A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
The genomic analysis of assemblages of organisms.
Sequential operating programs and data which instruct the functioning of a digital computer.
The portion of an interactive computer program that issues messages to and receives commands from a user.
A order of gram-negative bacteria whose members are found in a variety of aquatic habitats as well as animal hosts.
The genetic complement of a BACTERIA as represented in its DNA.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The relationships of groups of organisms as reflected by their genetic makeup.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
The variety of all native living organisms and their various forms and interrelationships.
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).
A group of different species of microorganisms that act together as a community.
A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).
An order of photosynthetic bacteria representing a physiological community of predominantly aquatic bacteria.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
Devices for generating biological products that use light as the energy source. They are used for controlled BIOMASS production such as growing cyanobacteria, mosses, or algae.
A genus of PROCHLOROPHYTES containing unicellular, spherical bacteria without a mucilaginous sheath. They are found almost exclusively as extracellular symbionts of colonial ASCIDIANS on subtropical or tropical marine shores.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Refuse liquid or waste matter carried off by sewers.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Databases devoted to knowledge about specific genes and gene products.
A genus of SPONGES in the family Chalinidae characterized by unispicular secondary lines in the choanosomal skeleton.
A genus of shallow-cupped SPONGES with a broad base in the family Theonellidae. They are characterized by ectosomal spicules dominated by phyllotriaenes.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc.
Organisms that live in water.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Enzymes which catalyze the endohydrolysis of 1,4-beta-D-xylosidic linkages in XYLANS.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
Physiological processes and properties of BACTERIA.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.
Software designed to store, manipulate, manage, and control data for specific uses.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Activities related to WEIGHT REDUCTION in patients with OBESITY. Treatment methods include DIET; EXERCISE; BEHAVIOR MODIFICATION; medications; and BARIATRIC SURGERY.
Metagenome analysis of moss-associated microbiome project's aim is to explore and analyze the ecology of the area-specific ... Disease Discovery Suites are based on the type of disease that is the focus of the investigation: chronic, rare, malignant and ... The purpose of the suites is the biological interpretation of structured NGS data - assisting the researcher in revealing the ... GenoMiner is high-performance IT platform for next generation sequencing data analysis for biologists with or without IT ...
A suite of computational methods was used to identify putative host virus connections. The isolate viral host information was ... Breitbart, M; Hewson, I; Felts, B; Mahaffy, JM; Nulton, J; Salamon, P; Rohwer, F (October 2003). "Metagenomic analyses of an ... Thurber, RV; Haynes, M; Breitbart, M; Wegley, L; Rohwer, F (2009). "Laboratory procedures to generate viral metagenomes". ... McDaniel, L; Breitbart, M; Mobberley, J; Long, A; Haynes, M; Rohwer, F; Paul, JH (23 September 2008). "Metagenomic analysis of ...
These new possibilities have revolutionized microbial ecology, because the analysis of genomes and metagenomes in a high- ... The worms do not contain a mouth or a digestive or excretory system, but are instead nourished with the help of a suite of ... Based on metagenome data, microbial genomes can be reconstructed. While first metagenome-assembled genomes were reconstructed ... The term microbiome is also sometimes confused with the metagenome. Metagenome is, however, clearly defined as a collection of ...
Multi-omic data analysis has been employed to gather novel insights about the immune response to infectious diseases, such as ... a meta-genome and/or meta-transcriptome, depending upon how it is sequenced); in other words, the use of multiple omics ... a suite of multivariate methods for data integration MultiDataSet, a package for encapsulating multiple data sets The OmicTools ... The integration of multi-omics data analysis and machine learning has led to the discovery of new biomarkers. For example, one ...
The worms do not contain a mouth or a digestive or excretory system, but are instead nourished with the help of a suite of ... Vollmers, John; Wiegand, Sandra; Kaster, Anne-Kristin (2017). "Comparing and Evaluating Metagenome Assembly Tools from a ... by using 16S rRNA sequence analysis and oligodeoxynucleotide probe hybridization". Applied and Environmental Microbiology. 57 ( ... "Symbiosis insights through metagenomic analysis of a microbial consortium". Nature, 443(7114): 950-955. doi:10.1038/nature05192 ...
Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, U.K. ... Gene Identification in Prokaryotic Genomes, Phages, Metagenomes, and EST Sequences with GeneMarkS Suite. ... An additional advantage of these sequence‐analysis tools is that the problem of algorithm parameterization is solved ...
Tool suite to conduct phylogenetic analysis of genomes and metagenomes. Bridges. Picard. Java-based command-line utilities that ... Biosequence analysis using profile hidden Markov models. Bridges. Homer. Suite of tools for motif discovery and next-gen ... Suite for finite element analysis and computer-aided engineering. Bridges. Abinit. Calculates electronic density and derived ... Suite of python tools for the efficient analysis of high-throughput sequencing data. Bridges. ...
Scientists have developed a new method for DNA analysis of microbial communities such as those found in the ocean, the soil, ... "Accurate read-based metagenome characterization using a hierarchical suite of unique signatures," the researchers present this ... Bioinformatics tool for metagenome analysis. Los Alamos creates bioinformatics tool for metagenome analysis. Scientists have ... LOS ALAMOS, N.M., March 18, 2015-Scientists at Los Alamos National Laboratory have developed a new method for DNA analysis of ...
The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose ... The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as ... TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun ... TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun ...
The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and ... Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these ... William P. Inskeep, Zackary J. Jay, Susannah G.Tringe, Markus J. Herrgård, Douglas B. Rusch and YNP Metagenome Project ... The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ...
AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite. Oct 23, 2013·Gene·Csaba KerepesiVince ... Finding a needle in the virus metagenome haystack--micro-metagenome analysis captures a snapshot of the diversity of a ... Mixture models for analysis of the taxonomic composition of metagenomes. May 7, 2011·Bioinformatics·Peter MeinickeThomas ... Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. Mar 5, 2011·BMC Bioinformatics·Suparna Mitra ...
Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic ... Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic ... have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to ... have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to ...
The core facility is well equipped to perform genomic analysis in human and common model organisms. We are experienced in all ... DNAstar Suite sequence analysis tools: These tools provide the software for next-generation sequence assembly and analysis. ... metagenome and population assemblies, large-scale multi-sample SNP analysis, RNAseq, ChIPseq, and miRNA alignment and analysis ... This software includes capabilities for pathway analysis, predictive casual analytics and NGS/RNAseq data analysis. ...
Metagenomic analysis of tuberculosis in a mummy. N. Engl. J. Med. 369:289-290. doi:10.1056/NEJMc1302295. ... We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the ... The pplacer suite of programs (16) was used to assign the sequence to a position on the tree. ... Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis. Lancet Infect. Dis. 14:319-326. doi:10.1016/S1473- ...
The hands-on components of the tutorial will introduce the bioBakery suite of metaomic analysis methods, which are publicly ... Metagenome taxonomic and strain profiling (20 minutes, Kevin Bonham). Lab: StrainPhlAn (25 minutes, Kevin Bonham). Metaomic ... This workshop will provide an introduction to study design tools and analysis methods for emerging molecular tools in human ... Workshop: Metagenomic, Metatranscriptomic and MultiOmic Microbiome Analyses (Joint) ...
The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose ... Going deeper: metagenome of a hadopelagic microbial community.. Emiley A Eloe, Douglas W Fadrosh, Mark Novotny, Lisa Zeigler ... Isolation and genome analysis of single virions using single virus genomics.. Lisa Zeigler Allen, Thomas Ishoey, Mark A Novotny ... Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and ...
... using metagenome sequencing in combination with quantitative metaproteomics. The taxonomic affiliation of the metagenomic data ... Extracellular metaproteome analysis further pinpointed the specific role and synergistic interaction of Firmicutes populations ... analysis of the coordinate expression patterns indicated that transport proteins and hypothetical proteins may play a role in ... The metagenome of EMSD5 harbored a full suite of genes for cellulose degradation, including 28 genes encoding GH5 and GH9 ...
"Accurate read-based metagenome characterization using a hierarchical suite of unique signatures," the researchers present this ... Scientists at Los Alamos National Laboratory have developed a new method for DNA analysis of microbial communities such as ... metagenome datasets that can be used to re-validate any current or future tools; and 3) addresses the issue of false positives ... and then it classifies the individual metagenome sequences or "reads." They have established a unique method to query these ...
By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new ... work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis ... and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern ... diversity of microbial communities and again demonstrate how this can be associated to sample metadata.These analyses are ...
1B) and Bayesian phylogenetic analyses (15) of the nxrA gene (Fig. 1C; Text S1) indicated that this metagenome bin is related ... As with Nitrospira moscoviensis, the new metagenome bin also contained a full suite of genes for urea transport and its ... This results in all metagenome bins included in the ESOM analyses appearing four times in the tiled view. (B) Enlarged view of ... S2D) to those of other scaffolds in this metagenome bin. Both analyses suggested that this scaffold was not an outlier with ...
MM participated in the sample collection and data analysis. SD participated in the data analysis. SC and ST recruited and ... 1d). Together, genes encoding for these functions accounted for 70% of the metagenome. ... the Human Microbiome Project and other studies promulgated a paradigm of a core microbiome consisting of a universal suite of ... Groups that are bracketed are significantly different from each other (p , 0.05, Dunns test). Principal component analysis of ...
Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We ... reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified ... inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome- ... Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We ...
Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading ... Marbouty M, Koszul R. Metagenome analysis exploiting high-throughput chromosome conformation capture (3c) data. Trends Genet. ... A standard cleaning procedure was applied to all WGS and Hi-C read-sets using bbduk from the BBTools suite (v37.25) [38], where ... Here, we describe a new open software tool bin3C which can retrieve MAGs from metagenomes by combining conventional metagenome ...
Jonathan Eisen: Phylogenetic approaches to the analysis of genomes and metagenomes Upcoming SlideShare ... E a ste rn Tropica l Pa cific_ G S 0 2 2 _ O pe n O ce a n W a te r de pth S ites S a rga sso S e a _ G S 0 0 1 c_ O pe n O ce ... Jonathan Eisen: Phylogenetic approaches to the analysis of genomes and metagenomes * 1. Phylogenetic and Phylogenomic ... experimental and computational analyses • Many diverse approaches • All improved both by "phylogenomic" type analyses that ...
Here we performed transcriptome analyses to investigate the genes controlled by EcfG of Sphingomonas melonis Fr1 and the ... phenotypic analyses, and biochemical assays. Transcriptional profiling of signaling components upstream of EcfG under complex ... IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 45, D507-D516 (2017). ... MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-208 (2009). ...
This report provides the first detailed analysis of the longitudinal changes in the intestinal microbiota due to anti- ... 4a). Interestingly, analysis of the TB + HRZ group data using the principle coordinates from the weighted UniFrac analysis ... Additionally, annotation of metagenome function based on the 16S sequence data using the Greengenes database [55] and PICRUSt ... Heat maps were generated with the Partek Genomics Suite 6.6 software (Partek Ink. St. Louis, MO, USA) using average species ...
Eikmeyer, F. G., et al. Metagenome analyses reveal the influence of the inoculant Lactobacillus buchneri CD034 on the microbial ... Hauser, M., Steinegger, M., Söding, J. MMseqs software suite for fast and deep clustering and searching of large protein ... Darling, A. E., et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2, (12), 243 (2014). ... Heberle, H., et al. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinf. 16, (1), 213 ( ...
We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of ... and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. ... Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Res. 2015;43(10 ... PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014;2:e243.View ArticleGoogle Scholar. ...
JGI researchers has developed standards for the minimum metadata to be supplied with single amplified genomes and metagenome- ... Metagenome-assembled genomes have similar quality challenges. For researchers who want to conduct comparative analyses, its ... "These extensions complement the MIxS suite of metadata standards by defining the key data elements pertinent for describing the ... Developing these novel metadata standards enables researchers to consistently report the most critical metadata for analysis. ...
... denaturing gradient gel electrophoresis fingerprint analysis, cloning and sequencing) and statistical analyses were used to ... A complex suite of abiotic factors is associatedwith seasonal changes in viral diversity across all sites over 14 months, with ... Generating viral metagenomes from the coral holobiont (2014). Front. Microbiol., 5. *High temporal and spatial diversity in ... Proteomic analyses showed that the virion is composed of at least 129 CroV-encoded proteins, including a large set of ...
A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. ... Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes Chhedi Lal Gupta et al. Environ Int. ... Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes Chhedi Lal Gupta 1 , Rohit Kumar ... Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the ...
Meme Suite. Tool. Command-line, Galaxy tool. 4.14. A collection of tools for the discovery and analysis of sequence motifs.. ... MEtaGenome ANalyzer provides tools for optimized analysis of large metagenomic datasets. All the interactive tools you need in ... European Molecular Biology Open Software Suite, a free open source software analysis package specially developed for the needs ... A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a ...
IMG/M: the integrated metagenome data management and comparative analysis system The Integrated Microbial Genomes (IMG) system ... CADRE facilitates visualisation and analyses of data using the Ensembl software suite. Much of our data has been extracted from ... serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative ... The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly ...
Assembly also reduces analysis runtime. Simulated data were utilized to evaluate the protocol by permuting common experimental ... Any metatranscriptome pipeline that includes assembly of reads can add this analysis with minimal additional cost of compute ... With the growing demand for analysis of the functional microbiome, metatranscriptome studies attract more interest. To make ... Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic Acids Research. 2015; ...
  • Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. (meta.org)
  • The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. (meta.org)
  • Dendroscope can be used for a variety of analyses of molecular data sets but is particularly designed for metagenomics or analyses of uncultured environmental samples. (77.235.253)
  • Recent developments in culture-independent methodologies based on large-scale comparative analyses of microbial small-subunit ribosomal RNA genes (16S ribosomal RNA) and metagenomics have revealed the extent of microbial diversity and metabolic potential in greater detail ( 2 - 7 ). (pnas.org)
  • I am a microbial ecologist, specializing in bioinformatic analyses of 'big data' (metagenomics, metatranscriptomics, metaproteomics) to better understand how interactions within microbial communities enable functional diversity and efficiency that is greater than the sum of its parts. (exeter.ac.uk)
  • The misuse of terms such as microbiome, microbiota, metabolomic, and metagenome and metagenomics among others has contributed to misunderstanding of many study results by the scientific community and the general public alike. (biomedcentral.com)
  • Metataxonomic analysis, because it relies on the amplification and sequencing of taxonomic marker genes, is not metagenomics. (biomedcentral.com)
  • Metagenomics is the process used to characterize the metagenome, from which information on the potential function of the microbiota can be gained. (biomedcentral.com)
  • Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. (nih.gov)
  • The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. (omictools.com)
  • MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. (nih.gov)
  • The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes," BMC Bioinformatics , vol. 9, no. 1, article 386, 2008. (hindawi.com)
  • We have developed and use the M-tools suite for microbial metagenomics and iVirus for viral metagenomics. (osu.edu)
  • The novel approach for the analysis of microbial communities in environmental samples is called "metagenomics", and is defined as the study of all the genetic material recovered directly from environmental samples bypassing the need to isolate and culture individual community members 3 . (worldgastroenterology.org)
  • The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally. (qiagenbioinformatics.com)
  • When we started these analysis, from the metagenomics to the chemical ones, we had a lot of questions and we were only looking for answers… After these first results, more questions have arisen and so did the concerns! (ageofautism.com)
  • The tool, named GOTTCHA (for Genomic Origins Through Taxonomic CHAllenge), makes use of a database of reference genomes that have been pre-processed to retain only unique segments of the genomes at any level of taxonomy, and then it classifies the individual metagenome sequences or "reads. (lanl.gov)
  • This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. (montana.edu)
  • Genomic information acquired from metagenomic sampling, has become a fundamental step for the elucidation of the taxonomic composition of the niche together with each organism's potent enzymatic capabilities and is derived through the proper analysis of the chunks of DNA sequences, i.e., the full documentation of the nucleotide sequences that constitute the metagenome that are generated from a metagenomic sequencing experiment. (frontiersin.org)
  • The core facility is well equipped to perform genomic analysis in human and common model organisms. (umc.edu)
  • This system provides a well-established, robust genomic analysis platform for human disease models (human, mouse, rat). (umc.edu)
  • While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. (jove.com)
  • MitoZoa has been specifically designed to address comparative analyses of mitochondrial genomic features in a given metazoan group or in species belonging to the same genus (congeneric species). (fairsharing.org)
  • A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. (cdc.gov)
  • NGS methods such as Metagenomic Analysis (measuring species composition and function of microbial communities) and Whole Genome Sequencing (entire genomic content of individual strains) are particularly suited for food and public health microbiology and these approaches are emerging rapidly in industrial-scale applications focused on ingredient and product quality, environmental monitoring, source-tracking, and sanitation. (metagenomeanalytics.com)
  • This microbial census is established using molecular methods relying predominantly on the analysis of 16S rRNA genes, 18S rRNA genes, or other marker genes and genomic regions, amplified and sequenced from given biological samples. (biomedcentral.com)
  • In addition, genomic epidemiological and phylogenetic analyses of K. pneumoniae KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database. (dovepress.com)
  • We present the whole genome sequence of SGAir0282, isolated from the outdoor air in Singapore, and its relevance to other ECC bacteria by in silico genomic analysis. (biomedcentral.com)
  • Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments. (montana.edu)
  • The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. (asm.org)
  • We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. (frontiersin.org)
  • Here we performed transcriptome analyses to investigate the genes controlled by EcfG of Sphingomonas melonis Fr1 and the plasticity of this regulation under stress conditions. (nature.com)
  • Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). (oregonstate.edu)
  • Today's digest features a collection of reviews, opinion pieces, discussion on prenatal microbiome, pipeline to extract metabolic models from whole metagenome sequencing data (metaGEM), novel type of colistin resistance genes, mechanisms that shape microbial pangenomes, and more. (microbiomedigest.com)
  • The team used a technique called whole exome sequencing an analysis of the makeup of all the genes to study a rare inherited form of hypertension characterized by excess levels of potassium in the blood. (bio-medicine.org)
  • Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment. (nih.gov)
  • However, using these methods for community level surveys of the thousands of genes found in metagenomes requires powerful computational systems and sophisticated software workflows. (wwu.edu)
  • A comparative analysis of metagenomic samples from the OMZ using our pipeline shows that while functional and SSU genes show similar spatial patterns of diversity across the oxygen gradient, higher overall diversity was identified via the functional genes. (wwu.edu)
  • Stress-response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. (mcgill.ca)
  • Comparing functional community composition of the LH spring to metagenomes from other saline/subzero environments revealed a close association between LH and another Canadian High Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. (mcgill.ca)
  • A phylogenetic analysis was performed using the putative amino acid sequences of these genes to identify their phylogenetic affiliation. (mcgill.ca)
  • Members of Oceanospirillales , a bacterial order belonging to the Deltaproteobacteria , recruited less than 2% of the assembled genes within the SBC metagenome. (standardsingenomics.org)
  • Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. (cdc.gov)
  • As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g. (peerj.com)
  • The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. (fairsharing.org)
  • The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available genome and metagenome datasets. (fairsharing.org)
  • The discovery was made possible by mining the datasets in the Integrated Microbial Genomes and Microbiomes (IMG/M) suite of tools managed by the JGI. (doe.gov)
  • As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared. (nih.gov)
  • In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software. (springer.com)
  • Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. (springer.com)
  • The M-tools suite is software designed and developed by the Australian Centre for Ecogenomics (ACE) and are used in the analysis of ecogenomic datasets. (osu.edu)
  • The decreasing cost and increasing speed of DNA sequencing, coupled with the advances in computational analyses of large datasets, have made it feasible to analyze complex mixtures of entire genomes with reasonable coverage. (worldgastroenterology.org)
  • The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. (meta.org)
  • We undertook a large-scale analysis of 16S rRNA gene sequences to profile microbial flora inhabiting the digestive system of giant pandas and used a metagenomic approach based on next-generation de novo sequencing to identify functional attributes encoded in the gut microbiome. (pnas.org)
  • We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. (nih.gov)
  • Insufficient reference sequence data for annotation of unknown environmental sequences and metagenomes has driven efforts to find alternative annotation methods that mitigate biases from missing information. (wwu.edu)
  • Users can perform taxonomic, functional or comparative analysis, map reads to reference sequences, reference-based multiple alignments and reference-guided assembly and integrate their own classifications. (omictools.com)
  • Within the Archaea , the phylum Euryarchaeota , recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales . (standardsingenomics.org)
  • This report provides the first detailed analysis of the longitudinal changes in the intestinal microbiota due to anti-tuberculosis therapy. (biomedcentral.com)
  • Such analyses allowed the identification of a core microbiota that was shown to be horizontally transmitted from dairy cattle to fresh Parmesan cheese. (nature.com)
  • CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. (cdc.gov)
  • CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. (osu.edu)
  • Three of the areas are comprised of formerly separate programs (isolates, metagenomes and single cell sequencing). (biomedcentral.com)
  • TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. (jcvi.org)
  • The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the classification and functional prediction of viral gene products. (jcvi.org)
  • A thorough analysis of a metagenomic sample requests certain successive bioinformatic tasks that comprise (i) quality control, (ii) assembly, (iii) gene detection, (iv) gene annotation, (v) taxonomic analysis, and (vi) comparative analysis, whilst storing the generated results under a database-structured computational repository enabling advanced data management, processing, mining, and meta-mining capabilities (Figure 1 ). (frontiersin.org)
  • Artemis is a free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. (77.235.253)
  • However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of ISs. (hindawi.com)
  • PredictProtein is a comprehensive sequence analysis server that incorporates an increasing number of services and databases that can be used for protein annotation. (iscb.org)
  • PIR ( http://pir.georgetown.edu/ ) provides bioinformatics resources for protein analysis, including databases and tools tailored for proteomics (expression data, unique proteins lists), ID mapping, text mining (information extraction, entity recognition), and protein annotation (protein entries, family classification). (iscb.org)
  • JGI users) and from the broader community wanting to use IMG resources for sequence analysis and annotation. (biomedcentral.com)
  • Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). (biomedcentral.com)
  • However, analysis based on the isolated strains might not be representative of the complete repertoire of host-associated features of L. reuteri because isolating and sequencing a single bacterial strain under appropriate culture conditions remains challenging ( Teeling and Glockner, 2012 ). (frontiersin.org)
  • Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. (cdc.gov)
  • Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. (oregonstate.edu)
  • For additional microbial analyses (microbial biomass collection for DNA and RNA extractions and bacterial production) were returned to the laboratory, which was within 10 minutes' drive of the field site. (bco-dmo.org)
  • Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. (microbe.net)
  • Proteomic tracking and analysis of a bacterial mixed culture. (mpg.de)
  • In this PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. (pacb.com)
  • But Sapkota's team took a more holistic approach using DNA microarray analysis to estimate the so-called bacterial metagenome, the totality of bacterial genetic material present in the tested cigarettes. (newswise.com)
  • The system also allows for genetic analysis in eukaryotic animal (Drosophila, zebrafish) and plant (rice, barley, cotton) systems, and prokaryotic organisms (E. coli). (umc.edu)
  • Sweeping genetic analysis of rare disease yields common mechanism of hy. (bio-medicine.org)
  • Meta-community analyses revealed just five ecological zones throughout the global ocean, and established local and global patterns and drivers in viral community diversity at levels of both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). (exeter.ac.uk)
  • To determine its total functional and genetic potential, we performed metagenomic analysis of the LH spring outlet microbial community. (mcgill.ca)
  • The purpose of the suites is the biological interpretation of structured NGS data - assisting the researcher in revealing the genetic background of diseases or providing an answer to related research questions. (wikipedia.org)
  • The metagenome is the collective genetic content of the combined genomes of the constituents of an ecological community. (worldgastroenterology.org)
  • Genome wide association of host genetic control of HIV in a meta-analysis of the five INSIGHT HIV+ cohorts. (ku.dk)
  • Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. (oregonstate.edu)
  • In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. (peerj.com)
  • Chipster is a user-friendly analysis software for high-throughput data. (77.235.253)
  • It contains over 300 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. (77.235.253)
  • Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations. (77.235.253)
  • CADRE facilitates visualisation and analyses of data using the Ensembl software suite. (fairsharing.org)
  • CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. (fairsharing.org)
  • MetaGenome Analytics (MGA) provides simple solutions to these barriers with commercial-scale software that unites bioinformatics, statistics, data sciences, with the power of cloud-based computing and delivers it to your fingertips in seamless, easy to use applications that are affordable. (metagenomeanalytics.com)
  • The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (phylogenomics.me)
  • This game-changing technology is fueled by the convergence of two rapidly evolving fields: DNA sequencing and the analysis of that sequencing data (i.e., bioinformatics). (foodsafetytech.com)
  • Analysis of sequence data is a specialized field called bioinformatics and has its own expert practitioners. (foodsafetytech.com)
  • For example, there is an online tool suite known as NEPHELE, which offers publically available online programs, software, and data handling capacity for sequence analysis. (foodsafetytech.com)
  • a guide from sampling to data analysis. (nih.gov)
  • QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. (scicombinator.com)
  • MEGAN is a comprehensive microbiome analysis toolbox for metagenome, meta-transcriptome, amplicon and from other sources data. (omictools.com)
  • An image processing and data analysis program for remotely sensed data. (westgrid.ca)
  • Tools for high-throughput data analysis and data mining, and data are provided. (iscb.org)
  • Fiesta provides features allowing for data sharing, online job invocation and tracking, a number of useful analysis features, and a friendly web interface. (iscb.org)
  • Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. (nih.gov)
  • While some urban metagenome studies are already published [ 9 , 10 ], more data and work is needed to be able to profile the metagenome of cities worldwide. (springer.com)
  • AstridBio's focus is biobanking software development, data management and analysis for genomics research. (wikipedia.org)
  • GenoMiner is high-performance IT platform for next generation sequencing data analysis for biologists with or without IT background. (wikipedia.org)
  • Here we report on the first metagenome exceeding 50 Gb of raw DNA sequence data from a microbial community associated with natural crude oil seeps of the Santa Barbara Channel (SBC), one of the world's largest natural hydrocarbon seep regions [ 16 ], which can be accessed publicly through IMG/M for further analysis by the scientific community. (standardsingenomics.org)
  • IsoGenie Co-PI Dr. Gene Tyson, Deputy Director of ACE, uses this suite of tools to analyze the data for this project. (osu.edu)
  • The M-tools are a suite of metagenomic analysis tools targeted toward the recovery of high-quality population genomes from metagenomic data. (osu.edu)
  • The M-tools suite also includes software for constructing strain-resolved community profiles, and the analysis of gene families within unassembled metagenomic data. (osu.edu)
  • GraftM is a tool for the analyses of gene families within sequence data. (osu.edu)
  • GraftM searches metagenome sequence data using either a DIAMOND database, or a hidden Markov model (HMM) search coupled to a rapid ORF caller (OrfM, see below). (osu.edu)
  • These apps cover nearly every stage of the viral analysis pipeline, including processing raw sequence data, assembly, post-assembly filtering, and sequence analysis. (osu.edu)
  • The DRAGEN Genome pipeline enables ultra rapid analysis of Next Generation Sequencing (NGS) data, reducing the time required for analyzing a whole genome at 30x coverage from 10 to 30 hours using the current industry standard, BWA-MEM+GATK-HC software, to ~22 minutes, with the same level of accuracy for both SNPs and INDELs. (edicogenome.com)
  • Aren't there quality issues with making data available before analysis? (bitsandbugs.org)
  • Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. (biomedcentral.com)
  • In particular, processing metagenome data in an efficient and reproducible manner is challenging because it requires implementation of several distinct tools, each designed for a specific task. (biomedcentral.com)
  • The most direct and frequently used way to analyze metagenome data is to map the sequence reads to reference genomes, when a suitable genome database from cultivated microbes is available (e.g. (biomedcentral.com)
  • The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation. (mpg.de)
  • Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. (mpg.de)
  • Published August 8, 2017 in Nature Biotechnology , an international team led by researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases. (eurekalert.org)
  • We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna . (nature.com)
  • Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira -like nitrite-oxidizing bacteria. (asm.org)
  • The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira . (asm.org)
  • Among these, we identified a novel negative GSR feedback regulator, termed NepR2, on the basis of gene reporter assays, phenotypic analyses, and biochemical assays. (nature.com)
  • Selective amplification (e.g. 16S, 18S, ITS) of specific gene regions has long been standard for microbial community sequencing, but it introduces bias and omits organisms and functional elements from analysis. (biomedcentral.com)
  • Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. (oregonstate.edu)
  • The main goal of this thesis is to outline a phylogenetic analysis pipeline built to process environmental metagenomic samples using the pplacer software suite, and a pilot study performed with this software pipeline to investigate community-level patterns in gene diversity for a marine oxygen minimum zone (OMZ) off the coast of Chile, South America. (wwu.edu)
  • The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose results are ranked according to a priority rules hierarchy. (jcvi.org)
  • The bioanalyzer is used for nucleic acid and protein analysis using an integrated lab chip system that performs multiple electrophoresis steps in up to 12 samples in one run. (umc.edu)
  • Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. (asm.org)
  • The DNA and protein sequence searches are based on a suite of BLAST programs (BLASTN, BLASTX, and BLASTP) [ 8 , 9 ]. (hindawi.com)
  • MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. (nih.gov)
  • In addition, analysis of the coordinate expression patterns indicated that transport proteins and hypothetical proteins may play a role in bacteria processing lignocellulose. (biomedcentral.com)
  • Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. (qiagenbioinformatics.com)
  • RNRs are universal among cellular life, common within viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDNA virioplankton sampled in this study. (jove.com)
  • The word is frequently used to describe environmental viral shotgun metagenomes. (wikipedia.org)
  • The IMG/VR systems serve as a starting point for the sequence analysis of viral fragments derived from metagenomic samples. (wikipedia.org)
  • Used primarily in the study of microorganisms, metagenome sequencing has now been carried out on a variety of environments where one finds microbes - from plants and animals to every kind of natural and man-made environment around the globe. (peerj.com)
  • The current use of molecular techniques that do not require the isolation and cultivation of microorganisms ( 1 , 33 ), including 16S rRNA analysis ( 6 , 13 , 20 ) and fluorescent in situ hybridization ( 8 ), have greatly expanded our understanding of wastewater microbial communities. (asm.org)
  • Random community genomes (metagenomes) are now commonly used to study microbes in different environments. (meta.org)
  • Principle coordinates analysis (PCoA) based on UniFrac scores of room and gut microbes. (nih.gov)
  • As a former professional software developer, I am interested in combining high-performance computing with multivariate statistical analyses to identify putative drivers of function and diversity in complex communities. (exeter.ac.uk)
  • A suite of computational methods was used to identify putative host virus connections. (wikipedia.org)
  • These analyses are implemented in an open source software pipeline called PhyloSift. (peerj.com)
  • Any metatranscriptome pipeline that includes assembly of reads can add this analysis with minimal additional cost of compute time. (beds.ac.uk)
  • The DRAGEN Transcriptome (RNA-Seq) pipeline performs Next Generation Sequencing (NGS) secondary analysis of RNA transcripts. (edicogenome.com)
  • In a paper this week in the journal Nucleic Acids Research , "Accurate read-based metagenome characterization using a hierarchical suite of unique signatures," the researchers present this novel method for shotgun metagenomic read classification, a method that is highly accurate, and outperforms all other most recent methods, they say. (lanl.gov)
  • DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (doe.gov)
  • As we enter a period of genome-centric analysis of metagenomes, accurate, fast population genome recovery methods are needed. (osu.edu)
  • We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. (biomedcentral.com)
  • While current methods rely on mutational analyses, we will genetically encode the incorporation of acetylated lysine and directly measure the functional role of each acetylation site in cancerous and non-cancerous cell lines. (europa.eu)
  • Metagenome processing pipelines commonly default to co-assembly of the samples rather than assembly of individual samples, resulting in more fragmented assemblies [ 18 ]. (biomedcentral.com)
  • The phylogenetic tree of amo A showed similar patterns of grouping as the analysis done by r16S rDNA. (mcgill.ca)
  • Assembly also reduces analysis runtime. (beds.ac.uk)
  • To truly characterize a natural microbial community and examine its functional potential, assembly-based metagenome analyses are needed. (biomedcentral.com)
  • The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. (montana.edu)
  • It finally compares metagenomic reads against this precomputed marker catalog using nucleotide BLAST searches in order to provide clade abundances for one or more sequenced metagenomes. (omictools.com)
  • This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. (springer.com)
  • Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. (oregonstate.edu)
  • We extended the model analysis to investigate metabolic costs. (asm.org)
  • The degree of connectivity between microbial populations based on metabolic network analysis reveals exquisite functional redundancy in hypersaline microbial communities. (manualzz.com)
  • 2014 (doi:10.1038/ismej.2015.57) B. Metabolic reconstruction of the aerobic n-alkane degradation by partially-recovered genome from a metagenome of an oil reservoir. (microbiomeinsights.com)
  • Assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. (omictools.com)
  • The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS), have revolutionized metagenomic analysis. (frontiersin.org)
  • We present here a comprehensive study on the community structure and enzyme systems of a lignocellulolytic microbial consortium EMSD5 during growth on corn stover, using metagenome sequencing in combination with quantitative metaproteomics. (biomedcentral.com)
  • This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. (asm.org)
  • By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. (peerj.com)
  • False positives, false negatives, and speed of analysis are critical concerns, in particular when sequencing is applied to medical diagnosis or tracking infectious agents. (biomedcentral.com)
  • Next Generation DNA Sequencing (NGS) is transforming diagnostic microbiology, allowing DNA sequence analysis to be used as an affordable, high-resolution analytical platform. (metagenomeanalytics.com)
  • High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. (qiagenbioinformatics.com)
  • Our vision is to revolutionize genome sequencing analysis by providing unprecedented speed, scale and accuracy. (edicogenome.com)
  • Cluster signatures provide a rapid and universal analysis tool to identify all possible short diagnostic DNA markers and variants from any DNA sequencing dataset. (biomedcentral.com)
  • Roary: rapid large-scale prokaryote pan genome analysis. (cdc.gov)
  • The QIAxcel system provides high-throughput RNA and DNA analysis (up to 96 samples) using a capillary-based gel system. (umc.edu)
  • We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. (cdc.gov)
  • Metagenome analysis of moss-associated microbiome project's aim is to explore and analyze the ecology of the area-specific community composition (the Alpine bog) with the help of metagenomic approaches using NGS technology. (wikipedia.org)
  • A fundamental step in taxonomy classification is to count taxa based on the shotgun read alignments to the metagenome. (beds.ac.uk)
  • Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. (frontiersin.org)
  • Results from the first urban metagenome studies show that a large proportion of the DNA found in these samples is still not present in public databases and is therefore missing in any reference-based method. (springer.com)
  • European Molecular Biology Open Software Suite, a free open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community. (77.235.253)