. (biomedcentral.com)
  • The student would further develop a metagenomics pipeline to compare abundance of different microbial symbionts between larvae feeding on their preferred and unpreferred host plant. (lu.se)
Genetic diversity8
  • It is likely that dsDNA viruses also comprise Earth's largest pool of unknown and novel genetic diversity. (udel.edu)
  • Genetic diversity and its use in under-utilized crops of the developing world. (uga.edu)
  • Using advanced data interaction and interactive visualizations, Stamen helped unravel these vast new landscapes of genetic diversity. (stamen.com)
  • The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. (nih.gov)
  • My scientific research focused on unravelling the mechanisms of plant-microbe interactions with a particular emphasis on the effect of drivers of global change such as land use intensity, climate change, as well as plant species identity and genetic diversity on the plant associated and rhizosphere soil microbiomes. (ufz.de)
  • This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species. (lu.se)
  • Our present-day genetic diversity was shaped by biological and demographic events that marked their signatures in the genome. (lu.se)
  • The student will evaluate gene expression in relation to measures of genetic diversity, differentiation, and neutrality across the genome to evaluate whether the sequences or the flanking regions of genes with stage-specific expression demonstrate signs of selection. (lu.se)
Amplicon based2
  • We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. (springer.com)
  • Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, fundamentally challenging the dogma that shotgun recovers more diversity than amplicon-based approaches. (phys.org)
High-throughput2
  • High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
  • and assessment of viral diversity through high-throughput DNA sequence analysis (viral metagenomics). (udel.edu)
Molecular2
  • We utilize genetics, metagenomics and molecular microbiology to answer questions related to this research area. (sdstate.edu)
  • Research Topic: Molecular diversity and community structure of arbuscular mycorrhizal fungi associated with indigenous tree species in a mountain forest in Ethiopia. (ufz.de)
Genome4
  • In metagenomics, binning is the process of grouping reads or contigs and assigning them to individual genome. (wikipedia.org)
  • From the metagenomics datasets, we reconstructed the near-complete genome of the M. leprae species (which we named KFMC-1) at 99.2% completeness when compared with M. leprae TN, a strain commonly used for reference ( 3 ). (cdc.gov)
  • In an article recently published in Genome Medicine , a group of UBC researchers discussed the implications of metagenomics for infectious disease surveillance, in public health. (ubc.ca)
  • Metagenomics for pathogen detection in public health " was written by Ruth R. Miller, Vincent Montoya, Jennifer L. Gardy, David M. Patrick and Patrick Tang, and published in Genome Medicine . (ubc.ca)
Genomes2
  • The rationale of using protein reference sequences, rather than DNA reference sequences, is that current DNA reference databases only cover a small fraction of the true diversity of genomes that exist in the environment. (wikipedia.org)
  • The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. (peerj.com)
Bacteria2
  • Given the diversity of microorganisms (bacteria, viruses, parasites) and the complex of biological phenomena that we seek to understand, data-driven research in microbiology requires researchers to collaborate and to share data. (sfu.ca)
  • Shifts in taxonomic and functional diversity, community composition and distribution patterns of soil microbiomes with main focus on general fungi, mycorrhizal fungi and bacteria along land use and simulated drought senarios. (ufz.de)
Genetics1
  • Now, the metagenomics approach is used widely in different research areas, including marine ecological research, plant and agriculture, human genetics and diagnosis of human diseases [ 10 ]. (biomedcentral.com)
Shotgun3
  • Using shotgun metagenomics, we identified an imported case of multidrug-resistant Mycobacterium leprae in a Filipino resident of Saudi Arabia in 2017. (cdc.gov)
  • We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farm s. (cdc.gov)
  • Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. (cdc.gov)
20211
  • 2021 ) Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples Metabarcoding and Metagenomics . (neurotree.org)
Genomic4
  • However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. (biomedcentral.com)
  • I am using next generation sequencing to survey the genomic diversity of viruses in East African maize. (cam.ac.uk)
  • Art illustration capturing giant virus genomic diversity. (doe.gov)
  • The genomic approaches are presented to highlight their diversity and relationships to other prokaryotes. (usda.gov)
Benthic1
  • The project also uses metagenomics to survey benthic habitats including coral mounds, cold seeps. (usgs.gov)
Microbes2
  • Current projects focus on coral disease dynamics, bacterial diversity, and using metagenomics to elucidate the functional roles of coral microbes. (usgs.gov)
  • The ecology and diversity of the biocontrol microbes, types and mechanisms of their predation, lifecycle, as well as their attributes and limitations are presented by highlighting examples from published research. (usda.gov)
Abundance4
  • However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. (springer.com)
  • Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. (peerj.com)
  • The vast abundance of viruses within natural ecosystems is paralleled by their extraordinary diversity. (udel.edu)
  • Throughout our studies in these disparate environments my lab seeks to define the abundance, diversity, and activity of indigenous viral assemblages with a particular focus on uncovering those genetic elements essential to key viral functions within a given microbial community. (udel.edu)
Bacterial diversity1
  • Thus, this study offers new clues pertaining to bacterial diversity pattern between the varied types of landfills studied. (um.edu.my)
Environments1
  • The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. (lu.se)
Pathogens2
  • Along with a high ecosystem diversity and the great fibrolytic potential, the Hadza gut microbiota was enriched in microorganisms commonly considered to be opportunistic pathogens - e.g. (frontiersin.org)
  • As progress in metagenomics and on PB effects on animal cells/tissues continues, it is anticipated that a better understanding of regulation of cellular metabolic events associated with growth of PB and prey degradation will ultimately enhance the utility of PB as biocontrol agents of foodborne and plant pathogens. (usda.gov)
Detection2
  • Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. (biomedcentral.com)
  • Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples. (biomedcentral.com)
Taxonomic1
  • Depending on the diversity and complexity of the sample, their degree of success vary: in some cases they can resolve the sequences up to individual species, while in some others the sequences are identified at best with very broad taxonomic groups. (wikipedia.org)
Analysis3
  • Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. (biomedcentral.com)
  • The first application of metagenomics study in virus discovery was the analysis of virus particles in soil samples from marine sites in San Diego [ 9 ]. (biomedcentral.com)
  • Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Micro" by Matthew D. Di Guglielmo, Karl R Franke et al. (jefferson.edu)
Viruses3
  • A metagenomics approach using NGS to characterise viruses in clinical samples was used. (biomedcentral.com)
  • JGI-led team significantly expands the global diversity of large and giant viruses. (doe.gov)
  • The ever-changing diversity of influenza viruses and the identification of influenza D emphasize the need for more virus surveillance. (cdc.gov)
Approaches1
  • To evaluate this complexity, the structures of bacterial communities in active (operational) and closed (non-operational) landfills in Malaysia were analysed with culture independent metagenomics approaches. (um.edu.my)
Infectious1
  • Metagenomics approach based on NGS has been used to detect different infectious agents in different samples [ 8 ]. (biomedcentral.com)
Enables1
  • Metagenomics enables us to investigate microbial ecology at a much larger scale than ever before and sheds light upon the previously invisible diversity of microscopic life. (phys.org)
20201
  • 2020 ) Corrigendum: Using DNA metabarcoding for assessing chironomid diversity and community change in mosquito controlled temporary wetlands. (neurotree.org)
Rhizosphere1
  • We are also interested in determining plant mechanisms that influence the microbial diversity in the rhizosphere and plant intercellular spaces. (sdstate.edu)
Mechanisms1
Sequences1
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
Soil2
Analyses1
  • In particular, the computationally-intensive analyses associated with viral metagenomics also means that the work of the lab is highly interdisciplinary requiring close interaction of computer scientists and environmental microbiologists. (udel.edu)
Https1
Habitats1
  • Ecological communities are defined by both the organisms that persist within habitats, and the interactions that shape the assembly and diversity patterns of these organisms. (springer.com)
Newly1
  • SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID. (who.int)
Assess1
  • The first studies that sampled DNA from multiple organisms used specific genes to assess diversity and origin of each sample. (wikipedia.org)
Data1
  • The application of MetaRon to metagenomic data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics. (biomedcentral.com)
Samples1
  • A Welch t-test of the Shannon diversity index for BF and FF samples approached significance ( p =0.061). (jefferson.edu)
Study1
  • We want to see if we can marry new sequencing science (including metagenomics) with state of the art epidemiological study design. (ubc.ca)
Complexity1
  • The diversity and complexity inherent to many natural ecosystems presents challenges in defining the ecological niches that describe the complex web of these interactions. (frontiersin.org)
Public1
Communities3
  • The municipal landfill is an example of human-made environment that harbours some complex diversity of microorganism communities. (um.edu.my)
  • Microbial communities in the human small intestine: coupling diversity to metagenomics. (springer.com)
  • Using noninvasive metagenomics to characterize viral communities from wildlife. (montana.edu)
Strain1
  • This library covers most of the phylogenetic diversity found in the human gut and contains extensive strain diversity. (nih.gov)
Diverse1
  • The probes' design makes possible simultaneous targeted capture of diverse metagenomics targets, Biocompare explained. (darkdaily.com)
Process1
  • Whereas metagenomics is indeed a field of research, bioprospecting is more akin to a strategy or process encompassing many techniques. (openwetware.org)
Identify1
  • Metagenomics sequencing can be used to identify multidrug-resistant M. leprae . (cdc.gov)