1078:. Shotgun sequencing reveals genes present in environmental samples. Historically, clone libraries were used to facilitate this sequencing. However, with advances in high throughput sequencing technologies, the cloning step is no longer necessary and greater yields of sequencing data can be obtained without this labour-intensive bottleneck step. Shotgun metagenomics provides information both about which organisms are present and what metabolic processes are possible in the community. Because the collection of DNA from an environment is largely uncontrolled, the most abundant organisms in an environmental sample are most highly represented in the resulting sequence data. To achieve the high coverage needed to fully resolve the genomes of under-represented community members, large samples, often prohibitively so, are needed. On the other hand, the random nature of shotgun sequencing ensures that many of these organisms, which would otherwise go unnoticed using traditional culturing techniques, will be represented by at least some small sequence segments.
1493:-based comparative metagenomic analysis application called Community-Analyzer has been developed by Kuntal et al. which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed microbial communities (in terms of their taxonomic composition), but also provides insights into the inherent inter-microbial interactions occurring therein. Notably, this layout algorithm also enables grouping of the metagenomes based on the probable inter-microbial interaction patterns rather than simply comparing abundance values of various taxonomic groups. In addition, the tool implements several interactive GUI-based functionalities that enable users to perform standard comparative analyses across microbiomes.
1980:
critically important for the health of the intestinal tract. There are two types of functions in these range clusters: housekeeping and those specific to the intestine. The housekeeping gene clusters are required in all bacteria and are often major players in the main metabolic pathways including central carbon metabolism and amino acid synthesis. The gut-specific functions include adhesion to host proteins and the harvesting of sugars from globoseries glycolipids. Patients with irritable bowel syndrome were shown to exhibit 25% fewer genes and lower bacterial diversity than individuals not suffering from irritable bowel syndrome indicating that changes in patients' gut biome diversity may be associated with this condition.
1111:; Ion Torrent PGM System and 454 pyrosequencing typically produces ~400 bp reads, Illumina MiSeq produces 400-700bp reads (depending on whether paired end options are used), and SOLiD produce 25–75 bp reads. Historically, these read lengths were significantly shorter than the typical Sanger sequencing read length of ~750 bp, however the Illumina technology is quickly coming close to this benchmark. However, this limitation is compensated for by the much larger number of sequence reads. In 2009, pyrosequenced metagenomes generate 200–500 megabases, and Illumina platforms generate around 20–50 gigabases, but these outputs have increased by orders of magnitude in recent years.
1009:
49:
1438:
MEGAN run slowly to annotate large samples (e.g., several hours to process a small/medium size dataset/sample ). Thus, ultra-fast classifiers have recently emerged, thanks to more affordable powerful servers. These tools can perform the taxonomic annotation at extremely high speed, for example CLARK (according to CLARK's authors, it can classify accurately "32 million metagenomic short reads per minute"). At such a speed, a very large dataset/sample of a billion short reads can be processed in about 30 minutes.
1894:
1881:
high-throughput bioinformatic analysis pipelines. The sequence-driven approach to screening is limited by the breadth and accuracy of gene functions present in public sequence databases. In practice, experiments make use of a combination of both functional and sequence-based approaches based upon the function of interest, the complexity of the sample to be screened, and other factors. An example of success using metagenomics as a biotechnology for drug discovery is illustrated with the
377:
1175:
218:
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754:
332:
1426:(MEta Genome ANalyzer). A first version of the program was used in 2005 to analyse the metagenomic context of DNA sequences obtained from a mammoth bone. 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
7846:
7806:
1709:. Functional metagenomics strategies are being used to explore the interactions between plants and microbes through cultivation-independent study of these microbial communities. By allowing insights into the role of previously uncultivated or rare community members in nutrient cycling and the promotion of plant growth, metagenomic approaches can contribute to improved disease detection in
1262:. The use of reference genomes allows researchers to improve the assembly of the most abundant microbial species, but this approach is limited by the small subset of microbial phyla for which sequenced genomes are available. After an assembly is created, an additional challenge is "metagenomic deconvolution", or determining which sequences come from which species in the sample.
570:
1140:
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1991:(HMP), gut microbial communities were assayed using high-throughput DNA sequencing. HMP showed that, unlike individual microbial species, many metabolic processes were present among all body habitats with varying frequencies. Microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals were studied as part of the
869:, it did support early microbial morphology-based observations that diversity was far more complex than was known by culturing methods. Soon after that in 1995, Healy reported the metagenomic isolation of functional genes from "zoolibraries" constructed from a complex culture of environmental organisms grown in the laboratory on dried
1872:
approach is limited by availability of a suitable screen and the requirement that the desired trait be expressed in the host cell. Moreover, the low rate of discovery (less than one per 1,000 clones screened) and its labor-intensive nature further limit this approach. In contrast, sequence-driven analysis uses
1407:) a community resource for metagenome data set analysis. As of June 2012 over 14.8 terabases (14x10 bases) of DNA have been analyzed, with more than 10,000 public data sets freely available for comparison within MG-RAST. Over 8,000 users now have submitted a total of 50,000 metagenomes to MG-RAST. The
1901:
Metagenomics can provide valuable insights into the functional ecology of environmental communities. Metagenomic analysis of the bacterial consortia found in the defecations of
Australian sea lions suggests that nutrient-rich sea lion faeces may be an important nutrient source for coastal ecosystems.
1632:
for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics. Viral metagenomes (also called viromes) should thus provide more and more information about viral diversity and evolution. For example, a metagenomic pipeline called
1542:
researchers can piece together a metabolic network that goes beyond species boundaries. Such studies require detailed knowledge about which versions of which proteins are coded by which species and even by which strains of which species. Therefore, community genomic information is another fundamental
1476:
Additionally, several studies have also utilized oligonucleotide usage patterns to identify the differences across diverse microbial communities. Examples of such methodologies include the dinucleotide relative abundance approach by
Willner et al. and the HabiSign approach of Ghosh et al. This latter
1441:
With the increasing availability of samples containing ancient DNA and due to the uncertainty associated with the nature of those samples (ancient DNA damage), a fast tool capable of producing conservative similarity estimates has been made available. According to FALCON's authors, it can use relaxed
1437:
With the advent of fast and inexpensive sequencing instruments, the growth of databases of DNA sequences is now exponential (e.g., the NCBI GenBank database ). Faster and efficient tools are needed to keep pace with the high-throughput sequencing, because the BLAST-based approaches such as MG-RAST or
6992:
Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M.; Izard, Jacques; Cantarel, Brandi L.; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T.; Methé, Barbara; Schloss, Patrick D.; Gevers, Dirk; Mitreva, Makedonka;
2028:
shows promise as a sensitive and rapid method to diagnose infection by comparing genetic material found in a patient's sample to databases of all known microscopic human pathogens and thousands of other bacterial, viral, fungal, and parasitic organisms and databases on antimicrobial resistances gene
1983:
While these studies highlight some potentially valuable medical applications, only 31–48.8% of the reads could be aligned to 194 public human gut bacterial genomes and 7.6–21.2% to bacterial genomes available in GenBank which indicates that there is still far more research necessary to capture novel
1840:
Microbial communities produce a vast array of biologically active chemicals that are used in competition and communication. Many of the drugs in use today were originally uncovered in microbes; recent progress in mining the rich genetic resource of non-culturable microbes has led to the discovery of
1472:
as a whole rather than taxonomic groups, and shows that the functional complements are analogous under similar environmental conditions. Consequently, metadata on the environmental context of the metagenomic sample is especially important in comparative analyses, as it provides researchers with the
1871:
of metagenomic data: function-driven screening for an expressed trait, and sequence-driven screening for DNA sequences of interest. Function-driven analysis seeks to identify clones expressing a desired trait or useful activity, followed by biochemical characterization and sequence analysis. This
1385:
associated with metagenomic projects. Metadata includes detailed information about the three-dimensional (including depth, or height) geography and environmental features of the sample, physical data about the sample site, and the methodology of the sampling. This information is necessary both to
1225:
while metagenomic data is usually highly non-redundant. Furthermore, the increased use of second-generation sequencing technologies with short read lengths means that much of future metagenomic data will be error-prone. Taken in combination, these factors make the assembly of metagenomic sequence
1979:
The study demonstrated that two bacterial divisions, Bacteroidetes and
Firmicutes, constitute over 90% of the known phylogenetic categories that dominate distal gut bacteria. Using the relative gene frequencies found within the gut these researchers identified 1,244 metagenomic clusters that are
1975:
Another medical study as part of the MetaHit (Metagenomics of the Human
Intestinal Tract) project consisted of 124 individuals from Denmark and Spain consisting of healthy, overweight, and irritable bowel disease patients. The study attempted to categorize the depth and phylogenetic diversity of
1880:
to screen clones for the sequence of interest. In comparison to cloning-based approaches, using a sequence-only approach further reduces the amount of bench work required. The application of massively parallel sequencing also greatly increases the amount of sequence data generated, which require
1488:
A key goal in comparative metagenomics is to identify microbial group(s) which are responsible for conferring specific characteristics to a given environment. However, due to issues in the sequencing technologies artifacts need to be accounted for like in metagenomeSeq. Others have characterized
968:
Seas. Analysis of the metagenomic data collected during this journey revealed two groups of organisms, one composed of taxa adapted to environmental conditions of 'feast or famine', and a second composed of relatively fewer but more abundantly and widely distributed taxa primarily composed of
1681:
in which plants grow are inhabited by microbial communities, with one gram of soil containing around 10-10 microbial cells which comprise about one gigabase of sequence information. The microbial communities which inhabit soils are some of the most complex known to science, and remain poorly
1976:
gastrointestinal bacteria. Using
Illumina GA sequence data and SOAPdenovo, a de Bruijn graph-based tool specifically designed for assembly short reads, they were able to generate 6.58 million contigs greater than 500 bp for a total contig length of 10.3 Gb and a N50 length of 2.2 kb.
500:
Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful way of understanding the microbial world that might revolutionize understanding of biology. As the price of DNA sequencing continues to fall, metagenomics now allows
940:(GOS), circumnavigating the globe and collecting metagenomic samples throughout the journey. All of these samples were sequenced using shotgun sequencing, in hopes that new genomes (and therefore new organisms) would be identified. The pilot project, conducted in the
1450:
Comparative analyses between metagenomes can provide additional insight into the function of complex microbial communities and their role in host health. Pairwise or multiple comparisons between metagenomes can be made at the level of sequence composition (comparing
6869:
Qin, Junjie; Li, Ruiqiang; Raes, Jeroen; Arumugam, Manimozhiyan; Burgdorf, Kristoffer
Solvsten; Manichanh, Chaysavanh; Nielsen, Trine; Pons, Nicolas; Levenez, Florence; Yamada, Takuji; Mende, Daniel R.; Li, Junhua; Xu, Junming; Li, Shaochuan; Li, Dongfang (2010).
1477:
study also indicated that differences in tetranucleotide usage patterns can be used to identify genes (or metagenomic reads) originating from specific habitats. Additionally some methods as TriageTools or
Compareads detect similar reads between two read sets. The
1459:
and other phylogenetic marker genes, or—in the case of low-diversity communities—by genome reconstruction from the metagenomic dataset. Functional comparisons between metagenomes may be made by comparing sequences against reference databases such as
1369:, use read coverage landscape of individual reference genomes to minimize false-positive hits and get reliable relative abundances. In composition based binning, methods use intrinsic features of the sequence, such as oligonucleotide frequencies or
1194:
gene catalog identified 3.3 million genes assembled from 567.7 gigabases of sequence data. Collecting, curating, and extracting useful biological information from datasets of this size represent significant computational challenges for researchers.
852:
to explore the diversity of ribosomal RNA sequences. The insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985. This led to the first report of isolating and
1086:
An advantage to high throughput sequencing is that this technique does not require cloning the DNA before sequencing, removing one of the main biases and bottlenecks in environmental sampling. The first metagenomic studies conducted using
1936:
and for cleaning up contaminated environments. Increased understanding of how microbial communities cope with pollutants improves assessments of the potential of contaminated sites to recover from pollution and increases the chances of
1905:
DNA sequencing can also be used more broadly to identify species present in a body of water, debris filtered from the air, sample of dirt, or animal's faeces, and even detect diet items from blood meals. This can establish the range of
1960:, but their composition and the mechanism by which they do so remains mysterious. Metagenomic sequencing is being used to characterize the microbial communities from 15–18 body sites from at least 250 individuals. This is part of the
2011:
In animals, metagenomics can be used to profile their gut microbiomes and enable detection of antibiotic-resistant bacteria. This can have implications in monitoring the spread of diseases from wildlife to farmed animals and humans.
7741:
1394:
Several tools have been developed to integrate metadata and sequence data, allowing downstream comparative analyses of different datasets using a number of ecological indices. In 2007, Folker Meyer and Robert
Edwards and a team at
2542:
Healy FG, Ray RM, Aldrich HC, Wilkie AC, Ingram LO, Shanmugam KT (1995). "Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose".
1230:
that make assembly especially difficult because of the difference in the relative abundance of species present in the sample. Misassemblies can also involve the combination of sequences from more than one species into chimeric
1390:
and to enable downstream analysis. Because of its importance, metadata and collaborative data review and curation require standardized data formats located in specialized databases, such as the
Genomes OnLine Database (GOLD).
533:, and Sean F. Brady, and first appeared in publication in 1998. 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
1314:
prediction is that it enables the detection of coding regions that lack homologs in the sequence databases; however, it is most accurate when there are large regions of contiguous genomic DNA available for comparison.
1809:. Furthermore, knowledge of how these microbial communities function is required to control them, and metagenomics is a key tool in their understanding. Metagenomic approaches allow comparative analyses between
1999:
degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. The HMP has brought to light the utility of metagenomics in diagnostics and
1571:
Metagenomics allows researchers to access the functional and metabolic diversity of microbial communities, but it cannot show which of these processes are active. The extraction and analysis of metagenomic
1902:
This is because the bacteria that are expelled simultaneously with the defecations are adept at breaking down the nutrients in the faeces into a bioavailable form that can be taken up into the food chain.
877:
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
5913:
1118:(Hi-C), which measures the proximity of any two DNA sequences within the same cell, to guide microbial genome assembly. Long read sequencing technologies, including PacBio RSII and PacBio Sequel by
3073:
Béjà O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, et al. (October 2000). "Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage".
2697:
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. (March 2004). "Community structure and metabolism through reconstruction of microbial genomes from the environment".
1062:, refinements of DNA amplification, and the proliferation of computational power have greatly aided the analysis of DNA sequences recovered from environmental samples, allowing the adaptation of
1411:(IMG/M) system also provides a collection of tools for functional analysis of microbial communities based on their metagenome sequence, based upon reference isolate genomes included from the
6346:
1203:
The first step of metagenomic data analysis requires the execution of certain pre-filtering steps, including the removal of redundant, low-quality sequences and sequences of probable
4404:
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, et al. (December 2013). "Metagenomic species profiling using universal phylogenetic marker genes".
1182:
The data generated by metagenomics experiments are both enormous and inherently noisy, containing fragmented data representing as many as 10,000 species. The sequencing of the cow
6743:"A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus)"
2020:
Differentiating between infectious and non-infectious illness, and identifying the underlying etiology of infection, can be challenging. For example, more than half of cases of
1178:
Schematic representation of the main steps necessary for the analysis of whole metagenome shotgun sequencing-derived data. The software related to each step is shown in italics.
1995:
project. The metagenomic analysis revealed variations in niche specific abundance among 168 functional modules and 196 metabolic pathways within the microbiome. These included
1468:, and tabulating the abundance by category and evaluating any differences for statistical significance. This gene-centric approach emphasizes the functional complement of the
1207:
origin (especially in metagenomes of human origin). The methods available for the removal of contaminating eukaryotic genomic DNA sequences include Eu-Detect and DeConseq.
837:
species in a sample. Much of the interest in metagenomics comes from these discoveries that showed that the vast majority of microorganisms had previously gone unnoticed.
1302:, uses intrinsic features of the sequence to predict coding regions based upon gene training sets from related organisms. This is the approach taken by programs such as
3470:
Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, et al. (January 2011). "Metagenomic discovery of biomass-degrading genes and genomes from cow rumen".
4963:
Pratas D, Pinho AJ, Silva RM, Rodrigues JM, Hosseini M, Caetano T, Ferreira PJ (February 2018). "FALCON: a method to infer metagenomic composition of ancient DNA".
3846:
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS (September 2011). "Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets".
2920:
Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B, et al. (January 2006). "Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA".
5921:
2802:
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the
Sargasso Sea".
865:
false positives and supported the existence of a complex community of unexplored species. Although this methodology was limited to exploring highly conserved,
6741:
Chua, Physilia Y. S.; Carøe, Christian; Crampton-Platt, Alex; Reyes-Avila, Claudia S.; Jones, Gareth; Streicker, Daniel G.; Bohmann, Kristine (4 July 2022).
1357:
are methods based on unique clade-specific markers for estimating organismal relative abundances with improved computational performances. Other tools, like
5481:
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils".
7736:
1455:
or genome size), taxonomic diversity, or functional complement. Comparisons of population structure and phylogenetic diversity can be made on the basis of
2041:(blood-feeding) insects such as mosquitoes and ticks. Metagenomics is routinely used by public health officials and organisations for the surveillance of
428:) to deduce the individual genomes or parts of genomes that constitute the original environmental sample. This information can then be used to study the
363:
1066:
to metagenomic samples (known also as whole metagenome shotgun or WMGS sequencing). The approach, used to sequence many cultured microorganisms and the
6509:"Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens"
897:(see below) to show that 200 liters of seawater contains over 5000 different viruses. Subsequent studies showed that there are more than a thousand
829:, indicating that there are numerous non-isolated organisms. These surveys of ribosomal RNA genes taken directly from the environment revealed that
545:) defined metagenomics as "the application of modern genomics technique without the need for isolation and lab cultivation of individual species".
785:
621:
6377:
1341:
are used to rapidly search for phylogenetic markers or otherwise similar sequences in existing public databases. This approach is implemented in
2457:
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986). "The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences". In Marshall KC (ed.).
2588:"Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon"
1365:
is possible to profile species without a reference genome, improving the estimation of microbial community diversity. Recent methods, such as
7778:
6850:
6799:
6326:
6040:
3665:
2474:
2230:
652:
5997:
1624:
Metagenomic sequencing is particularly useful in the study of viral communities. As viruses lack a shared universal phylogenetic marker (as
1897:
Metagenomics allows the study of microbial communities like those present in this stream receiving acid drainage from surface coal mining.
1610:
to measure whole-genome expression and quantification of a microbial community, first employed in analysis of ammonia oxidation in soils.
1649:
Metagenomics has the potential to advance knowledge in a wide variety of fields. It can also be applied to solve practical challenges in
806:. However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be
7893:
1408:
7463:
910:
739:
542:
6607:"High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces"
5837:
Kerepesi C, Grolmusz V (June 2017). "The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys".
1797:
with higher productivity and lower cost. Metagenomic approaches to the analysis of complex microbial communities allow the targeted
1280:
use two approaches in the annotation of coding regions in the assembled contigs. The first approach is to identify genes based upon
1968:, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and
6690:
Chua, Physilia Y. S.; Crampton-Platt, Alex; Lammers, Youri; Alsos, Inger G.; Boessenkool, Sanne; Bohmann, Kristine (25 May 2021).
7898:
937:
734:
729:
7810:
7756:
2025:
1381:
The massive amount of exponentially growing sequence data is a daunting challenge that is complicated by the complexity of the
1115:
1039:
953:
857:
bulk DNA from an environmental sample, published by Pace and colleagues in 1991 while Pace was in the Department of Biology at
909:. Essentially all of the viruses in these studies were new species. In 2004, Gene Tyson, Jill Banfield, and colleagues at the
356:
6058:"Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics"
7784:
2037:
Metagenomics has been an invaluable tool to help characterise the diversity and ecology of pathogens that are vectored by
1221:
DNA sequence data from genomic and metagenomic projects are essentially the same, but genomic sequence data offers higher
1151:
about quality assessment: on assembly (N50, MetaQUAST), on genome (universal single-copy marker genes – CheckM and BUSCO).
6664:
4660:"The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes"
1607:
1560:
1123:
1096:
6995:"PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome"
1008:
7700:
7428:
3176:
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW (July 2010). Gilbert JA (ed.).
1790:
1396:
723:
7274:"Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus"
6217:
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, et al. (September 2010). Sonnenburg J (ed.).
5891:
1333:
provide the "who". In order to connect community composition and function in metagenomes, sequences must be binned.
7836:
6160:"Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing"
1877:
1337:
is the process of associating a particular sequence with an organism. In similarity-based binning, methods such as
1043:
997:
709:
125:
6816:
4611:"The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata"
3691:"Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies"
513:
directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities.
7790:
5532:
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016).
5152:"HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences"
862:
849:
778:
693:
510:
349:
5638:"IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes"
7746:
7591:
7523:
6558:"Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data"
5299:"Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes"
1988:
1961:
143:
6031:
Charles T (2010). "The Potential for Investigation of Plant-microbe Interactions Using Metagenomics Methods".
5935:
Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R, Philippot L (2009).
7883:
7731:
7603:
3418:"Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses"
2299:"Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products"
2001:
1227:
830:
807:
598:
486:
6790:
George I, Stenuit B, Agathos SN (2010). "Application of Metagenomics to Bioremediation". In Marco D (ed.).
6158:
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, et al. (January 2011). Aziz RK (ed.).
48:
7772:
7688:
7491:
7456:
6458:"Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library"
4914:"CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers"
2819:
2248:"Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes"
2222:
2054:
1893:
1547:
and proteomics) in the quest to determine how metabolites are transferred and transformed by a community.
1334:
914:
771:
758:
493:
gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of
6841:
Nelson KE and White BA (2010). "Metagenomics and Its Applications to the Study of the Human Microbiome".
1841:
new genes, enzymes, and natural products. The application of metagenomics has allowed the development of
1514:), during which the waste products of some organisms are metabolites for others. In one such system, the
1373:. Once sequences are binned, it is possible to carry out comparative analysis of diversity and richness.
7878:
7751:
7705:
2005:
1953:
1400:
1338:
1289:
1258:, have been optimized for the shorter reads produced by second-generation sequencing through the use of
977:
921:
system. This effort resulted in the complete, or nearly complete, genomes for a handful of bacteria and
316:
296:
261:
173:
168:
4008:"MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads"
2971:
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, et al. (March 2006).
5686:
1126:, is another choice to get long shotgun sequencing reads that should make ease in assembling process.
7511:
7496:
7336:
7179:
7006:
6948:
6883:
6618:
6171:
5996:
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007).
5545:
5490:
5351:
5114:
5057:
4964:
4463:
4267:
3902:
3751:
3646:
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007).
3534:
3479:
3323:
3189:
3082:
2929:
2876:
2811:
2706:
2648:
2411:
2352:
2119:
1825:
1810:
1767:
1762:. This process is dependent upon microbial consortia (association) that transform the cellulose into
1254:
but nevertheless produce good results when assembling metagenomic data sets. Other programs, such as
1104:
1067:
933:
608:
603:
3689:
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, et al. (2015).
2824:
376:
7721:
7695:
7553:
7540:
7501:
4812:
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (January 2013).
3738:
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, et al. (23 February 2012).
1854:
1842:
1806:
1683:
1566:
1523:
1277:
1174:
1119:
679:
613:
444:
291:
271:
236:
206:
163:
157:
148:
120:
5199:"TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data"
2024:
remain undiagnosed, despite extensive testing using state-of-the-art clinical laboratory methods.
7675:
7486:
7089:
6772:
6006:
5872:
5846:
5819:
5793:
5717:
5569:
5514:
4429:
3891:"Fast identification and removal of sequence contamination from genomic and metagenomic datasets"
3871:
3503:
3260:
3106:
2953:
2845:
2730:
2568:
1911:
1873:
1759:
1634:
1619:
1478:
1281:
1100:
1075:
1063:
918:
894:
858:
818:
704:
688:
668:
626:
506:
417:
286:
281:
256:
178:
2170:"Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity"
1721:
practices which improve crop health by harnessing the relationship between microbes and plants.
5338:
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, et al. (March 2011).
4106:"Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps"
2635:
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (October 2002).
7888:
7726:
7535:
7449:
7423:
7403:
7362:
7305:
7254:
7205:
7148:
7130:
7081:
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7034:
6974:
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6899:
6846:
6795:
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6723:
6646:
6587:
6538:
6489:
6438:
6369:
6322:
6299:
6250:
6199:
6140:
6089:
6036:
5864:
5811:
5766:
5709:
5667:
5618:
5561:
5506:
5463:
5428:
5379:
5320:
5279:
5228:
5179:
5132:
5083:
5015:
4945:
4894:
4843:
4794:
4740:
4709:
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. (January 2012).
4691:
4640:
4591:
4540:
4489:
4421:
4386:
4337:
4285:
4236:
4187:
4135:
4086:
4037:
3988:
3930:
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3828:
3779:
3720:
3671:
3661:
3615:
3560:
3495:
3449:
3398:
3349:
3310:
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. (February 2018).
3252:
3217:
3158:
3098:
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3004:
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2894:
2837:
2784:
2722:
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2617:
2560:
2524:
2470:
2439:
2380:
2320:
2279:
2226:
2199:
2147:
2069:
2004:. Thus metagenomics is a powerful tool to address many of the pressing issues in the field of
1996:
1691:
1687:
1629:
1625:
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1031:
1027:
989:
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841:
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646:
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526:
505:
to be investigated at a much greater scale and detail than before. Recent studies use either "
502:
490:
475:
429:
421:
409:
336:
221:
100:
5587:
Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. (January 2017).
4450:
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, et al. (March 2019).
7650:
7645:
7393:
7352:
7344:
7295:
7285:
7244:
7236:
7195:
7187:
7138:
7120:
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7014:
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6907:
6891:
6754:
6713:
6703:
6636:
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6528:
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6479:
6469:
6428:
6420:
6361:
6289:
6281:
6240:
6230:
6189:
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6130:
6120:
6079:
6069:
5948:
5856:
5803:
5756:
5748:
5701:
5657:
5649:
5636:
Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. (January 2019).
5608:
5600:
5553:
5498:
5455:
5418:
5410:
5369:
5359:
5310:
5269:
5259:
5218:
5210:
5169:
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5122:
5073:
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4997:
4935:
4925:
4884:
4874:
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4784:
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4730:
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4630:
4622:
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4571:
4530:
4520:
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4368:
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4319:
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4226:
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4125:
4117:
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4019:
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3818:
3810:
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3710:
3702:
3653:
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3542:
3487:
3439:
3429:
3388:
3380:
3339:
3331:
3290:
3244:
3207:
3197:
3148:
3140:
3090:
3045:
3035:
2994:
2984:
2937:
2884:
2829:
2774:
2764:
2714:
2666:
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2607:
2599:
2552:
2514:
2506:
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2429:
2419:
2370:
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2310:
2269:
2259:
2189:
2181:
2137:
2127:
1992:
1965:
1907:
1861:
1858:
1695:
1422:
One of the first standalone tools for analysing high-throughput metagenome shotgun data was
1370:
1255:
483:
228:
4609:
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, et al. (January 2012).
2863:
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, et al. (November 2010).
7862:
7665:
7655:
7640:
7576:
6507:
Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, et al. (April 2018).
4658:
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, et al. (September 2008).
1938:
1585:
1581:
1271:
1259:
902:
5687:"Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data"
5340:"Bacterial community structures are unique and resilient in full-scale bioenergy systems"
4761:
Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, et al. (February 2011).
1602:
metatranscriptomic studies of microbial communities to date. While originally limited to
1226:
reads into genomes difficult and unreliable. Misassemblies are caused by the presence of
7340:
7183:
7010:
6952:
6887:
6622:
6175:
5549:
5494:
5355:
5118:
5061:
4986:"Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes"
4467:
4271:
3906:
3755:
3538:
3483:
3327:
3193:
3086:
2933:
2880:
2815:
2710:
2652:
2415:
2356:
2123:
1153:
Please expand the section to include this information. Further details may exist on the
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7249:
7224:
7200:
7167:
7143:
7108:
7029:
6994:
6969:
6936:
6912:
6871:
6718:
6691:
6641:
6606:
6582:
6557:
6533:
6508:
6484:
6457:
6433:
6408:
6294:
6269:
6245:
6218:
6194:
6159:
6135:
6108:
6084:
6057:
5761:
5736:
5662:
5637:
5613:
5588:
5423:
5398:
5374:
5339:
5274:
5247:
5223:
5198:
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5078:
5045:
5010:
4985:
4940:
4913:
4889:
4862:
4838:
4813:
4789:
4762:
4735:
4710:
4686:
4659:
4635:
4610:
4586:
4559:
4535:
4509:"Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences"
4508:
4484:
4451:
4381:
4356:
4332:
4307:
4231:
4206:
4182:
4157:
4130:
4105:
4081:
4056:
4032:
4007:
3983:
3958:
3925:
3890:
3823:
3798:
3774:
3739:
3715:
3690:
3610:
3585:
3555:
3522:
3444:
3417:
3393:
3368:
3344:
3311:
3212:
3177:
3153:
3128:
3050:
3023:
2999:
2972:
2490:
2375:
2340:
2274:
2247:
2142:
2107:
2064:
1969:
1942:
1923:
1868:
1846:
1829:
1798:
1662:
1603:
1239:
1092:
1088:
1059:
1017:
985:
981:
980:
and colleagues published the first sequences of an environmental sample generated with
906:
879:
845:
401:
389:
276:
201:
7325:"Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool"
6365:
4984:
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. (August 2007).
4355:
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (June 2012).
2779:
2752:
2671:
2636:
2612:
2587:
2519:
2494:
2434:
2399:
2315:
2298:
2194:
2169:
7872:
7635:
7581:
7545:
7093:
7053:
6935:
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010).
6776:
5127:
5102:
3521:
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010).
3235:
Schuster SC (January 2008). "Next-generation sequencing transforms today's biology".
3094:
2510:
2495:"Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing"
2185:
2074:
2038:
1556:
1387:
1222:
993:
898:
890:
886:
874:
866:
580:
576:
561:
522:
7166:
Zakrzewski M, Rašić G, Darbro J, Krause L, Poo YS, Filipović I, et al. (2018).
5823:
4357:"Metagenomic microbial community profiling using unique clade-specific marker genes"
3875:
3814:
3740:"Assessment of metagenomic assembly using simulated next generation sequencing data"
3507:
2957:
2769:
2572:
1361:
and MetaPhyler, use universal marker genes to profile prokaryotic species. With the
7625:
7586:
7398:
7381:
5914:"Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes Print E-mail"
5876:
5721:
5573:
5518:
4433:
3264:
3127:
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (May 2013).
3110:
2849:
2734:
2021:
1850:
1461:
1346:
1330:
941:
929:
538:
494:
471:
392:
directly from samples taken from the environment (e.g. soil, sea water, human gut,
266:
7290:
6605:
Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012). Steinke D (ed.).
6424:
4711:"IMG/M: the integrated metagenome data management and comparative analysis system"
2603:
1442:
thresholds and edit distances without affecting the memory and speed performance.
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6631:
6235:
6184:
5459:
5446:
Klitgord N, Segrè D (August 2011). "Ecosystems biology of microbial metabolism".
5414:
5264:
3915:
3764:
3369:"Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond"
3202:
2365:
2264:
2132:
7598:
7530:
5315:
5298:
5164:
4779:
3312:"Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen"
2466:
1783:
1755:
1718:
1699:
1658:
1654:
1544:
1530:) working together in order to turn raw resources into fully metabolized waste (
1527:
854:
17:
7845:
7348:
7191:
7069:
5533:
5344:
Proceedings of the National Academy of Sciences of the United States of America
4763:"Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG"
4525:
4475:
3335:
2641:
Proceedings of the National Academy of Sciences of the United States of America
2404:
Proceedings of the National Academy of Sciences of the United States of America
1350:
7683:
7630:
7620:
7615:
7125:
6524:
6285:
5860:
5807:
5752:
4930:
3859:
3649:
The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
2400:"Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses"
1779:
1539:
1535:
1515:
1507:
1473:
ability to study the effect of habitat upon community structure and function.
1452:
1416:
1403:
released the Metagenomics Rapid Annotation using Subsystem Technology server (
1204:
1191:
1095:. Three other technologies commonly applied to environmental sampling are the
957:
799:
530:
448:
196:
110:
90:
65:
7134:
7077:
6903:
6768:
6074:
2341:"Bioinformatics for whole-genome shotgun sequencing of microbial communities"
1190:, or 279 billion base pairs of nucleotide sequence data, while the human gut
7742:
Matrix-assisted laser desorption ionization-time of flight mass spectrometer
7610:
6937:"A human gut microbial gene catalogue established by metagenomic sequencing"
6872:"A human gut microbial gene catalogue established by metagenomic sequencing"
6708:
5589:"IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses"
5364:
5001:
4879:
4676:
4452:"Microbial abundance, activity and population genomic profiling with mOTUs2"
3957:
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (December 2008).
3523:"A human gut microbial gene catalogue established by metagenomic sequencing"
3491:
2941:
2833:
2424:
2042:
1933:
1929:
1882:
1821:
1775:
1747:
1714:
1588:
profiles of complex communities. Because of the technical difficulties (the
1519:
1511:
1412:
1298:
1238:
There are several assembly programs, most of which can use information from
1107:
system. These techniques for sequencing DNA generate shorter fragments than
1023:
965:
811:
153:
7407:
7366:
7309:
7258:
7225:"Targeted Metagenomics Offers Insights into Potential Tick-Borne Pathogens"
7209:
7152:
7085:
7038:
6978:
6921:
6727:
6650:
6591:
6542:
6493:
6442:
6373:
6303:
6254:
6219:"An insect herbivore microbiome with high plant biomass-degrading capacity"
6203:
6144:
6125:
6093:
5868:
5815:
5770:
5713:
5705:
5671:
5622:
5565:
5510:
5467:
5432:
5383:
5324:
5283:
5232:
5183:
5136:
5087:
5019:
4949:
4898:
4847:
4798:
4744:
4695:
4644:
4595:
4544:
4493:
4425:
4390:
4341:
4289:
4240:
4191:
4139:
4090:
4057:"Velvet: algorithms for de novo short read assembly using de Bruijn graphs"
4041:
3992:
3934:
3867:
3832:
3783:
3724:
3675:
3619:
3564:
3499:
3453:
3402:
3353:
3256:
3221:
3162:
3102:
3059:
3008:
2989:
2949:
2898:
2865:"Genomic and functional adaptation in surface ocean planktonic prokaryotes"
2841:
2788:
2726:
2680:
2661:
2384:
2283:
2151:
1139:
6742:
6474:
6317:
Wong D (2010). "Applications of Metagenomics for Industrial Bioproducts".
5784:
Kerepesi C, Grolmusz V (March 2016). "Giant viruses of the Kutch Desert".
5653:
5604:
4829:
4626:
4280:
4255:
4173:
4121:
4072:
3974:
3434:
3384:
3295:
3278:
3040:
2621:
2564:
2528:
2443:
2324:
2203:
7472:
7240:
7168:"Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok"
6759:
5214:
5069:
4726:
4222:
4156:
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (September 2011).
4023:
1650:
1382:
1303:
1187:
970:
949:
479:
440:
212:
95:
85:
40:
7436:
The “Critical Assessment of Metagenome Interpretation” (CAMI) initiative
6960:
6895:
6109:"Bioprospecting metagenomes: glycosyl hydrolases for converting biomass"
5953:
5936:
5557:
5502:
4560:"SLIMM: species level identification of microorganisms from metagenomes"
3647:
3546:
3144:
2889:
2864:
2718:
2297:
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (October 1998).
901:
in human stool and possibly a million different viruses per kilogram of
7571:
6573:
6409:"Size Does Matter: Application-driven Approaches for Soil Metagenomics"
4576:
4417:
4372:
4323:
3706:
3601:
2556:
2398:
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (October 1985).
1802:
1794:
1771:
1743:
1735:
1730:
1666:
1598:
1531:
1404:
1354:
1307:
1242:
in order to improve the accuracy of assemblies. Some programs, such as
992:. Another early paper in this area appeared in 2006 by Robert Edwards,
945:
922:
834:
826:
489:, early environmental gene sequencing cloned specific genes (often the
432:
and functional potential of the microbial community of the environment.
5685:
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC (August 2017).
3248:
1489:
inter-microbial interactions between the resident microbial groups. A
1481:
they apply on reads is based on a number of identical words of length
6107:
Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (May 2009).
2059:
1957:
1818:
1814:
1251:
1247:
1232:
534:
105:
80:
6270:"Achievements and new knowledge unraveled by metagenomic approaches"
825:
sequences have been found which do not belong to any known cultured
821:
within a species, and generally different between species. Many 16S
5999:
Understanding Our Microbial Planet: The New Science of Metagenomics
5937:"TerraGenome: A consortium for the sequencing of a soil metagenome"
5851:
5737:"New dimensions of the virus world discovered through metagenomics"
4969:
3657:
3586:"Differential abundance analysis for microbial marker-gene surveys"
2973:"Using pyrosequencing to shed light on deep mine microbial ecology"
2106:
Wooley JC, Godzik A, Friedberg I (February 2010). Bourne PE (ed.).
1427:
7382:"Metagenomic arbovirus detection using MinION nanopore sequencing"
5798:
5246:
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P (2012).
1892:
1763:
1751:
1706:
1638:
1534:). Using comparative gene studies and expression experiments with
1518:
bioreactor, functional stability requires the presence of several
1423:
1342:
1293:
1243:
1183:
870:
375:
5735:
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV (January 2010).
5150:
Ghosh TS, Mohammed MH, Rajasingh H, Chadaram S, Mande SS (2011).
2586:
Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (February 1996).
1928:
Metagenomics can improve strategies for monitoring the impact of
1366:
810:
and thus cannot be sequenced. These early studies focused on 16S
7380:
Batovska J, Lynch SE, Rodoni BC, Sawbridge TI, Cogan NO (2017).
7052:
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022).
1739:
1710:
1702:
1678:
1589:
1573:
1465:
1431:
822:
7445:
6692:"Metagenomics: A viable tool for reconstructing herbivore diet"
7323:
Batovska J, Mee PT, Lynch SE, Sawbridge TI, Rodoni BC (2019).
5968:
5103:"Metagenomic signatures of 86 microbial and viral metagenomes"
4863:"A comparative evaluation of sequence classification programs"
4158:"Integrative analysis of environmental sequences using MEGAN4"
1506:
In many bacterial communities, natural or engineered (such as
1490:
1292:
searches. This type of approach is implemented in the program
1133:
814:
803:
381:
75:
70:
6556:
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (March 2011).
4006:
Namiki T, Hachiya T, Tanaka H, Sakakibara Y (November 2012).
956:, and completed a two-year expedition in 2006 to explore the
420:. These short sequences can then be put together again using
7435:
4558:
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K (2017).
1805:
with industrial applications in biofuel production, such as
7441:
1329:
Gene annotations provide the "what", while measurements of
1070:, randomly shears DNA, sequences many short sequences, and
3129:"Computational meta'omics for microbial community studies"
2637:"Genomic analysis of uncultured marine viral communities"
1606:
technology, metatranscriptomics studies have made use of
1510:), there is significant division of labor in metabolism (
1362:
1358:
4912:
Ounit R, Wanamaker S, Close TJ, Lonardi S (March 2015).
4207:"Ab initio gene identification in metagenomic sequences"
4104:
Burton JN, Liachko I, Dunham MJ, Shendure J (May 2014).
3799:"Filtering duplicate reads from 454 pyrosequencing data"
802:
begins with a culture of identical cells as a source of
3797:
Balzer S, Malde K, Grohme MA, Jonassen I (April 2013).
3584:
Paulson JN, Stine OC, Bravo HC, Pop M (December 2013).
3024:"Metagenomics - a guide from sampling to data analysis"
1250:
Assembler, were designed to be used to assemble single
925:
that had previously resisted attempts to culture them.
5920:. Vol. 6, no. 7. p. 309. Archived from
5397:
McInerney MJ, Sieber JR, Gunsalus RP (December 2009).
4507:
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M (2011).
7834:
3416:
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C (2020).
1114:
An emerging approach combines shotgun sequencing and
1022:
Recovery of DNA sequences longer than a few thousand
833:
based methods find less than 1% of the bacterial and
5248:"Compareads: comparing huge metagenomic experiments"
2753:"Exploring prokaryotic diversity in the genomic era"
7765:
7714:
7674:
7562:
7479:
4306:Huson DH, Auch AF, Qi J, Schuster SC (March 2007).
2219:
Metagenomics: Current Innovations and Future Trends
2168:Hugenholtz P, Goebel BM, Pace NR (September 1998).
1964:with primary goals to determine if there is a core
1417:
Genomic Encyclopedia of Bacteria and Archaea (GEBA)
861:. Considerable efforts ensured that these were not
817:(rRNA) sequences which are relatively short, often
6407:Kakirde KS, Parsley LC, Liles MR (November 2010).
3652:. Washington, D.C.: The National Academies Press.
3178:"Unlocking short read sequencing for metagenomics"
1284:with genes that are already publicly available in
952:never before seen. Venter thoroughly explored the
6665:"What's Swimming in the River? Just Look For DNA"
1641:in a saline desert and in Antarctic dry valleys.
932:, leader of the privately funded parallel of the
3641:
3639:
3637:
3635:
3633:
3631:
3629:
3367:Hiraoka S, Yang CC, Iwasaki W (September 2016).
1774:. Microbes also produce a variety of sources of
5973:TerraGenome international sequencing consortium
5197:Fimereli D, Detours V, Konopka T (April 2013).
4445:
4443:
2163:
2161:
2029:sequences with associated clinical phenotypes.
6843:Metagenomics: Theory, Methods and Applications
6792:Metagenomics: Theory, Methods and Applications
6402:
6400:
6398:
6347:"Biotechnological prospects from metagenomics"
6340:
6338:
6319:Metagenomics: Theory, Methods and Applications
6033:Metagenomics: Theory, Methods and Applications
6005:. The National Academies Press. Archived from
5991:
5989:
5297:Kuntal BK, Ghosh TS, Mande SS (October 2013).
5046:"Metagenomic analyses: past and future trends"
3579:
3577:
3022:Thomas T, Gilbert J, Meyer F (February 2012).
1682:understood despite their economic importance.
1122:, and Nanopore MinION, GridION, PromethION by
497:had been missed by cultivation-based methods.
7457:
5399:"Syntrophy in anaerobic global carbon cycles"
5101:Willner D, Thurber RV, Rohwer F (July 2009).
4205:Zhu W, Lomsadze A, Borodovsky M (July 2010).
3952:
3950:
3948:
3946:
3944:
3122:
3120:
2915:
2913:
2911:
779:
451:. The broad field may also be referred to as
357:
8:
7107:Chiu, Charles Y.; Miller, Steven A. (2019).
6456:Parachin NS, Gorwa-Grauslund MF (May 2011).
5039:
5037:
5035:
5033:
5031:
5029:
4756:
4754:
4301:
4299:
4151:
4149:
3959:"A bioinformatician's guide to metagenomics"
2692:
2690:
2101:
2099:
2097:
2095:
2093:
2091:
2089:
1030:was very difficult until recent advances in
1012:Flow diagram of a typical metagenome project
7737:Matrix-assisted laser desorption ionization
3465:
3463:
2461:. Vol. 9. Springer US. pp. 1–55.
1592:of mRNA, for example) in the collection of
7805:
7464:
7450:
7442:
3963:Microbiology and Molecular Biology Reviews
1637:showed the first evidence of existence of
786:
772:
552:
521:The term "metagenomics" was first used by
364:
350:
31:
7397:
7356:
7299:
7289:
7248:
7199:
7142:
7124:
7028:
7018:
6968:
6911:
6758:
6717:
6707:
6640:
6630:
6581:
6532:
6483:
6473:
6432:
6293:
6244:
6234:
6193:
6183:
6134:
6124:
6083:
6073:
5952:
5850:
5797:
5760:
5661:
5612:
5422:
5373:
5363:
5314:
5273:
5263:
5222:
5173:
5163:
5126:
5077:
5009:
4968:
4939:
4929:
4888:
4878:
4837:
4788:
4778:
4734:
4685:
4675:
4634:
4585:
4575:
4534:
4524:
4483:
4380:
4331:
4279:
4230:
4181:
4129:
4080:
4031:
3982:
3924:
3914:
3822:
3773:
3763:
3714:
3609:
3554:
3443:
3433:
3392:
3343:
3294:
3211:
3201:
3152:
3049:
3039:
3028:Microbial Informatics and Experimentation
2998:
2988:
2888:
2823:
2778:
2768:
2670:
2660:
2611:
2518:
2433:
2423:
2374:
2364:
2314:
2273:
2263:
2193:
2141:
2131:
1791:efficient industrial-scale deconstruction
1409:Integrated Microbial Genomes/Metagenomes
1173:
1007:
380:In metagenomics, the genetic materials (
7841:
2085:
1034:techniques allowed the construction of
944:, found DNA from nearly 2000 different
637:
589:
560:
447:or clinical samples by a method called
39:
27:Study of genes found in the environment
6864:
6862:
6345:Schloss PD, Handelsman J (June 2003).
6274:Applied Microbiology and Biotechnology
5890:Copeland CS (September–October 2017).
5050:Applied and Environmental Microbiology
4256:"What is microbial community ecology?"
2545:Applied Microbiology and Biotechnology
1867:Two types of analysis are used in the
1690:necessary for plant growth, including
7779:European Molecular Biology Laboratory
7054:"Taking metagenomics under the wings"
3889:Schmieder R, Edwards R (March 2011).
873:. After leaving the Pace laboratory,
7:
7272:Parry R, James ME, Asgari S (2021).
4861:Bazinet AL, Cummings MP (May 2012).
4308:"MEGAN analysis of metagenomic data"
1956:play a key role in preserving human
1746:conversion, as in the conversion of
893:, and colleagues used environmental
7438:to evaluate methods in metagenomics
6817:"How Microbes Defend and Define Us"
6268:Simon C, Daniel R (November 2009).
5158:. 12 Suppl 13 (Supplement 13): S9.
5044:Simon C, Daniel R (February 2011).
3695:Bioinformatics and Biology Insights
1097:Ion Torrent Personal Genome Machine
6056:Bringel F, Couée I (22 May 2015).
2493:, DeLong EF, Pace NR (July 1991).
1914:, and track seasonal populations.
984:, in this case massively parallel
911:University of California, Berkeley
740:Consortium for the Barcode of Life
543:University of California, Berkeley
25:
5899:Healthcare Journal of New Orleans
4055:Zerbino DR, Birney E (May 2008).
3279:"Metagenomics versus Moore's law"
443:material recovered directly from
7856:
7844:
7817:
7816:
7804:
6354:Current Opinion in Biotechnology
5448:Current Opinion in Biotechnology
5403:Current Opinion in Biotechnology
5128:10.1111/j.1462-2920.2009.01901.x
3969:(4): 557–78, Table of Contents.
3095:10.1046/j.1462-2920.2000.00133.x
2511:10.1128/jb.173.14.4371-4378.1991
2186:10.1128/JB.180.18.4765-4774.1998
1138:
1040:bacterial artificial chromosomes
938:Global Ocean Sampling Expedition
917:sequenced DNA extracted from an
753:
752:
568:
331:
330:
217:
216:
47:
7757:Chromosome conformation capture
6413:Soil Biology & Biochemistry
2770:10.1186/gb-2002-3-2-reviews0003
2339:Chen K, Pachter L (July 2005).
2026:Clinical metagenomic sequencing
1717:and the adaptation of enhanced
1596:there have been relatively few
1434:classifications, respectively.
1116:chromosome conformation capture
976:In 2005 Stephan C. Schuster at
954:West Coast of the United States
7399:10.1016/j.jviromet.2017.08.019
6747:Metabarcoding and Metagenomics
1972:tools to support these goals.
1628:for bacteria and archaea, and
1580:) provides information on the
1345:. Another tool, PhymmBL, uses
1042:(BACs), which provided better
844:in the field was conducted by
1:
7785:National Institutes of Health
7291:10.3390/microorganisms9081653
6425:10.1016/j.soilbio.2010.07.021
6366:10.1016/S0958-1669(03)00067-3
3815:10.1093/bioinformatics/btt047
2604:10.1128/jb.178.3.591-599.1996
2459:Advances in Microbial Ecology
2316:10.1016/S1074-5521(98)90108-9
7020:10.1371/journal.pcbi.1002358
6993:Huttenhower, Curtis (2012).
6632:10.1371/journal.pone.0036478
6236:10.1371/journal.pgen.1001129
6185:10.1371/journal.pone.0014519
5460:10.1016/j.copbio.2011.04.018
5415:10.1016/j.copbio.2009.10.001
5265:10.1186/1471-2105-13-S19-S10
3916:10.1371/journal.pone.0017288
3765:10.1371/journal.pone.0031386
3203:10.1371/journal.pone.0011840
2366:10.1371/journal.pcbi.0010024
2265:10.1371/journal.pbio.0050082
2133:10.1371/journal.pcbi.1000667
2016:Infectious disease diagnosis
1949:Gut microbe characterization
1864:is increasingly recognized.
1608:transcriptomics technologies
1561:Transcriptomics technologies
1413:Integrated Microbial Genomes
1124:Oxford Nanopore Technologies
7701:Structure-based drug design
7429:Nature Reviews Microbiology
7058:Nature Reviews Microbiology
6696:Molecular Ecology Resources
5941:Nature Reviews Microbiology
5534:"Uncovering Earth's virome"
5316:10.1016/j.ygeno.2013.08.004
5165:10.1186/1471-2105-12-s13-s9
4780:10.1186/1471-2105-12-S1-S21
4254:Konopka A (November 2009).
2467:10.1007/978-1-4757-0611-6_1
1962:Human Microbiome initiative
1698:, disease suppression, and
1692:fixing atmospheric nitrogen
1397:Argonne National Laboratory
7915:
7894:Environmental microbiology
7349:10.1038/s41598-019-55741-3
7192:10.1038/s41598-018-22945-y
7070:10.1038/s41579-022-00746-5
6999:PLOS Computational Biology
6845:. Caister Academic Press.
6794:. Caister Academic Press.
6462:Biotechnology for Biofuels
6321:. Caister Academic Press.
6113:Biotechnology for Biofuels
6035:. Caister Academic Press.
5107:Environmental Microbiology
4824:(Database issue): D36-42.
4721:(Database issue): D123-9.
4621:(Database issue): D571-9.
4526:10.1186/1471-2164-12-S2-S4
4476:10.1038/s41467-019-08844-4
3336:10.1038/s41467-018-03317-6
3075:Environmental Microbiology
2345:PLOS Computational Biology
2112:PLOS Computational Biology
2108:"A primer on metagenomics"
1921:
1793:of biomass requires novel
1728:
1686:perform a wide variety of
1617:
1564:
1554:
1485:shared by pairs of reads.
1347:interpolated Markov models
1322:
1269:
1214:
1089:high-throughput sequencing
1082:High-throughput sequencing
1015:
998:San Diego State University
982:high-throughput sequencing
710:High throughput sequencing
537:. In 2005, Kevin Chen and
408:) after multiplication by
7800:
7791:Wellcome Sanger Institute
7126:10.1038/s41576-019-0113-7
6815:Zimmer C (13 July 2010).
6562:Molecular Systems Biology
6525:10.1038/s41564-018-0110-1
6286:10.1007/s00253-009-2233-z
6062:Frontiers in Microbiology
5861:10.1007/s00705-017-3286-4
5808:10.1007/s00705-015-2720-8
5753:10.1016/j.tim.2009.11.003
4931:10.1186/s12864-015-1419-2
3860:10.1007/s12038-011-9105-2
3373:Microbes and Environments
3133:Molecular Systems Biology
1918:Environmental remediation
1758:, and other biomass into
1186:metagenome generated 279
948:, including 148 types of
848:and colleagues, who used
7747:Microfluidic-based tools
7592:Human Connectome Project
7524:Human Microbiome Project
6075:10.3389/fmicb.2015.00486
1989:Human Microbiome Project
1446:Comparative metagenomics
1310:. The main advantage of
1228:repetitive DNA sequences
1105:Applied Biosystems SOLiD
1091:used massively parallel
867:non-protein coding genes
647:Environmental DNA (eDNA)
416:) in an approach called
7899:Microbiology techniques
7732:Electrospray ionization
7604:Human Epigenome Project
7113:Nature Reviews Genetics
7109:"Clinical metagenomics"
6709:10.1111/1755-0998.13425
5365:10.1073/pnas.1015676108
4880:10.1186/1471-2105-13-92
4677:10.1186/1471-2105-9-386
3570:(subscription required)
3492:10.1126/science.1200387
2942:10.1126/science.1123360
2904:(subscription required)
2834:10.1126/science.1093857
2740:(subscription required)
2592:Journal of Bacteriology
2499:Journal of Bacteriology
2425:10.1073/pnas.82.20.6955
2303:Chemistry & Biology
2246:Eisen JA (March 2007).
2174:Journal of Bacteriology
2060:Epidemiology and sewage
2002:evidence-based medicine
1874:conserved DNA sequences
1813:microbial systems like
1103:MiSeq or HiSeq and the
7773:DNA Data Bank of Japan
7689:Human proteome project
7492:Computational genomics
6702:(7): 1755–0998.13425.
6126:10.1186/1754-6834-2-10
5969:"TerraGenome Homepage"
5741:Trends in Microbiology
5706:10.1038/nprot.2017.063
5642:Nucleic Acids Research
5593:Nucleic Acids Research
5203:Nucleic Acids Research
4818:Nucleic Acids Research
4715:Nucleic Acids Research
4615:Nucleic Acids Research
4211:Nucleic Acids Research
4012:Nucleic Acids Research
3848:Journal of Biosciences
2990:10.1186/1471-2164-7-57
2662:10.1073/pnas.202488399
2223:Caister Academic Press
2217:Marco, D, ed. (2011).
2033:Arbovirus surveillance
1898:
1199:Sequence pre-filtering
1179:
1149:is missing information
1013:
915:Joint Genome Institute
529:, Michelle R. Rondon,
495:microbial biodiversity
453:environmental genomics
433:
7752:Isotope affinity tags
7706:Expression proteomics
7424:Focus on Metagenomics
6475:10.1186/1754-6834-4-9
5892:"The World Within Us"
5002:10.1093/dnares/dsm018
4456:Nature Communications
4281:10.1038/ismej.2009.88
4174:10.1101/gr.120618.111
4122:10.1534/g3.114.011825
4073:10.1101/gr.074492.107
3975:10.1128/MMBR.00009-08
3435:10.1099/mgen.0.000409
3385:10.1264/jsme2.ME16024
3316:Nature Communications
3296:10.1038/nmeth0909-623
3041:10.1186/2042-5783-2-3
2751:Hugenholtz P (2002).
2006:personalized medicine
1954:Microbial communities
1896:
1857:where the benefit of
1555:Further information:
1415:(IMG) system and the
1401:University of Chicago
1276:Metagenomic analysis
1177:
1011:
978:Penn State University
482:rely upon cultivated
379:
317:Personalized medicine
311:Personalized medicine
174:Quantitative genetics
169:Mendelian inheritance
7512:Human Genome Project
7497:Comparative genomics
7241:10.1128/JCM.01893-20
6760:10.3897/mbmg.6.78756
5839:Archives of Virology
5786:Archives of Virology
5070:10.1128/AEM.02345-10
1807:glycoside hydrolases
1502:Community metabolism
1054:Shotgun metagenomics
1032:molecular biological
996:, and colleagues at
934:Human Genome Project
541:(researchers at the
237:Branches of genetics
7722:2-D electrophoresis
7696:Call-map proteomics
7554:Structural genomics
7541:Population genomics
7502:Functional genomics
7341:2019NatSR...919398B
7223:Thoendel M (2020).
7184:2018NatSR...8.4690Z
7011:2012PLSCB...8E2358A
6961:10.1038/nature08821
6953:2010Natur.464...59.
6896:10.1038/nature08821
6888:2010Natur.464...59.
6623:2012PLoSO...736478L
6513:Nature Microbiology
6176:2011PLoSO...614519J
5954:10.1038/nrmicro2119
5654:10.1093/nar/gky1127
5605:10.1093/nar/gkw1030
5558:10.1038/nature19094
5550:2016Natur.536..425P
5503:10.1038/nature04983
5495:2006Natur.442..806L
5356:2011PNAS..108.4158W
5119:2009EnvMi..11.1752W
5062:2011ApEnM..77.1153S
4830:10.1093/nar/gks1195
4627:10.1093/nar/gkr1100
4468:2019NatCo..10.1014M
4272:2009ISMEJ...3.1223K
3907:2011PLoSO...617288S
3756:2012PLoSO...731386M
3547:10.1038/nature08821
3539:2010Natur.464...59.
3484:2011Sci...331..463H
3328:2018NatCo...9..870S
3194:2010PLoSO...511840R
3145:10.1038/msb.2013.22
3087:2000EnvMi...2..516B
2934:2006Sci...311..392P
2890:10.1038/nature09530
2881:2010Natur.468...60Y
2816:2004Sci...304...66V
2719:10.1038/nature02340
2711:2004Natur.428...37T
2653:2002PNAS...9914250B
2416:1985PNAS...82.6955L
2357:2005PLSCB...1...24C
2124:2010PLSCB...6E0667W
1984:bacterial genomes.
1945:trials to succeed.
1770:of the sugars into
1684:Microbial consortia
1567:Metatranscriptomics
1551:Metatranscriptomics
1524:Syntrophobacterales
1120:Pacific Biosciences
1026:from environmental
928:Beginning in 2003,
840:In the 1980s early
680:Metatranscriptomics
556:Part of a series on
396:) after filtering (
207:Genetic engineering
164:Population genetics
35:Part of a series on
7676:Structural biology
7487:Cognitive genomics
6574:10.1038/msb.2011.6
6012:on 30 October 2012
5912:Jansson J (2011).
5252:BMC Bioinformatics
5215:10.1093/nar/gkt094
5156:BMC Bioinformatics
4867:BMC Bioinformatics
4767:BMC Bioinformatics
4727:10.1093/nar/gkr975
4664:BMC Bioinformatics
4577:10.7717/peerj.3138
4418:10.1038/nmeth.2693
4373:10.1038/nmeth.2066
4324:10.1101/gr.5969107
4223:10.1093/nar/gkq275
4024:10.1093/nar/gks678
3707:10.4137/BBI.S12462
3602:10.1038/nmeth.2658
3422:Microbial Genomics
2763:(2): REVIEWS0003.
2557:10.1007/BF00164771
1912:endangered species
1899:
1878:design PCR primers
1766:, followed by the
1760:cellulosic ethanol
1688:ecosystem services
1635:Giant Virus Finder
1620:Viral metagenomics
1479:similarity measure
1286:sequence databases
1180:
1093:454 pyrosequencing
1076:consensus sequence
1064:shotgun sequencing
1014:
919:acid mine drainage
895:shotgun sequencing
859:Indiana University
705:Shotgun sequencing
622:macroinvertebrates
470:While traditional
461:community genomics
434:
418:shotgun sequencing
179:Molecular genetics
138:History and topics
7832:
7831:
7727:Mass spectrometer
7536:Personal genomics
6852:978-1-904455-54-7
6801:978-1-904455-54-7
6419:(11): 1911–1923.
6328:978-1-904455-54-7
6042:978-1-904455-54-7
5924:on 31 March 2012.
5648:(D1): D678–D686.
5599:(D1): D457–D465.
5258:(Suppl 19): S10.
3667:978-0-309-10676-4
3249:10.1038/nmeth1156
2476:978-1-4757-0611-6
2232:978-1-904455-87-5
2070:Microbial ecology
1997:glycosaminoglycan
1594:environmental RNA
1578:metatranscriptome
1349:to assign reads.
1331:species diversity
1325:Species diversity
1319:Species diversity
1217:Sequence assembly
1172:
1171:
1109:Sanger sequencing
1048:molecular cloning
990:454 Life Sciences
905:, including many
796:
795:
719:Extracellular RNA
653:environmental RNA
527:Robert M. Goodman
503:microbial ecology
476:genome sequencing
430:species diversity
374:
373:
101:Genetic variation
16:(Redirected from
7906:
7861:
7860:
7859:
7849:
7848:
7840:
7820:
7819:
7808:
7807:
7651:Pharmacogenomics
7646:Pharmacogenetics
7466:
7459:
7452:
7443:
7412:
7411:
7401:
7377:
7371:
7370:
7360:
7320:
7314:
7313:
7303:
7293:
7269:
7263:
7262:
7252:
7229:J Clin Microbiol
7220:
7214:
7213:
7203:
7163:
7157:
7156:
7146:
7128:
7104:
7098:
7097:
7049:
7043:
7042:
7032:
7022:
6989:
6983:
6982:
6972:
6932:
6926:
6925:
6915:
6866:
6857:
6856:
6838:
6832:
6831:
6829:
6827:
6812:
6806:
6805:
6787:
6781:
6780:
6762:
6738:
6732:
6731:
6721:
6711:
6687:
6681:
6680:
6678:
6676:
6661:
6655:
6654:
6644:
6634:
6602:
6596:
6595:
6585:
6553:
6547:
6546:
6536:
6504:
6498:
6497:
6487:
6477:
6453:
6447:
6446:
6436:
6404:
6393:
6392:
6390:
6388:
6382:
6376:. Archived from
6351:
6342:
6333:
6332:
6314:
6308:
6307:
6297:
6265:
6259:
6258:
6248:
6238:
6214:
6208:
6207:
6197:
6187:
6155:
6149:
6148:
6138:
6128:
6104:
6098:
6097:
6087:
6077:
6053:
6047:
6046:
6028:
6022:
6021:
6019:
6017:
6011:
6004:
5993:
5984:
5983:
5981:
5979:
5965:
5959:
5958:
5956:
5932:
5926:
5925:
5909:
5903:
5902:
5896:
5887:
5881:
5880:
5854:
5845:(6): 1671–1676.
5834:
5828:
5827:
5801:
5781:
5775:
5774:
5764:
5732:
5726:
5725:
5700:(8): 1673–1682.
5694:Nature Protocols
5691:
5682:
5676:
5675:
5665:
5633:
5627:
5626:
5616:
5584:
5578:
5577:
5544:(7617): 425–30.
5529:
5523:
5522:
5478:
5472:
5471:
5443:
5437:
5436:
5426:
5394:
5388:
5387:
5377:
5367:
5335:
5329:
5328:
5318:
5294:
5288:
5287:
5277:
5267:
5243:
5237:
5236:
5226:
5194:
5188:
5187:
5177:
5167:
5147:
5141:
5140:
5130:
5098:
5092:
5091:
5081:
5041:
5024:
5023:
5013:
4981:
4975:
4974:
4972:
4960:
4954:
4953:
4943:
4933:
4909:
4903:
4902:
4892:
4882:
4858:
4852:
4851:
4841:
4809:
4803:
4802:
4792:
4782:
4773:(Suppl 1): S21.
4758:
4749:
4748:
4738:
4706:
4700:
4699:
4689:
4679:
4655:
4649:
4648:
4638:
4606:
4600:
4599:
4589:
4579:
4555:
4549:
4548:
4538:
4528:
4504:
4498:
4497:
4487:
4447:
4438:
4437:
4401:
4395:
4394:
4384:
4352:
4346:
4345:
4335:
4303:
4294:
4293:
4283:
4260:The ISME Journal
4251:
4245:
4244:
4234:
4202:
4196:
4195:
4185:
4153:
4144:
4143:
4133:
4101:
4095:
4094:
4084:
4052:
4046:
4045:
4035:
4003:
3997:
3996:
3986:
3954:
3939:
3938:
3928:
3918:
3886:
3880:
3879:
3843:
3837:
3836:
3826:
3794:
3788:
3787:
3777:
3767:
3735:
3729:
3728:
3718:
3686:
3680:
3679:
3643:
3624:
3623:
3613:
3581:
3572:
3571:
3568:
3558:
3518:
3512:
3511:
3467:
3458:
3457:
3447:
3437:
3413:
3407:
3406:
3396:
3364:
3358:
3357:
3347:
3307:
3301:
3300:
3298:
3289:(9): 623. 2009.
3275:
3269:
3268:
3232:
3226:
3225:
3215:
3205:
3173:
3167:
3166:
3156:
3124:
3115:
3114:
3070:
3064:
3063:
3053:
3043:
3019:
3013:
3012:
3002:
2992:
2968:
2962:
2961:
2917:
2906:
2905:
2902:
2892:
2860:
2854:
2853:
2827:
2799:
2793:
2792:
2782:
2772:
2748:
2742:
2741:
2738:
2694:
2685:
2684:
2674:
2664:
2632:
2626:
2625:
2615:
2583:
2577:
2576:
2539:
2533:
2532:
2522:
2487:
2481:
2480:
2454:
2448:
2447:
2437:
2427:
2395:
2389:
2388:
2378:
2368:
2336:
2330:
2328:
2318:
2294:
2288:
2287:
2277:
2267:
2243:
2237:
2236:
2214:
2208:
2207:
2197:
2165:
2156:
2155:
2145:
2135:
2103:
1993:human microbiome
1966:human microbiome
1908:invasive species
1862:chiral synthesis
1859:enzyme-catalyzed
1696:nutrient cycling
1377:Data integration
1371:codon usage bias
1260:de Bruijn graphs
1256:Velvet assembler
1167:
1164:
1158:
1142:
1134:
788:
781:
774:
761:
756:
755:
572:
553:
439:is the study of
422:assembly methods
366:
359:
352:
339:
334:
333:
229:Medical genetics
225:
220:
219:
51:
32:
21:
18:Human metagenome
7914:
7913:
7909:
7908:
7907:
7905:
7904:
7903:
7869:
7868:
7867:
7857:
7855:
7843:
7835:
7833:
7828:
7796:
7761:
7710:
7670:
7666:Transcriptomics
7656:Systems biology
7641:Paleopolyploidy
7577:Cheminformatics
7558:
7475:
7470:
7432:journal website
7420:
7415:
7386:J Virol Methods
7379:
7378:
7374:
7322:
7321:
7317:
7271:
7270:
7266:
7222:
7221:
7217:
7165:
7164:
7160:
7106:
7105:
7101:
7051:
7050:
7046:
7005:(6): e1002358.
6991:
6990:
6986:
6947:(7285): 59–65.
6934:
6933:
6929:
6882:(7285): 59–65.
6868:
6867:
6860:
6853:
6840:
6839:
6835:
6825:
6823:
6814:
6813:
6809:
6802:
6789:
6788:
6784:
6740:
6739:
6735:
6689:
6688:
6684:
6674:
6672:
6663:
6662:
6658:
6604:
6603:
6599:
6555:
6554:
6550:
6506:
6505:
6501:
6455:
6454:
6450:
6406:
6405:
6396:
6386:
6384:
6383:on 4 March 2016
6380:
6349:
6344:
6343:
6336:
6329:
6316:
6315:
6311:
6267:
6266:
6262:
6229:(9): e1001129.
6216:
6215:
6211:
6157:
6156:
6152:
6106:
6105:
6101:
6055:
6054:
6050:
6043:
6030:
6029:
6025:
6015:
6013:
6009:
6002:
5995:
5994:
5987:
5977:
5975:
5967:
5966:
5962:
5934:
5933:
5929:
5911:
5910:
5906:
5894:
5889:
5888:
5884:
5836:
5835:
5831:
5783:
5782:
5778:
5734:
5733:
5729:
5689:
5684:
5683:
5679:
5635:
5634:
5630:
5586:
5585:
5581:
5531:
5530:
5526:
5489:(7104): 806–9.
5480:
5479:
5475:
5445:
5444:
5440:
5396:
5395:
5391:
5350:(10): 4158–63.
5337:
5336:
5332:
5296:
5295:
5291:
5245:
5244:
5240:
5196:
5195:
5191:
5149:
5148:
5144:
5100:
5099:
5095:
5043:
5042:
5027:
4983:
4982:
4978:
4962:
4961:
4957:
4911:
4910:
4906:
4860:
4859:
4855:
4811:
4810:
4806:
4760:
4759:
4752:
4708:
4707:
4703:
4657:
4656:
4652:
4608:
4607:
4603:
4557:
4556:
4552:
4519:(Suppl 2): S4.
4506:
4505:
4501:
4449:
4448:
4441:
4403:
4402:
4398:
4354:
4353:
4349:
4312:Genome Research
4305:
4304:
4297:
4266:(11): 1223–30.
4253:
4252:
4248:
4204:
4203:
4199:
4162:Genome Research
4155:
4154:
4147:
4103:
4102:
4098:
4061:Genome Research
4054:
4053:
4049:
4005:
4004:
4000:
3956:
3955:
3942:
3888:
3887:
3883:
3845:
3844:
3840:
3796:
3795:
3791:
3737:
3736:
3732:
3688:
3687:
3683:
3668:
3645:
3644:
3627:
3583:
3582:
3575:
3569:
3533:(7285): 59–65.
3520:
3519:
3515:
3478:(6016): 463–7.
3469:
3468:
3461:
3415:
3414:
3410:
3366:
3365:
3361:
3309:
3308:
3304:
3277:
3276:
3272:
3234:
3233:
3229:
3175:
3174:
3170:
3126:
3125:
3118:
3072:
3071:
3067:
3021:
3020:
3016:
2970:
2969:
2965:
2928:(5759): 392–4.
2919:
2918:
2909:
2903:
2862:
2861:
2857:
2825:10.1.1.124.1840
2810:(5667): 66–74.
2801:
2800:
2796:
2750:
2749:
2745:
2739:
2705:(6978): 37–43.
2696:
2695:
2688:
2647:(22): 14250–5.
2634:
2633:
2629:
2585:
2584:
2580:
2541:
2540:
2536:
2489:
2488:
2484:
2477:
2456:
2455:
2451:
2397:
2396:
2392:
2338:
2337:
2333:
2296:
2295:
2291:
2245:
2244:
2240:
2233:
2216:
2215:
2211:
2180:(18): 4765–74.
2167:
2166:
2159:
2118:(2): e1000667.
2105:
2104:
2087:
2083:
2051:
2035:
2018:
1951:
1939:bioaugmentation
1926:
1920:
1891:
1855:pharmaceuticals
1838:
1830:leafcutter ants
1733:
1727:
1675:
1647:
1622:
1616:
1590:short half-life
1569:
1563:
1553:
1504:
1499:
1448:
1379:
1327:
1321:
1296:4. The second,
1274:
1272:Gene prediction
1268:
1266:Gene prediction
1240:paired-end tags
1219:
1213:
1201:
1168:
1162:
1159:
1152:
1143:
1132:
1084:
1056:
1020:
1006:
903:marine sediment
792:
751:
744:
735:Diet assessment
726:
714:
700:
684:
675:
659:
649:
633:
585:
583:
575:
551:
519:
370:
329:
322:
321:
312:
304:
303:
302:
301:
250:
242:
241:
233:
211:
192:
184:
183:
139:
131:
130:
117:
116:
115:
59:
28:
23:
22:
15:
12:
11:
5:
7912:
7910:
7902:
7901:
7896:
7891:
7886:
7884:Bioinformatics
7881:
7871:
7870:
7866:
7865:
7853:
7830:
7829:
7827:
7826:
7814:
7801:
7798:
7797:
7795:
7794:
7788:
7782:
7776:
7769:
7767:
7763:
7762:
7760:
7759:
7754:
7749:
7744:
7739:
7734:
7729:
7724:
7718:
7716:
7715:Research tools
7712:
7711:
7709:
7708:
7703:
7698:
7693:
7692:
7691:
7680:
7678:
7672:
7671:
7669:
7668:
7663:
7661:Toxicogenomics
7658:
7653:
7648:
7643:
7638:
7633:
7628:
7623:
7618:
7613:
7608:
7607:
7606:
7596:
7595:
7594:
7584:
7579:
7574:
7568:
7566:
7564:Bioinformatics
7560:
7559:
7557:
7556:
7551:
7543:
7538:
7533:
7528:
7527:
7526:
7516:
7515:
7514:
7507:Genome project
7504:
7499:
7494:
7489:
7483:
7481:
7477:
7476:
7471:
7469:
7468:
7461:
7454:
7446:
7440:
7439:
7433:
7419:
7418:External links
7416:
7414:
7413:
7372:
7315:
7278:Microorganisms
7264:
7215:
7158:
7119:(6): 341–355.
7099:
7044:
6984:
6927:
6858:
6851:
6833:
6821:New York Times
6807:
6800:
6782:
6733:
6682:
6671:. 24 July 2013
6656:
6597:
6548:
6519:(4): 415–422.
6499:
6448:
6394:
6334:
6327:
6309:
6260:
6209:
6150:
6099:
6048:
6041:
6023:
5985:
5960:
5927:
5904:
5882:
5829:
5776:
5727:
5677:
5628:
5579:
5524:
5473:
5438:
5389:
5330:
5289:
5238:
5189:
5142:
5113:(7): 1752–66.
5093:
5056:(4): 1153–61.
5025:
4976:
4970:10.1101/267179
4955:
4904:
4853:
4804:
4750:
4701:
4650:
4601:
4550:
4499:
4439:
4412:(12): 1196–9.
4406:Nature Methods
4396:
4361:Nature Methods
4347:
4295:
4246:
4197:
4168:(9): 1552–60.
4145:
4116:(7): 1339–46.
4096:
4047:
3998:
3940:
3881:
3838:
3803:Bioinformatics
3789:
3730:
3681:
3666:
3658:10.17226/11902
3625:
3596:(12): 1200–2.
3590:Nature Methods
3573:
3513:
3459:
3408:
3359:
3302:
3283:Nature Methods
3270:
3237:Nature Methods
3227:
3168:
3116:
3065:
3014:
2963:
2907:
2875:(7320): 60–6.
2855:
2794:
2757:Genome Biology
2743:
2686:
2627:
2578:
2534:
2505:(14): 4371–8.
2482:
2475:
2449:
2410:(20): 6955–9.
2390:
2331:
2309:(10): R245-9.
2289:
2238:
2231:
2209:
2157:
2084:
2082:
2079:
2078:
2077:
2072:
2067:
2065:Metaproteomics
2062:
2057:
2050:
2047:
2034:
2031:
2017:
2014:
1970:bioinformatics
1950:
1947:
1943:biostimulation
1924:Bioremediation
1922:Main article:
1919:
1916:
1890:
1887:
1869:bioprospecting
1847:fine chemicals
1837:
1834:
1817:fermenters or
1729:Main article:
1726:
1723:
1674:
1671:
1663:sustainability
1646:
1643:
1618:Main article:
1615:
1612:
1565:Main article:
1552:
1549:
1503:
1500:
1498:
1495:
1447:
1444:
1378:
1375:
1363:mOTUs profiler
1323:Main article:
1320:
1317:
1270:Main article:
1267:
1264:
1215:Main article:
1212:
1209:
1200:
1197:
1170:
1169:
1146:
1144:
1137:
1131:
1130:Bioinformatics
1128:
1083:
1080:
1060:bioinformatics
1055:
1052:
1018:DNA sequencing
1016:Main article:
1005:
1002:
986:pyrosequencing
936:, has led the
907:bacteriophages
846:Norman R. Pace
842:molecular work
794:
793:
791:
790:
783:
776:
768:
765:
764:
763:
762:
746:
745:
743:
742:
737:
732:
727:
721:
715:
713:
712:
707:
701:
699:
698:
697:
696:
685:
683:
682:
676:
674:
673:
672:
671:
660:
658:
657:
656:
655:
643:
640:
639:
635:
634:
632:
631:
630:
629:
624:
616:
611:
606:
601:
595:
592:
591:
587:
586:
573:
565:
564:
558:
557:
550:
547:
518:
515:
474:and microbial
372:
371:
369:
368:
361:
354:
346:
343:
342:
341:
340:
324:
323:
320:
319:
313:
310:
309:
306:
305:
300:
299:
294:
289:
284:
279:
277:Immunogenetics
274:
269:
264:
259:
253:
252:
251:
248:
247:
244:
243:
240:
239:
232:
231:
226:
209:
204:
202:DNA sequencing
199:
193:
190:
189:
186:
185:
182:
181:
176:
171:
166:
161:
151:
146:
140:
137:
136:
133:
132:
129:
128:
123:
114:
113:
108:
103:
98:
93:
88:
83:
78:
73:
68:
62:
61:
60:
58:Key components
57:
56:
53:
52:
44:
43:
37:
36:
26:
24:
14:
13:
10:
9:
6:
4:
3:
2:
7911:
7900:
7897:
7895:
7892:
7890:
7887:
7885:
7882:
7880:
7877:
7876:
7874:
7864:
7854:
7852:
7847:
7842:
7838:
7825:
7824:
7815:
7813:
7812:
7803:
7802:
7799:
7792:
7789:
7786:
7783:
7780:
7777:
7774:
7771:
7770:
7768:
7766:Organizations
7764:
7758:
7755:
7753:
7750:
7748:
7745:
7743:
7740:
7738:
7735:
7733:
7730:
7728:
7725:
7723:
7720:
7719:
7717:
7713:
7707:
7704:
7702:
7699:
7697:
7694:
7690:
7687:
7686:
7685:
7682:
7681:
7679:
7677:
7673:
7667:
7664:
7662:
7659:
7657:
7654:
7652:
7649:
7647:
7644:
7642:
7639:
7637:
7636:Nutrigenomics
7634:
7632:
7629:
7627:
7624:
7622:
7619:
7617:
7614:
7612:
7609:
7605:
7602:
7601:
7600:
7597:
7593:
7590:
7589:
7588:
7585:
7583:
7582:Chemogenomics
7580:
7578:
7575:
7573:
7570:
7569:
7567:
7565:
7561:
7555:
7552:
7550:
7548:
7544:
7542:
7539:
7537:
7534:
7532:
7529:
7525:
7522:
7521:
7520:
7517:
7513:
7510:
7509:
7508:
7505:
7503:
7500:
7498:
7495:
7493:
7490:
7488:
7485:
7484:
7482:
7478:
7474:
7467:
7462:
7460:
7455:
7453:
7448:
7447:
7444:
7437:
7434:
7431:
7430:
7425:
7422:
7421:
7417:
7409:
7405:
7400:
7395:
7391:
7387:
7383:
7376:
7373:
7368:
7364:
7359:
7354:
7350:
7346:
7342:
7338:
7334:
7330:
7326:
7319:
7316:
7311:
7307:
7302:
7297:
7292:
7287:
7283:
7279:
7275:
7268:
7265:
7260:
7256:
7251:
7246:
7242:
7238:
7234:
7230:
7226:
7219:
7216:
7211:
7207:
7202:
7197:
7193:
7189:
7185:
7181:
7177:
7173:
7169:
7162:
7159:
7154:
7150:
7145:
7140:
7136:
7132:
7127:
7122:
7118:
7114:
7110:
7103:
7100:
7095:
7091:
7087:
7083:
7079:
7075:
7071:
7067:
7063:
7059:
7055:
7048:
7045:
7040:
7036:
7031:
7026:
7021:
7016:
7012:
7008:
7004:
7000:
6996:
6988:
6985:
6980:
6976:
6971:
6966:
6962:
6958:
6954:
6950:
6946:
6942:
6938:
6931:
6928:
6923:
6919:
6914:
6909:
6905:
6901:
6897:
6893:
6889:
6885:
6881:
6877:
6873:
6865:
6863:
6859:
6854:
6848:
6844:
6837:
6834:
6822:
6818:
6811:
6808:
6803:
6797:
6793:
6786:
6783:
6778:
6774:
6770:
6766:
6761:
6756:
6752:
6748:
6744:
6737:
6734:
6729:
6725:
6720:
6715:
6710:
6705:
6701:
6697:
6693:
6686:
6683:
6670:
6666:
6660:
6657:
6652:
6648:
6643:
6638:
6633:
6628:
6624:
6620:
6617:(5): e36478.
6616:
6612:
6608:
6601:
6598:
6593:
6589:
6584:
6579:
6575:
6571:
6567:
6563:
6559:
6552:
6549:
6544:
6540:
6535:
6530:
6526:
6522:
6518:
6514:
6510:
6503:
6500:
6495:
6491:
6486:
6481:
6476:
6471:
6467:
6463:
6459:
6452:
6449:
6444:
6440:
6435:
6430:
6426:
6422:
6418:
6414:
6410:
6403:
6401:
6399:
6395:
6379:
6375:
6371:
6367:
6363:
6360:(3): 303–10.
6359:
6355:
6348:
6341:
6339:
6335:
6330:
6324:
6320:
6313:
6310:
6305:
6301:
6296:
6291:
6287:
6283:
6280:(2): 265–76.
6279:
6275:
6271:
6264:
6261:
6256:
6252:
6247:
6242:
6237:
6232:
6228:
6224:
6223:PLOS Genetics
6220:
6213:
6210:
6205:
6201:
6196:
6191:
6186:
6181:
6177:
6173:
6170:(1): e14519.
6169:
6165:
6161:
6154:
6151:
6146:
6142:
6137:
6132:
6127:
6122:
6118:
6114:
6110:
6103:
6100:
6095:
6091:
6086:
6081:
6076:
6071:
6067:
6063:
6059:
6052:
6049:
6044:
6038:
6034:
6027:
6024:
6008:
6001:
6000:
5992:
5990:
5986:
5974:
5970:
5964:
5961:
5955:
5950:
5946:
5942:
5938:
5931:
5928:
5923:
5919:
5915:
5908:
5905:
5900:
5893:
5886:
5883:
5878:
5874:
5870:
5866:
5862:
5858:
5853:
5848:
5844:
5840:
5833:
5830:
5825:
5821:
5817:
5813:
5809:
5805:
5800:
5795:
5791:
5787:
5780:
5777:
5772:
5768:
5763:
5758:
5754:
5750:
5746:
5742:
5738:
5731:
5728:
5723:
5719:
5715:
5711:
5707:
5703:
5699:
5695:
5688:
5681:
5678:
5673:
5669:
5664:
5659:
5655:
5651:
5647:
5643:
5639:
5632:
5629:
5624:
5620:
5615:
5610:
5606:
5602:
5598:
5594:
5590:
5583:
5580:
5575:
5571:
5567:
5563:
5559:
5555:
5551:
5547:
5543:
5539:
5535:
5528:
5525:
5520:
5516:
5512:
5508:
5504:
5500:
5496:
5492:
5488:
5484:
5477:
5474:
5469:
5465:
5461:
5457:
5453:
5449:
5442:
5439:
5434:
5430:
5425:
5420:
5416:
5412:
5409:(6): 623–32.
5408:
5404:
5400:
5393:
5390:
5385:
5381:
5376:
5371:
5366:
5361:
5357:
5353:
5349:
5345:
5341:
5334:
5331:
5326:
5322:
5317:
5312:
5309:(4): 409–18.
5308:
5304:
5300:
5293:
5290:
5285:
5281:
5276:
5271:
5266:
5261:
5257:
5253:
5249:
5242:
5239:
5234:
5230:
5225:
5220:
5216:
5212:
5208:
5204:
5200:
5193:
5190:
5185:
5181:
5176:
5171:
5166:
5161:
5157:
5153:
5146:
5143:
5138:
5134:
5129:
5124:
5120:
5116:
5112:
5108:
5104:
5097:
5094:
5089:
5085:
5080:
5075:
5071:
5067:
5063:
5059:
5055:
5051:
5047:
5040:
5038:
5036:
5034:
5032:
5030:
5026:
5021:
5017:
5012:
5007:
5003:
4999:
4996:(4): 169–81.
4995:
4991:
4987:
4980:
4977:
4971:
4966:
4959:
4956:
4951:
4947:
4942:
4937:
4932:
4927:
4923:
4919:
4915:
4908:
4905:
4900:
4896:
4891:
4886:
4881:
4876:
4872:
4868:
4864:
4857:
4854:
4849:
4845:
4840:
4835:
4831:
4827:
4823:
4819:
4815:
4808:
4805:
4800:
4796:
4791:
4786:
4781:
4776:
4772:
4768:
4764:
4757:
4755:
4751:
4746:
4742:
4737:
4732:
4728:
4724:
4720:
4716:
4712:
4705:
4702:
4697:
4693:
4688:
4683:
4678:
4673:
4669:
4665:
4661:
4654:
4651:
4646:
4642:
4637:
4632:
4628:
4624:
4620:
4616:
4612:
4605:
4602:
4597:
4593:
4588:
4583:
4578:
4573:
4569:
4565:
4561:
4554:
4551:
4546:
4542:
4537:
4532:
4527:
4522:
4518:
4514:
4510:
4503:
4500:
4495:
4491:
4486:
4481:
4477:
4473:
4469:
4465:
4461:
4457:
4453:
4446:
4444:
4440:
4435:
4431:
4427:
4423:
4419:
4415:
4411:
4407:
4400:
4397:
4392:
4388:
4383:
4378:
4374:
4370:
4366:
4362:
4358:
4351:
4348:
4343:
4339:
4334:
4329:
4325:
4321:
4318:(3): 377–86.
4317:
4313:
4309:
4302:
4300:
4296:
4291:
4287:
4282:
4277:
4273:
4269:
4265:
4261:
4257:
4250:
4247:
4242:
4238:
4233:
4228:
4224:
4220:
4216:
4212:
4208:
4201:
4198:
4193:
4189:
4184:
4179:
4175:
4171:
4167:
4163:
4159:
4152:
4150:
4146:
4141:
4137:
4132:
4127:
4123:
4119:
4115:
4111:
4107:
4100:
4097:
4092:
4088:
4083:
4078:
4074:
4070:
4066:
4062:
4058:
4051:
4048:
4043:
4039:
4034:
4029:
4025:
4021:
4017:
4013:
4009:
4002:
3999:
3994:
3990:
3985:
3980:
3976:
3972:
3968:
3964:
3960:
3953:
3951:
3949:
3947:
3945:
3941:
3936:
3932:
3927:
3922:
3917:
3912:
3908:
3904:
3901:(3): e17288.
3900:
3896:
3892:
3885:
3882:
3877:
3873:
3869:
3865:
3861:
3857:
3854:(4): 709–17.
3853:
3849:
3842:
3839:
3834:
3830:
3825:
3820:
3816:
3812:
3808:
3804:
3800:
3793:
3790:
3785:
3781:
3776:
3771:
3766:
3761:
3757:
3753:
3750:(2): e31386.
3749:
3745:
3741:
3734:
3731:
3726:
3722:
3717:
3712:
3708:
3704:
3700:
3696:
3692:
3685:
3682:
3677:
3673:
3669:
3663:
3659:
3655:
3651:
3650:
3642:
3640:
3638:
3636:
3634:
3632:
3630:
3626:
3621:
3617:
3612:
3607:
3603:
3599:
3595:
3591:
3587:
3580:
3578:
3574:
3566:
3562:
3557:
3552:
3548:
3544:
3540:
3536:
3532:
3528:
3524:
3517:
3514:
3509:
3505:
3501:
3497:
3493:
3489:
3485:
3481:
3477:
3473:
3466:
3464:
3460:
3455:
3451:
3446:
3441:
3436:
3431:
3427:
3423:
3419:
3412:
3409:
3404:
3400:
3395:
3390:
3386:
3382:
3379:(3): 204–12.
3378:
3374:
3370:
3363:
3360:
3355:
3351:
3346:
3341:
3337:
3333:
3329:
3325:
3321:
3317:
3313:
3306:
3303:
3297:
3292:
3288:
3284:
3280:
3274:
3271:
3266:
3262:
3258:
3254:
3250:
3246:
3242:
3238:
3231:
3228:
3223:
3219:
3214:
3209:
3204:
3199:
3195:
3191:
3188:(7): e11840.
3187:
3183:
3179:
3172:
3169:
3164:
3160:
3155:
3150:
3146:
3142:
3138:
3134:
3130:
3123:
3121:
3117:
3112:
3108:
3104:
3100:
3096:
3092:
3088:
3084:
3081:(5): 516–29.
3080:
3076:
3069:
3066:
3061:
3057:
3052:
3047:
3042:
3037:
3033:
3029:
3025:
3018:
3015:
3010:
3006:
3001:
2996:
2991:
2986:
2982:
2978:
2974:
2967:
2964:
2959:
2955:
2951:
2947:
2943:
2939:
2935:
2931:
2927:
2923:
2916:
2914:
2912:
2908:
2900:
2896:
2891:
2886:
2882:
2878:
2874:
2870:
2866:
2859:
2856:
2851:
2847:
2843:
2839:
2835:
2831:
2826:
2821:
2817:
2813:
2809:
2805:
2798:
2795:
2790:
2786:
2781:
2776:
2771:
2766:
2762:
2758:
2754:
2747:
2744:
2736:
2732:
2728:
2724:
2720:
2716:
2712:
2708:
2704:
2700:
2693:
2691:
2687:
2682:
2678:
2673:
2668:
2663:
2658:
2654:
2650:
2646:
2642:
2638:
2631:
2628:
2623:
2619:
2614:
2609:
2605:
2601:
2597:
2593:
2589:
2582:
2579:
2574:
2570:
2566:
2562:
2558:
2554:
2551:(4): 667–74.
2550:
2546:
2538:
2535:
2530:
2526:
2521:
2516:
2512:
2508:
2504:
2500:
2496:
2492:
2486:
2483:
2478:
2472:
2468:
2464:
2460:
2453:
2450:
2445:
2441:
2436:
2431:
2426:
2421:
2417:
2413:
2409:
2405:
2401:
2394:
2391:
2386:
2382:
2377:
2372:
2367:
2362:
2358:
2354:
2351:(2): 106–12.
2350:
2346:
2342:
2335:
2332:
2326:
2322:
2317:
2312:
2308:
2304:
2300:
2293:
2290:
2285:
2281:
2276:
2271:
2266:
2261:
2257:
2253:
2249:
2242:
2239:
2234:
2228:
2224:
2220:
2213:
2210:
2205:
2201:
2196:
2191:
2187:
2183:
2179:
2175:
2171:
2164:
2162:
2158:
2153:
2149:
2144:
2139:
2134:
2129:
2125:
2121:
2117:
2113:
2109:
2102:
2100:
2098:
2096:
2094:
2092:
2090:
2086:
2080:
2076:
2075:Pathogenomics
2073:
2071:
2068:
2066:
2063:
2061:
2058:
2056:
2053:
2052:
2048:
2046:
2044:
2040:
2039:hematophagous
2032:
2030:
2027:
2023:
2015:
2013:
2009:
2007:
2003:
1998:
1994:
1990:
1985:
1981:
1977:
1973:
1971:
1967:
1963:
1959:
1955:
1948:
1946:
1944:
1940:
1935:
1931:
1925:
1917:
1915:
1913:
1909:
1903:
1895:
1888:
1886:
1885:antibiotics.
1884:
1879:
1875:
1870:
1865:
1863:
1860:
1856:
1852:
1851:agrochemicals
1848:
1844:
1836:Biotechnology
1835:
1833:
1831:
1827:
1826:fungus garden
1823:
1820:
1816:
1812:
1808:
1804:
1800:
1796:
1792:
1787:
1785:
1781:
1777:
1773:
1769:
1765:
1761:
1757:
1753:
1750:contained in
1749:
1745:
1742:derived from
1741:
1737:
1732:
1724:
1722:
1720:
1716:
1712:
1708:
1704:
1701:
1697:
1693:
1689:
1685:
1680:
1672:
1670:
1668:
1664:
1660:
1656:
1652:
1644:
1642:
1640:
1639:giant viruses
1636:
1631:
1627:
1621:
1613:
1611:
1609:
1605:
1601:
1600:
1595:
1591:
1587:
1583:
1579:
1575:
1568:
1562:
1558:
1557:Transcriptome
1550:
1548:
1546:
1541:
1537:
1533:
1529:
1525:
1521:
1517:
1513:
1509:
1501:
1497:Data analysis
1496:
1494:
1492:
1486:
1484:
1480:
1474:
1471:
1467:
1463:
1458:
1454:
1445:
1443:
1439:
1435:
1433:
1429:
1425:
1420:
1418:
1414:
1410:
1406:
1402:
1398:
1392:
1389:
1388:replicability
1384:
1376:
1374:
1372:
1368:
1364:
1360:
1356:
1352:
1348:
1344:
1340:
1336:
1332:
1326:
1318:
1316:
1313:
1309:
1305:
1301:
1300:
1295:
1291:
1288:, usually by
1287:
1283:
1279:
1273:
1265:
1263:
1261:
1257:
1253:
1249:
1245:
1241:
1236:
1234:
1229:
1224:
1218:
1210:
1208:
1206:
1198:
1196:
1193:
1189:
1185:
1176:
1166:
1163:February 2022
1156:
1150:
1147:This section
1145:
1141:
1136:
1135:
1129:
1127:
1125:
1121:
1117:
1112:
1110:
1106:
1102:
1098:
1094:
1090:
1081:
1079:
1077:
1073:
1069:
1065:
1061:
1053:
1051:
1049:
1045:
1041:
1037:
1033:
1029:
1025:
1019:
1010:
1003:
1001:
999:
995:
994:Forest Rohwer
991:
988:developed by
987:
983:
979:
974:
972:
967:
963:
962:Mediterranean
959:
955:
951:
947:
943:
939:
935:
931:
926:
924:
920:
916:
912:
908:
904:
900:
899:viral species
896:
892:
891:Forest Rohwer
888:
887:Mya Breitbart
883:
881:
876:
875:Edward DeLong
872:
868:
864:
860:
856:
851:
847:
843:
838:
836:
832:
828:
824:
820:
816:
813:
809:
805:
801:
798:Conventional
789:
784:
782:
777:
775:
770:
769:
767:
766:
760:
750:
749:
748:
747:
741:
738:
736:
733:
731:
728:
725:
722:
720:
717:
716:
711:
708:
706:
703:
702:
695:
692:
691:
690:
689:Amplification
687:
686:
681:
678:
677:
670:
667:
666:
665:
662:
661:
654:
651:
650:
648:
645:
644:
642:
641:
636:
628:
625:
623:
620:
619:
617:
615:
612:
610:
607:
605:
602:
600:
597:
596:
594:
593:
588:
582:
581:Metabarcoding
578:
577:DNA barcoding
571:
567:
566:
563:
562:DNA barcoding
559:
555:
554:
548:
546:
544:
540:
536:
532:
528:
524:
523:Jo Handelsman
516:
514:
512:
508:
504:
498:
496:
492:
488:
485:
481:
477:
473:
468:
466:
462:
458:
454:
450:
446:
445:environmental
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2022:encephalitis
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1900:
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1824:such as the
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1645:Applications
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1074:them into a
1072:reconstructs
1068:human genome
1058:Advances in
1057:
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975:
942:Sargasso Sea
930:Craig Venter
927:
884:
839:
797:
664:Metagenomics
663:
539:Lior Pachter
520:
499:
472:microbiology
469:
465:microbiomics
464:
460:
456:
452:
437:Metagenomics
436:
435:
425:
413:
405:
397:
393:
385:
297:Quantitative
267:Cytogenetics
262:Conservation
144:Introduction
29:
7599:Epigenomics
7531:Pangenomics
7284:(8): 1653.
7178:(1): 4690.
6826:29 December
6016:30 December
5978:30 December
5747:(1): 11–9.
4462:(1): 1014.
3243:(1): 16–8.
2043:arboviruses
1756:switchgrass
1673:Agriculture
1659:agriculture
1655:engineering
1543:tool (with
1536:microarrays
1528:Synergistia
1508:bioreactors
831:cultivation
457:ecogenomics
400:), and are
7873:Categories
7684:Proteomics
7621:Lipidomics
7616:Immunomics
7064:(8): 447.
6753:: e78756.
6675:10 October
6387:20 January
5947:(4): 252.
5852:1503.05575
5209:(7): e86.
4924:(1): 236.
3322:(1): 870.
2491:Schmidt TM
2258:(3): e82.
2081:References
1934:ecosystems
1930:pollutants
1822:herbivores
1811:convergent
1778:including
1705:and other
1604:microarray
1586:expression
1582:regulation
1540:proteomics
1520:syntrophic
1453:GC-content
1205:eukaryotic
1192:microbiome
1024:base pairs
1004:Sequencing
800:sequencing
730:Healthcare
531:Jon Clardy
449:sequencing
292:Population
272:Ecological
197:Geneticist
111:Amino acid
91:Nucleotide
66:Chromosome
7611:Glycomics
7392:: 79–84.
7135:1471-0064
7094:248739527
7078:1740-1534
6904:1476-4687
6777:248041252
6769:2534-9708
5799:1410.1278
4814:"GenBank"
4570:: e3138.
3701:: 75–88.
2820:CiteSeerX
1883:malacidin
1843:commodity
1799:screening
1776:bioenergy
1748:cellulose
1715:livestock
1700:sequester
1522:species (
1512:syntrophy
1470:community
1419:project.
1351:MetaPhlAn
1312:ab initio
1299:ab initio
1278:pipelines
1188:gigabases
1155:talk page
1036:libraries
885:In 2002,
882:samples.
819:conserved
812:ribosomal
599:Microbial
517:Etymology
402:sequenced
390:extracted
287:Molecular
282:Microbial
257:Classical
158:molecular
154:Evolution
7889:Genomics
7863:Medicine
7823:Category
7549:genomics
7473:Genomics
7408:28855093
7367:31852942
7310:34442732
7259:32878948
7210:29549363
7153:30918369
7086:35546350
7039:22719234
6979:20203603
6922:20203603
6728:33971086
6651:22606263
6611:PLOS ONE
6592:21407210
6543:29434326
6494:21545702
6468:(1): 9.
6443:21076656
6374:12849784
6304:19760178
6255:20885794
6204:21297863
6164:PLOS ONE
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5869:28247094
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5511:16915287
5468:21592777
5433:19897353
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5325:23978768
5303:Genomics
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5233:23408855
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3403:27383682
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2789:11864374
2727:14961025
2681:12384570
2573:31384119
2385:16110337
2284:17355177
2152:20195499
2049:See also
1784:hydrogen
1754:stalks,
1736:Biofuels
1651:medicine
1457:16S rRNA
1399:and the
1383:metadata
1304:GeneMark
1282:homology
1223:coverage
1211:Assembly
1101:Illumina
971:plankton
950:bacteria
913:and the
835:archaeal
808:cultured
759:Category
618:Aquatic
491:16S rRNA
487:cultures
480:genomics
337:Category
222:template
213:Genomics
191:Research
96:Mutation
86:Heredity
41:Genetics
7851:Biology
7837:Portals
7572:Biochip
7358:6920425
7337:Bibcode
7329:Sci Rep
7301:8398489
7250:7587107
7201:5856816
7180:Bibcode
7172:Sci Rep
7144:6858796
7030:3374609
7007:Bibcode
6970:3779803
6949:Bibcode
6913:3779803
6884:Bibcode
6719:8518049
6669:NPR.org
6642:3350522
6619:Bibcode
6583:3094067
6568:: 473.
6534:5874163
6485:3113934
6434:2976544
6295:2773367
6246:2944797
6195:3027613
6172:Bibcode
6136:2694162
6085:4440916
6068:: 486.
5918:Microbe
5877:1925728
5762:3293453
5722:2127494
5663:6323928
5614:5210529
5574:4466854
5546:Bibcode
5519:4380804
5491:Bibcode
5424:2790021
5375:3053989
5352:Bibcode
5275:3526429
5224:3627586
5175:3278849
5115:Bibcode
5079:3067235
5058:Bibcode
5011:2533590
4965:bioRxiv
4941:4428112
4890:3428669
4839:3531190
4790:3044276
4736:3245048
4687:2563014
4670:: 386.
4636:3245063
4587:5372838
4536:3194235
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4464:Bibcode
4434:7728395
4382:3443552
4333:1800929
4268:Bibcode
4232:2896542
4183:3166839
4131:4455782
4082:2336801
4033:3488206
3984:2593568
3926:3052304
3903:Bibcode
3824:3605598
3775:3285633
3752:Bibcode
3716:4426941
3611:4010126
3556:3779803
3535:Bibcode
3480:Bibcode
3472:Science
3445:7641418
3394:5017796
3345:5830445
3324:Bibcode
3265:1465786
3213:2911387
3190:Bibcode
3154:4039370
3111:8267748
3083:Bibcode
3051:3351745
3000:1483832
2930:Bibcode
2922:Science
2877:Bibcode
2850:1454587
2812:Bibcode
2804:Science
2735:4420754
2707:Bibcode
2649:Bibcode
2622:8550487
2565:7546604
2529:2066334
2444:2413450
2412:Bibcode
2376:1185649
2353:Bibcode
2325:9818143
2275:1821061
2204:9733676
2143:2829047
2120:Bibcode
2055:Binning
1987:In the
1889:Ecology
1828:of the
1803:enzymes
1795:enzymes
1780:methane
1772:ethanol
1744:biomass
1731:Biofuel
1725:Biofuel
1719:farming
1667:ecology
1630:18S RNA
1626:16S RNA
1614:Viruses
1599:in situ
1532:methane
1405:MG-RAST
1386:ensure
1355:AMPHORA
1335:Binning
1308:GLIMMER
1252:genomes
1233:contigs
1044:vectors
1028:samples
946:species
923:archaea
871:grasses
855:cloning
827:species
724:Chimera
669:viruses
590:By taxa
574:
549:History
507:shotgun
441:genetic
410:cloning
149:History
121:Outline
7480:Fields
7406:
7365:
7355:
7308:
7298:
7257:
7247:
7235:(11).
7208:
7198:
7151:
7141:
7133:
7092:
7084:
7076:
7037:
7027:
6977:
6967:
6941:Nature
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2948:
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2869:Nature
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2699:Nature
2679:
2672:137870
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2195:107498
2192:
2150:
2140:
1958:health
1819:insect
1815:biogas
1764:sugars
1707:metals
1248:Celera
1099:, the
964:, and
958:Baltic
880:marine
757:
609:Pollen
604:Fungal
584:
535:genome
484:clonal
388:) are
335:
249:Fields
106:Allele
81:Genome
7787:(USA)
7547:Socio
7090:S2CID
6773:S2CID
6381:(PDF)
6350:(PDF)
6010:(PDF)
6003:(PDF)
5895:(PDF)
5873:S2CID
5847:arXiv
5820:S2CID
5794:arXiv
5718:S2CID
5690:(PDF)
5570:S2CID
5515:S2CID
4564:PeerJ
4430:S2CID
3872:S2CID
3504:S2CID
3428:(8).
3261:S2CID
3107:S2CID
2954:S2CID
2846:S2CID
2731:S2CID
2569:S2CID
1740:fuels
1711:crops
1679:soils
1576:(the
1424:MEGAN
1367:SLIMM
1359:mOTUs
1343:MEGAN
1339:BLAST
1294:MEGAN
1290:BLAST
1244:Phrap
1184:rumen
966:Black
638:Other
614:Algae
509:" or
126:Index
7811:List
7793:(UK)
7781:(EU)
7775:(JP)
7404:PMID
7363:PMID
7306:PMID
7255:PMID
7206:PMID
7149:PMID
7131:ISSN
7082:PMID
7074:ISSN
7035:PMID
6975:PMID
6918:PMID
6900:ISSN
6847:ISBN
6828:2011
6796:ISBN
6765:ISSN
6724:PMID
6677:2014
6647:PMID
6588:PMID
6539:PMID
6490:PMID
6439:PMID
6389:2012
6370:PMID
6323:ISBN
6300:PMID
6251:PMID
6200:PMID
6141:PMID
6090:PMID
6037:ISBN
6018:2011
5980:2011
5865:PMID
5812:PMID
5767:PMID
5710:PMID
5668:PMID
5619:PMID
5562:PMID
5507:PMID
5464:PMID
5429:PMID
5380:PMID
5321:PMID
5280:PMID
5229:PMID
5180:PMID
5133:PMID
5084:PMID
5016:PMID
4946:PMID
4895:PMID
4844:PMID
4795:PMID
4741:PMID
4692:PMID
4641:PMID
4592:PMID
4541:PMID
4490:PMID
4422:PMID
4387:PMID
4338:PMID
4286:PMID
4237:PMID
4188:PMID
4136:PMID
4087:PMID
4038:PMID
3989:PMID
3931:PMID
3864:PMID
3829:PMID
3780:PMID
3721:PMID
3672:PMID
3662:ISBN
3616:PMID
3561:PMID
3496:PMID
3450:PMID
3399:PMID
3350:PMID
3253:PMID
3218:PMID
3159:PMID
3099:PMID
3056:PMID
3005:PMID
2946:PMID
2895:PMID
2838:PMID
2785:PMID
2723:PMID
2677:PMID
2618:PMID
2561:PMID
2525:PMID
2471:ISBN
2440:PMID
2381:PMID
2321:PMID
2280:PMID
2227:ISBN
2200:PMID
2148:PMID
1910:and
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