Metagenomics

metagenomicmetagenomemetagenomesmetagenomic analysisComputational metagenomicsenvironmentalfunctional metagenomicsmeta-genomemeta-transcriptomemeta-transcriptomics
Metagenomics is the study of genetic material recovered directly from environmental samples.wikipedia
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Edward DeLong

Edward F. DeLong
After leaving the Pace laboratory, Edward DeLong continued in the field and has published work that has largely laid the groundwork for environmental phylogenies based on signature 16S sequences, beginning with his group's construction of libraries from marine samples.
Edward Francis DeLong, born 1958, is a marine microbiologist and professor in the Department of Oceanography at the University of Hawaii, Manoa, and is considered a pioneer in the field of metagenomics.

Mya Breitbart

Breitbart, M.
In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing (see below) to show that 200 liters of seawater contains over 5000 different viruses.
She is best known for her contributions to the field of viral metagenomics.

DNA sequencing

DNA sequencesequencesequencing
In 2005 Stephan C. Schuster at Penn State University and colleagues published the first sequences of an environmental sample generated with high-throughput sequencing, in this case massively parallel pyrosequencing developed by 454 Life Sciences.
The field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms.

Forest Rohwer

In 2002, Mya Breitbart, Forest Rohwer, and colleagues used environmental shotgun sequencing (see below) to show that 200 liters of seawater contains over 5000 different viruses.
In 2002, as a research scientist San Diego State University, Rohwer performed the first shotgun metagenome (Breitbart et al. 2002).

Microbiota

microbiomemicroflorabacterial flora
The sequencing of the cow rumen metagenome generated 279 gigabases, or 279 billion base pairs of nucleotide sequence data, while the human gut microbiome gene catalog identified 3.3 million genes assembled from 567.7 gigabases of sequence data.
Metagenomics is also used extensively for studying microbial communities.

Genomics

genomicgenome biologygenomic analysis
While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample.
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples.

Microbial ecology

environmental microbiologymicrobial ecologistEverything is everywhere
As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.
For example, molecular techniques such as community fingerprinting or metagenomics can be used to track changes in microbial communities over time or assess their biodiversity.

Binning (metagenomics)

Binningidentify species in metagenomic samples
Binning is the process of associating a particular sequence with an organism.
In metagenomics, binning is the process of grouping reads or contigs and assigning them to operational taxonomic units.

MEGAN

This type of approach is implemented in the program MEGAN4.
MEGAN ("MEtaGenome ANalyzer") is a computer program that allows optimized analysis of large metagenomic datasets.

Robert M. Goodman

The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.
He and collaborators also pioneered the field now known as "metagenomics."

Sargasso Sea

SargassoNorth Atlantic Subtropical Gyre
The pilot project, conducted in the Sargasso Sea, found DNA from nearly 2000 different species, including 148 types of bacteria never before seen.
In the early 2000s, the Sargasso Sea was sampled as part of the Global Ocean Sampling survey, to evaluate its diversity of microbial life through metagenomics.

Global Ocean Sampling Expedition

Global Ocean SamplingGlobal Ocean Survey
Beginning in 2003, Craig Venter, leader of the privately funded parallel of the Human Genome Project, has led the Global Ocean Sampling Expedition (GOS), circumnavigating the globe and collecting metagenomic samples throughout the journey.
The GOS datasets were submitted to both NCBI and [[Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis]] (CAMERA), a new online resource for marine metagenomics funded by the Gordon and Betty Moore Foundation, developed by JCVI and hosted by UC San Diego's Division of the California Institute for Telecommunications and Information Technology (Calit2).

KEGG

Kyoto Encyclopedia of Genes and GenomesKEGG PATHWAY Database
Based on a BLAST comparison against a reference database, this tool performs both taxonomic and functional binning, by placing the reads onto the nodes of the NCBI taxonomy using a simple lowest common ancestor (LCA) algorithm or onto the nodes of the SEED or KEGG classifications, respectively.
KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.

Jo Handelsman

Handelsman
The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.
She is responsible for coining the term metagenomics and is particularly known for her work in pioneering the use of functional metagenomics to study antibiotic resistance.

MG-RAST

RASTRAST annotation service
In 2007, Folker Meyer and Robert Edwards and a team at Argonne National Laboratory and the University of Chicago released the Metagenomics Rapid Annotation using Subsystem Technology server (MG-RAST) a community resource for metagenome data set analysis.
MG-RAST is an open-source web application server that suggests automatic phylogenetic and functional analysis of metagenomes.

Joint Genome Institute

JGIDOE Joint Genome InstituteDOE Joint Genome Institute (JGI)
In 2004, Gene Tyson, Jill Banfield, and colleagues at the University of California, Berkeley and the Joint Genome Institute sequenced DNA extracted from an acid mine drainage system.
The projects involve many important multicellular organisms, microbes and communities of microbes called metagenomes (or microbiomes) related to the DOE mission areas of bioenergy, understanding global cycles such as the carbon cycle, and biogeochemistry and are chosen primarily based on scientific merit as determined by outside review.

Conserved sequence

sequence conservationconservedhighly conserved
These early studies focused on 16S ribosomal RNA sequences which are relatively short, often conserved within a species, and generally different between species.
For example, the most highly conserved genes such as the 16S RNA and other ribosomal sequences are useful for reconstructing deep phylogenetic relationships and identifying bacterial phyla in metagenomics studies.

Genome

genomesgenetic materialgenomic
The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way analogous to the study of a single genome.

Jon Clardy

Jon Christel Clardy
The term "metagenomics" was first used by Jo Handelsman, Jon Clardy, Robert M. Goodman, Sean F. Brady, and others, and first appeared in publication in 1998.
Clardy is also known for his work in elucidating natural products made by unculturable bacteria and is credited, along with Jo Handelsman and Robert M. Goodman, for pioneering the field of metagenomics.

AMPHORA

MetaPhlAn and AMPHORA are methods based on unique clade-specific markers for estimating organismal relative abundances with improved computational performances.
AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets.

Bacteriophage

phagebacteriophagesphages
Subsequent studies showed that there are more than a thousand viral species in human stool and possibly a million different viruses per kilogram of marine sediment, including many bacteriophages.
Metagenomics has allowed the in-water detection of bacteriophages that was not possible previously.

Giant Virus Finder

Viral metagenomes (also called viromes) should thus provide more and more information about viral diversity and evolution For example, a metagenomic pipeline called Giant Virus Finder showed the first evidence of existence of giant viruses in a saline desert and in Antarctic dry valleys
The Giant Virus Finder is a free bioinformatics software for finding giant viruses in metagenomes.

Craig Venter

J. Craig VenterDr. Craig VenterJ. Craig Venter Ph.D.
Beginning in 2003, Craig Venter, leader of the privately funded parallel of the Human Genome Project, has led the Global Ocean Sampling Expedition (GOS), circumnavigating the globe and collecting metagenomic samples throughout the journey.

Metadata

meta datameta-datacommunications metadata
The massive amount of exponentially growing sequence data is a daunting challenge that is complicated by the complexity of the metadata associated with metagenomic projects.
Research studies in the fields of biomedicine and molecular biology frequently yield large quantities of data, including results of genome or meta-genome sequencing, proteomics data, and even notes or plans created during the course of research itself.

Pyrosequencing

Biotage454 pyrosequencingBiotage Pyrosequencer
In 2005 Stephan C. Schuster at Penn State University and colleagues published the first sequences of an environmental sample generated with high-throughput sequencing, in this case massively parallel pyrosequencing developed by 454 Life Sciences.
454 developed an array-based pyrosequencing technology which emerged as a platform for large-scale DNA sequencing, including genome sequencing and metagenomics.