Metagenomics: The genomic analysis of assemblages of organisms.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.Bacteria: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Gastrointestinal Tract: Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).Chenopodium ambrosioides: A plant species of the genus Chenopodium known for toxicity to intestinal worms and other simple organisms.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Microbial Consortia: A group of different species of microorganisms that act together as a community.Oceans and Seas: 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).Microbiota: 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.DNA Viruses: Viruses whose nucleic acid is DNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Computational Biology: 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.Fusobacteria: A phylum of anaerobic, gram-negative bacteria with a chemoorganotrophic heterotrophic metabolism. They are resident flora of the OROPHARYNX.Circoviridae: A family of very small viruses containing circular, single-stranded DNA and possessing no envelope. The modes of transmission are not known.Viruses: 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.Archaea: 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.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Methylophilaceae: A family of gram-negative bacteria in the order Methylophilales.Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.Proteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Ecology: The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Genetics, Microbial: A subdiscipline of genetics which deals with the genetic mechanisms and processes of microorganisms.Aquatic Organisms: Organisms that live in water.Heterotrophic Processes: The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements from light. Depending on environmental conditions some organisms can switch between different nutritional modes (AUTOTROPHY; heterotrophy; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrients and energy requirements.Marine Biology: The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.Cluster Analysis: 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.Biotechnology: 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.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.High-Throughput Nucleotide Sequencing: 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.Ecosystem: 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)Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Actinobacteria: 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)RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Hot Springs: 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.Molecular Sequence Data: 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.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Genes, Archaeal: The functional genetic units of ARCHAEA.Internet: 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.Sequence Alignment: 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.

*  PLOS ONE: MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit. Figure 1. The MOCAT data processing pipeline.. Metagenomic samples ...

*  Frontiers | Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the...

2012a). Assessing the diversity and specificity of two freshwater viral communities through metagenomics. PLoS ONE 7:e33641. ...

*  Metagenomics.

In this respect, metagenomics has and will continue to play an essential part in the new and evolving area of microbial systems ... Metagenomics constitutes the functional and sequence-based analysis of the collective microbial genomes (microbiome) in a ...

*  Bracken: estimating species abundance in metagenomics data [PeerJ]

Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively ... As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to ... accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. ... When used to identify the taxonomic label of metagenomics sequences, the Kraken system for classification of metagenomics ...

*  Urban Microbial Dynamics and Metagenomics | CUREnet

The project is carried out over 8-10 weeks of the 14-week lab, with an introduction to microbial diversity and metagenomics at ... The goal of the urban metagenomics project is to involve undergraduates in determining the microbial community composition of ...

*  Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

Background: Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. ... While metagenomics provides information on the gene content, metatranscriptomics aims at understanding gene expression patterns ...

*  Publication : USDA ARS

Ironically, the technology that has made the concept of deep sequencing/metagenomics real, may present a challenge for ...

*  Metagenomics | Byte Size Biology

Bioinformatics, Biology, Genomics, Metagenomics Comments turned off Metagenomics Metadata and Metaanalysis By Iddo on February ... Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful ... Bioinformatics, Metagenomics, Microbiology, stuctural biology Comments turned off Photosynthesis, phages and structures: ... The power of metagenomics and bioinfromatics: in a mass of data you just have to know what you are looking for, and […] ...

*  16s metagenomics

AOAC meeting recap: metagenomics, Meiothermus and an award-winning poster. For over a century - a whopping 131 years, to be ... AOAC meeting recap: metagenomics, Meiothermus and an award-winning poster * Study: groundnuts can be made immune to aflatoxin- ... June 19th, 2017 , Category: Corporate news, Food industry, Genomics (Agrigenomics) , Tags: 16s metagenomics, GeneSeek, ... Neogen's new NeoSeek™ genomic services utilize a novel application of 16s metagenomics to determine all bacteria in a sample, ...

*  Sample: SRS294929 | EBI metagenomics | EMBL-EBI

EBI Metagenomics is a free resource for the analysis, archiving and browsing of metagenomic and metatranscriptomic data ...

*  Psych Central - Better sludge through metagenomics

Better sludge through metagenomics. Researchers seek to master wastewater treatment failures. WALNUT CREEK, CA--Few stop to ...

*  Biogas Consortium Using Genedata Selector for Metagenomics-based Process Optimization

Full support of bioprocess engineering: from metagenomics, biomass to microbiome analysis * Integrative, scalable, and secure ...

*  Metagenomics of bacteria and bacteriophages of ants and their nests

... Principal Supervisor: Dr Rob Hammond - Department of ... PhD project title: Metagenomics of bacteria and bacteriophages of ants and their nests ...

*  Recent Articles | Metagenomics And Microbiology | The Scientist Magazine®

Vaginal birth leads to changes in the development of offsprings' microbiomes not seen among mice born via C-section, which researchers suspect might contribute to the weight differences.. 0 Comments. ...,10/tags/metagenomics,microbiology/

*  Metagenomics of skin reveals insights into the human microbiome | EurekAlert! Science News

Metagenomics of skin reveals insights into the human microbiome. Cold Spring Harbor Laboratory ...

*  Project: Beta Lactam Antibiotics and Human Gut Microbiota | EBI metagenomics | EMBL-EBI

EBI Metagenomics is a free resource for the analysis, archiving and browsing of metagenomic and metatranscriptomic data ...

*  Difference between revisions of "Talk:CH391L/S13/Metagenomics & Bioprospecting" - OpenWetWare

Siddharth Das 21:11, 2/21/2013 (EST): You provided an thorough overview of both metagenomics and bioprospecting. Nevertheless, ... Retrieved from "" ...

*  Recent Articles | Metagenomics And Culture | The Scientist Magazine®| Page 4

Winners in the Physiology or Medicine category are trending older, even though they're completing their award-winning research when they are about the same age, according to an analysis.. 1 Comment. ...,3/tags/metagenomics,culture/pageNo/4/

*  25th JGI Microbial Genomics and Metagenomics (MGM-25) Workshop - Attendees | Online Registration by Cvent

25th JGI Microbial Genomics and Metagenomics (MGM-25) Workshop. Online registration by Cvent ... 25th JGI Microbial Genomics and Metagenomics (MGM-25) Workshop. Attendees Search Attendees. ...

*  Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics | Scientific...

Metagenomics. Abstract. Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are ... The benefit of metagenomics is that no prior knowledge of the ARG sequences is needed, whereas PCR based methods require this ... Metagenomics does not require prior knowledge of ARGs and is in a sense an open-ended method for studying the resistome. ... Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. . ...

*  Sciblogs | Metagenomics-finding organisms from their genomes

Metagenomics-finding organisms from their genomes. By Grant Jacobs • 20/10/2009 • 10 ... Metagenomics exploits the power of high-throughput, where large amounts of DNA can be sequenced very quickly. If you have time ... A recent blog article on metagenomics can be found at one of the blogs on my blogroll Mystery Rays from Outer Space. Despite ... Metagenomics provides another way to find new species of organisms, one that doesn't involve painstakingly culturing micro- ...

*  "Comparative metagenomics of toxic freshwater cyanobacteria bloom communities on two continents" by Steven...

Comparative metagenomics of toxic freshwater cyanobacteria bloom communities on two continents. PLoS One (2012) * Steven ... "Comparative metagenomics of toxic freshwater cyanobacteria bloom communities on two continents" PLoS One Vol. 7 (2012) ...

Microbiota: A microbiota is "the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space". Joshua Lederberg coined the term, emphasising the importance of microorganisms inhabiting the human body in health and disease.Lung microbiome: The lung microbiota (or pulmonary microbial community) is a complex variety of microbes found in the lower respiratory tract particularly on the mucus layer and the epithelial surfaces (the lung microbiome refer to their genomes). These microbes include bacteria, yeasts, viruses and bacteriophages.Gijs Kuenen: Johannes Gijsbrecht Kuenen (born 9 December 1940, Heemstede) is a Dutch microbiologist who is professor emeritus at the Delft University of Technology and a visiting scientist at the University of Southern California. His research is influenced by, and a contribution to, the scientific tradition of the Delft School of Microbiology.Exogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Antestiopsis: Antestiopsis is a genus of shield bug, commonly known as antestia and the variegated coffee bug. Several species in eastern Africa are pests of coffee plants, giving the coffee beans a distinctive 'potato taste', which is thought to be caused indirectly by bacteria entering through wounds created by the insects, leading to an increase in the concentration of isopropyl methoxy pyrazine.Anoxic event: Oceanic anoxic events or anoxic events (anoxia conditions) refer to intervals in the Earth's past where portions of oceans become depleted in oxygen (O2) at depths over a large geographic area. During some of these events, euxinia develops - euxinia refers to anoxic waters that contain hydrogen sulfide.Nudivirus: A nudivirus (family Nudiviridae) is a large, rod-shaped virus with a circular, double stranded DNA genome of 96–231 kb. The genome encodes 98 to 154 open reading frames.Global microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Deep chlorophyll maximum: A deep chlorophyll maximum (DCM) is a subsurface maximum in the concentration of chlorophyll in the ocean or a lake. A DCM is not always present--sometimes there is more chlorophyll at the surface than at any greater depth--but it is a common feature of most aquatic ecosystems.Mac OS X Server 1.0PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Domain (biology): In biological taxonomy, a domain (also superregnum, superkingdom, empire, or regio) is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains: Archaea (a term which Woese created), Bacteria, and Eukaryota.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.Salt lake: Salt Lake (Disambiguation)}}Zetaproteobacteria: The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria. Zetaproteobacteria can also refer to the group of organisms assigned to this class.Spatial ecology: Spatial ecology is a specialization in ecology and geography that is concerned with the identification of spatial patterns and their relationships to ecological phenomena. Ecological events can be explained through the detection of patterns at a given spatial scale: local, regional, or global.Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Lacandonia: Lacandonia is a mycoheterotrophic plant that contains no chlorophyll and has the unusual characteristic of inverted positions of the male (androecium) and female (gynoecium) floral parts, something that had not been seen in any other plants with the occasional exception of some individuals of the related 'Esteban Martinez and Clara Hilda Ramos Lacandoniaceae (Triuridales): Una Nueva Familia de Mexico. Ann.Bodega Marine Reserve: Bodega Marine Reserve is a nature reserve and marine reserve on the coast of northern California, located in the vicinity of the Bodega Marine Laboratory on Bodega Head. It is a unit of the University of California Natural Reserve System, that is administered by the University of California, Davis.Biotechnology Industry Organization: The Biotechnology Industry Organization (BIO) is the largest trade organization to serve and represent the biotechnology industry in the United States and around the world.Anna Edney, "Biosciences Defy U.Library (biology): In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated).Gemmatimonadetes: The Gemmatimonadetes are a family of bacteria, given their own phylum (Gemmatimonadetes). This bacterium makes up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.EcosystemAdlercreutzia: Adlercreutzia is a genus in the phylum Actinobacteria (Bacteria).List of sequenced eukaryotic genomesList of hot springs: There are hot springs on all continents and in many countries around the world. Countries that are renowned for their hot springs include Honduras, Canada, Chile, Hungary, Iceland, Israel, Japan, New Zealand and United States, but there are interesting and unique hot springs in many other places as well.Coles PhillipsFecal coliform: A fecal coliform (British: faecal coliform) is a facultatively anaerobic, rod-shaped, gram-negative, non-sporulating bacterium. Coliform bacteria generally originate in the intestines of warm-blooded animals.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.CS-BLAST

(1/752) Contribution of exogenous genetic elements to the group A Streptococcus metagenome.

Variation in gene content among strains of a bacterial species contributes to biomedically relevant differences in phenotypes such as virulence and antimicrobial resistance. Group A Streptococcus (GAS) causes a diverse array of human infections and sequelae, and exhibits a complex pathogenic behavior. To enhance our understanding of genotype-phenotype relationships in this important pathogen, we determined the complete genome sequences of four GAS strains expressing M protein serotypes (M2, M4, and 2 M12) that commonly cause noninvasive and invasive infections. These sequences were compared with eight previously determined GAS genomes and regions of variably present gene content were assessed. Consistent with the previously determined genomes, each of the new genomes is approximately 1.9 Mb in size, with approximately 10% of the gene content of each encoded on variably present exogenous genetic elements. Like the other GAS genomes, these four genomes are polylysogenic and prophage encode the majority of the variably present gene content of each. In contrast to most of the previously determined genomes, multiple exogenous integrated conjugative elements (ICEs) with characteristics of conjugative transposons and plasmids are present in these new genomes. Cumulatively, 242 new GAS metagenome genes were identified that were not present in the previously sequenced genomes. Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. Two large ICEs, designated 2096-RD.2 (63 kb) and 10750-RD.2 (49 kb), have multiple genes encoding resistance to antimicrobial agents, including tetracycline and erythromycin, respectively. Also resident on these ICEs are three genes encoding inferred extracellular proteins of unknown function, including a predicted cell surface protein that is only present in the genome of the serotype M12 strain cultured from a patient with acute poststreptococcal glomerulonephritis. The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, and population genomics.  (+info)

(2/752) Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments.


(3/752) An interlaboratory comparison of 16S rRNA gene-based terminal restriction fragment length polymorphism and sequencing methods for assessing microbial diversity of seafloor basalts.


(4/752) Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.


(5/752) The population genomics of trans-specific inversion polymorphisms in Anopheles gambiae.


(6/752) Ancestral population genomics: the coalescent hidden Markov model approach.


(7/752) Population genomics of the Arabidopsis thaliana flowering time gene network.


(8/752) TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population.



  • Metagenomics constitutes the functional and sequence-based analysis of the collective microbial genomes (microbiome) in a particular environment or environmental niche. (

genomics and metagenomics

  • Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. (


  • Metagenomics provides another way to find new species of organisms, one that doesn't involve painstakingly culturing micro-organisms, trying to find what conditions (think: temperature, food, etc.) the organisms need to grow. (
  • Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. (
  • Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. (


  • As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. (


  • Metagenomics exploits the power of high-throughput, where large amounts of DNA can be sequenced very quickly. (


  • However, there are two major challenges in applying metagenomics for studying environmental ARGs. (
  • Metagenomics is the moniker given to genomic, or DNA sequence, surveys of environmental samples. (


  • In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances. (


  • In the context of metagenomics experiments, this makes it possible to sample a complex mixture of microbes by "shotgun" sequencing, which involves simply isolating DNA, preparing the DNA for sequencing, and sequencing the mixture as deeply as possible. (


  • In this respect, metagenomics has and will continue to play an essential part in the new and evolving area of microbial systems biology. (