Wikipedia

Khác biệt giữa bản sửa đổi của “Metagenomics”

Duyệt lịch sử tương tác
← Thay đổi trướcThay đổi sau →
Nội dung được xóa Nội dung được thêm vào
Trực quanMã wiki
Cheers!-bot (thảo luận | đóng góp)
5.681.853 sửa đổi
n replaced: {{Main| → {{chính| (6), {{main| → {{chính| using AWB
Không có tóm lược sửa đổi
Dòng 1:
{{Đang dịch 2 (nguồn)|ngày=20
|tháng=02
|năm=2014
|1 = tiếng Anh
}}
{{good article}}
[[Tập tin:Iron hydroxide precipitate in stream.jpg|thumb|right|Với Metagenomics ta có thể nghiên cứu các quần xã vi sinh vật, ví dụ như quần xã vi sinh ở dòng suối bị axit hóa do khai khoáng như ở hình trên.]]
Hàng 93 ⟶ 88:
 
Việc chú thích gen giúp trả lời cho câu hỏi "cái gì", trong khi việc xác định độ đa dạng loài giúp trả lời cho câu hỏi "ai".<ref name="konopka2008" /> Để xác định cấu trúc và chức năng của quần xã trong metagenomes, các đoạn trình tự phải được cố định hóa. Việc cố định này được hiểu là quá trình gắn một đoạn trình tự với một sinh vật cụ thể.<ref name="koonin2008" /> Cố định hóa dựa trên sự tương đồng bao gồm các phương pháp như BLAST, được sử dụng để tìm kiếm marker hoặc các đoạn trình tự tương tự trong những dữ liệu có sẵn đã công bố. Theo cách này có thể sử dụng chương trình MEGAN.<ref name="MEGAN2007" /> Một công cụ nữa để cố định hóa các reads là PhymmBL.<ref name="wooley2010" /> Cố định hóa dựa trên thành phần tập trung vào đặc tính của các đoạn trình tự, như tần số của các oligonucleotide hoặc codon biểu hiện (codon usage bias).<ref name="wooley2010" /> Sau khi phân nhóm các đoạn trình tự có thể phân tích so sánh độ đa dạng và phong phú của chúng nhờ một số chương trình khác, vd. như Unifrac.   
 
===Nhập dữ liệu===
 
<!-- Deleted image removed: [[Tập tin:F2.large.jpg|thumb|Metagenome data analysis in [[Integrated Microbial Genomes System|IMG]]/M 3.4]] -->
 
The massive amount of exponentially growing sequence data is a daunting challenge that is complicated by the complexity of the [[metadata]] associated with metagenomic projects. 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.<ref name="committee2007"/> This information is necessary both to ensure [[replicability]] 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).<ref name="pagani2011"/>
 
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 [[Argonne National Laboratory]] and the [[University of Chicago]] released the Metagenomics Rapid Annotation using Subsystem Technology server ([[MG-RAST]]) a community resource for metagenome data set analysis.<ref name="Meyer2008"/> As of June 2012 over 14.8 terabases (14x10<sup>12</sup> 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 [[Integrated Microbial Genomes System|Integrated Microbial Genomes/Metagenomes]] (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 [http://img.jgi.doe.gov/cgi-bin/w/main.cgi Integrated Microbial Genomes] (IMG) system and the [http://jgi.doe.gov/programs/GEBA/index.html Genomic Encyclopedia of Bacteria and Archaea (GEBA)] project.<ref name="markowitz2012"/>
 
One of the first standalone tools for analysing high-throughput metagenome shotgun data was [[MEGAN]] (MEta Genome ANalyzer).<ref name="MEGAN2011"/><ref name="MEGAN2007"/> A first version of the program was used in 2005 to analyse the metagenomic context of DNA sequences obtained from a mammoth bone.<ref name="Poinar2005" /> 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 [http://www.theseed.org/wiki/Main_Page SEED] or [[KEGG]] classifications, respectively.<ref name="mitra2011"/>
 
===So sánh metagenomics===
 
Comparative analyses between metagenomes can provide additional insight into the function of complex microbial communities and their role in host health.<ref name="kurokawa2007"/> Pairwise or multiple comparisons between metagenomes can be made at the level of sequence composition (comparing [[GC-content]] or genome size), taxonomic diversity, or functional complement. Comparisons of population structure and phylogenetic diversity can be made on the basis of 16S and other phylogenetic marker genes, or—in the case of low-diversity communities—by genome reconstruction from the metagenomic dataset.<ref name="simon2011"/> Functional comparisons between metagenomes may be made by comparing sequences against reference databases such as [[Gene cluster|COG]] or [[KEGG]], and tabulating the abundance by category and evaluating any differences for statistical significance.<ref name="mitra2011"/> This gene-centric approach emphasizes the functional complement of the ''community'' as a whole rather than taxonomic groups, and shows that the functional complements are analogous under similar environmental conditions.<ref name="simon2011"/> Consequently, metadata on the environmental context of the metagenomic sample is especially important in comparative analyses, as it provides researchers with the ability to study the effect of habitat upon community structure and function.<ref name="wooley2010" />
 
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.<ref name="willner2009">{{chú thích tạp chí
| volume = 11
| issue = 7
| pages = 1752–66
| last = Willner
| first = D
| coauthors = RV Thurber and F Rohwer.
| title = Metagenomic signatures of 86 microbial and viral metagenomes.
| journal = Environmental Microbiology
| year = 2009
}}</ref> and the HabiSign approach of Ghosh et al.<ref name = "ghosh2011">{{chú thích tạp chí
| volume = 12
| issue = Supplement 13
| pages = S9
| last = Ghosh
| first = Tarini Shankar
| coauthors = Monzoorul Haque Mohammed, Hannah Rajasingh, Sudha Chadaram and Sharmila S Mande
| title = HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences.
| journal = BMC Bioinformatics
| year = 2011
}}</ref> Ghosh et al. (2011) <ref name="ghosh2011"/> also indicated that differences in tetranucleotide usage patterns can be used to identify genes (or metagenomic reads) originating from specific habitats.
 
==Phân tích dữ liệu==
 
===Trao đổi chát trong quần xã sinh vật===
Đối với nhiều quần xã vi khuẩn tự nhiên hoặc nuôi cấy thì "sự phân công lao động" giữa các sinh vật hay còn gọi là đồng dưỡng (syntrophy) là một điều rất phổ biến. Cụ thể như trong nồi lên men methanogen cần có một số loài đồng dưỡng hoạt động cùng nhau để biến nguồn chất thô thành methane.<ref name="mcinerney2009" />  Các nghiên cứu về gen và biểu hiện gen bằng microarray hoặc proteomics giúp các nhà nghiên cứu lắp ghép các dữ liệu để có được bức tranh toàn diện về cơ chế trao đổi chất của các vi sinh vật trong quần xã.<ref name="kiltgord2011" />.  
 
===Metatranscriptomics===
{{Further|Transcriptome}}
Với Metagenomics các nhà khoa học có thể tìm hiểu được đa dạng chức năng và trao đổi chất của quần xã vi sinh, nhưng không thể biết được quá trình nào trong số đó đang diễn ra.<ref name="simon2011" /> Nhờ tách chiết và phân tích metagenomic mRNA (còn gọi là '''metatranscriptome''') mà có thể biết được đặc tính điều hòa và biểu hiện của hệ quần xã. Do các khó khăn kỹ thuật (vd. như thời gian bán rã ngắn (short half-life) của mRNA) trong thu thập RNA môi trường mà hiện nay các nhà khoa học đã phát triển một số nghiên cứu metatranscriptomic in situ.<ref name="simon2011" /> Và cũng không chỉ giới hạn trong kỹ thuật microarray, đến nay nghiên cứu metatranscriptomic cũng đã ứng dụng giải trình tự cDNA theo phương pháp hiện đại để xác định biểu hiện của toàn bộ genome và định lượng quần xã vi sinh.<ref name="simon2011" /><ref name="leininger2006" />
 
===Metagenomics với virus===
{{chính|Viral metagenomics}}
 
Giải trình trự metagenomic có ý nghĩa rất lớn trong nghiên cứu quần xã virus. Vì virus không có marker để phân loại (như 16S RNA đối với vi khuẩn và vi khuẩn cổ, 18S RNA cho các sinh vật nhân chuẩn) nên cách duy nhất để nghiên cứu đa dạng di truyền của virus là thông qua metagenomics. Nhờ metagenomic mà ta có thể nghiên cứu kỹ hơn và rõ hơn về sự tiến hóa và đa dạng của hệ virus.<ref name="Kristensen"/>
 
==Ứng dụng==
 
Metagenomics has the potential to advance knowledge in a wide variety of fields. It can also be applied to solve practical challenges in [[medicine]], [[engineering]], [[agriculture]], [[sustainability]] and [[ecology]].<ref name="committee2007"/>
 
===Y học===
[[Microbial communities]] play a key role in preserving human [[health]], but their composition and the mechanism by which they do so remains mysterious.<ref name="zimmer2010"/> 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 Human [[Microbiome]] initiative with primary goals to determine if there is a core human microbiome, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and [[bioinformatics]] tools to support these goals.<ref name="NelsonWhite"/>
 
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 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.
 
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 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 bacteria 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 or in harvesting sugars of the 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 bowel disease or obesity.
 
While these study highlights 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 bacterial genomes.<ref>{{chú thích tạp chí|last=Qin|first=Junjie|coauthors=Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvesten Burgdorf|title=A human gut microbial gene catalogue established by metagenomic sequencing|journal=Nature|date=March 2010|volume=464|pages=59–65|accessdate=7 October 2013|doi=10.1038/nature08821|pmid=20203603|issue=7285}}</ref>
 
===Nhiên liệu sinh học===
{{chính|Biofuel}}
[[Tập tin:Pg166 bioreactor.jpg|thumb|[[w:Bioreactor|Bioreactors]] allow the observation of microbial communities as they convert [[biomass]] into [[w:Cellulosic ethanol|cellulosic ethanol]].]]
 
[[Biofuel]]s are [[fuel]]s derived from [[biomass]] conversion, as in the conversion of [[cellulose]] contained in [[Maize|corn]] stalks, [[switchgrass]], and other biomass into [[cellulosic ethanol]].<ref name="committee2007"/> This process is dependent upon microbial consortia that transform the cellulose into [[sugar]]s, followed by the [[Ethanol fermentation|fermentation]] of the sugars into [[ethanol]]. Microbes also produce a variety of sources of [[bioenergy]] including [[Methanogen|methane]] and [[Biohydrogen|hydrogen]].<ref name="committee2007"/>
 
The [[Issues relating to biofuels#Technical issues|efficient industrial-scale deconstruction]] of biomass requires novel [[enzymes]] with higher productivity and lower cost.<ref name="hess2011"/> Metagenomic approaches to the analysis of complex microbial communities allow the targeted [[Genetic screen|screening]] of [[enzymes]] with industrial applications in biofuel production, such as [[glycoside hydrolase]]s.<ref name="li2009"/> 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 [[convergent evolution|convergent]] microbial systems like [[biogas]] fermenters<ref name="jaenicke2011"/> or [[insect]] [[herbivore]]s such as the [[ant-fungus mutualism|fungus garden]] of the [[leafcutter ant]]s.<ref name="suen2010"/>
 
===Xử lý môi trường===
{{chính|Bioremediation}}
Metagenomics can improve strategies for monitoring the impact of [[pollutant]]s on [[ecosystem]]s 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 [[bioaugmentation]] or [[biostimulation]] trials to succeed.<ref name="george2010"/>
 
===Công nghệ sinh học===
 
Microbial communities produce a vast array of biologically active chemicals that are used in competition and communication.<ref name="booklet2007"/> 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 new genes, enzymes, and natural products.<ref name="simon2011"/><ref name="simon2009a"/> The application of metagenomics has allowed the development of [[Commodity chemicals|commodity]] and [[fine chemicals]], [[agrochemical]]s and [[Pharmaceutical drug|pharmaceuticals]] where the benefit of [[Enzyme catalysis|enzyme-catalyzed]] [[chiral synthesis]] is increasingly recognized.<ref name="wong2010"/>
 
Two types of analysis are used in the [[bioprospecting]] of metagenomic data: function-driven screening for an expressed trait, and sequence-driven screening for DNA sequences of interest.<ref name="schloss2003"/> Function-driven analysis seeks to identify clones expressing a desired trait or useful activity, followed by biochemical characterization and sequence analysis. This 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.<ref name="kakirde2010"/> In contrast, sequence-driven analysis uses [[Conserved sequence|conserved DNA sequences]] to [[Primer (molecular biology)#PCR primer design|design PCR primers]] to screen clones for the sequence of interest.<ref name="schloss2003" /> 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 high-throughput bioinformatic analysis pipelines.<ref name="kakirde2010" /> 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.<ref name="kakirde2010"/><ref name="parachin2011"/>
 
===Nông nghiệp===
 
The [[soil]]s in which plants grow are inhabited by microbial communities, with one gram of soil containing around 10<sup>9</sup>-10<sup>10</sup> microbial cells which comprise about one gigabase of sequence information.<ref name="jansson2011"/><ref name="vogel2009"/> The microbial communities which inhabit soils are some of the most complex known to science, and remain poorly understood despite their economic importance.<ref name="terra"/> Microbial consortia perform a wide variety of [[ecosystem service]]s necessary for plant growth, including fixing atmospheric nitrogen, [[nutrient cycling]], disease suppression, and [[Siderophore|sequester]] [[iron]] and other [[metal]]s.<ref name="booklet2007"/> Functional metagenomics strategies are being used to explore the interactions between plants and microbes through cultivation-independent study of these microbial communities.<ref name="charles2010"/> 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 [[crop]]s and [[livestock]] and the adaptation of enhanced [[Agriculture|farming]] practices which improve crop health by harnessing the relationship between microbes and plants.<ref name="committee2007" />
 
===Sinh thái học===
 
Metagenomics can provide valuable insights into the functional ecology of environmental communities.<ref name="raes2011">{{cite pmid|21407210}}</ref> 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. 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.<ref name="lavery2012">{{cite doi|10.1371/journal.pone.0036478}}</ref>
 
DNA sequencing can also be used more broadly to identify species present in a body of water,<ref>[http://www.npr.org/2013/07/24/205178477/whats-swimming-in-the-river-just-look-for-dna What's Swimming In The River? Just Look For DNA]</ref> debris filtered from the air, or sample of dirt. This can establish the range of [[invasive species]] and [[endangered species]], and track seasonal populations.
 
== Xem thêm ==
Hàng 191 ⟶ 95:
*[[Pathogenomics]]
 
==Tài liệu thamTham khảo==
{{tham khảo|2|refs=}}
<!-- Converted to LDR format
using [[User:PleaseStand/References segregator]] -->
 
<ref name="Hugenholz1998">
{{chú thích tạp chí
| last = Hugenholz
| first = P
| coauthors = Goebel BM, Pace NR
| date=1 September 1998| title = Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
| journal = J. Bacteriol
| volume = 180
| pages = 4765–74
| pmid = 9733676
| issue = 18
| pmc = 107498 }}
</ref>
<ref name="Eisen2007">
{{chú thích tạp chí
| last=Eisen| first= JA
| year= 2007| title= Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes
| doi= 10.1371/journal.pbio.0050082| journal= PLoS Biology
| volume= 5| issue=3| pages= e82
| pmid=17355177
| pmc=1821061}}
</ref>
<ref name= MarcoD2011>
{{chú thích sách
| editor = Marco, D
| year=2011
| title=Metagenomics: Current Innovations and Future Trends
| publisher=[[Caister Academic Press]]
| isbn= 978-1-904455-87-5}}
</ref>
<ref name="Handelsman1998">
{{cite doi|10.1016/S1074-5521(98)90108-9}}.</ref>
<ref name="Chen2005">
{{cite doi
|10.1371/journal.pcbi.0010024}}</ref>
<ref name="Lane1985">
{{chú thích tạp chí
| last = Lane
| first = DJ
| coauthors = Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR
| year = 1985
| title = Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
| journal = [[Proceedings of the National Academy of Sciences]]
| volume = 82
| pages = 6955–9
| doi = 10.1073/pnas.82.20.6955
| pmid = 2413450
| issue = 20
| pmc = 391288|bibcode = 1985PNAS...82.6955L }}</ref>
<ref name="Pace1985">
{{chú thích tạp chí
| last = Pace
| first = NR
| coauthors = DA Stahl, DJ Lane, GJ Olsen
| year = 1985
| title = Analyzing natural microbial populations by rRNA sequences
| journal = ASM News
| volume = 51
| pages = 4–12
| url=http://md1.csa.com/partners/viewrecord.php?requester=gs&collection=ENV&recid=913954&q=Analyzing+natural+microbial+populations+by+rRNA+sequences&uid=790164755&setcookie=yes }}</ref>
<ref name="Healy1995">
{{chú thích tạp chí
| last = Healy
| first = FG
| coauthors = RM Ray, HC Aldrich, AC Wilkie, LO Ingram, KT Shanmugam
| year = 1995
| title = Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose
| journal = Appl. Microbiol Biotechnol.
| volume = 43
| pages = 667–74
| doi = 10.1007/BF00164771
| pmid = 7546604
| issue = 4}}</ref>
<ref name="Stein1996">
{{chú thích tạp chí
| last = Stein
| first = JL
| coauthors = TL Marsh, KY Wu, H Shizuya, EF DeLong
| year = 1996
| title = Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon
| journal = Journal of Bacteriology
| volume = 178
| issue = 3
| pages = 591–599
| pmid=8550487
| pmc = 177699}}
</ref>
<ref name="Breitbart2002">
{{chú thích tạp chí
| last = Breitbart
| first = M
| coauthors = Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F
| year = 2002
| title = Genomic analysis of uncultured marine viral communities
| journal = Proceedings of the National Academy of Sciences of the United States of America
| volume = 99
| pages = 14250–14255
| doi = 10.1073/pnas.202488399
| pmid = 12384570
| issue = 22
| pmc = 137870|bibcode = 2002PNAS...9914250B }}</ref>
<ref name="Tyson2004">
{{chú thích tạp chí
| last = Tyson
| first = GW
| coauthors = Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF
| year = 2004
| title = Insights into community structure and metabolism by reconstruction of microbial genomes from the environment
| journal = Nature
| volume = 428
| pages = 37–43
| url = http://www.nature.com/nature/journal/v428/n6978/full/nature02340.html
| doi = 10.1038/nature02340
| pmid = 14961025
| issue = 6978 |bibcode = 2004Natur.428...37T }}{{subscription required}}</ref>
<ref name="Hugenholz2002">
{{chú thích tạp chí
| last = Hugenholz
| first = P
| year = 2002
| title = Exploring prokaryotic diversity in the genomic era
| journal = Genome Biology
| volume = 3
| pages = 1–8
| doi = 10.1186/gb-2002-3-2-reviews0003
| pmid=11864374
| pmc=139013
| issue = 2}}</ref>
<ref name="Poinar2005">
{{chú thích tạp chí
| volume = 311
| pages = 392–394
| last = Poinar
| first = HN
| coauthors = Schwarz, C, Qi, J, Shapiro, B, Macphee, RD, Buigues, B, Tikhonov, A, Huson, D, Tomsho, LP, Auch, A, Rampp, M, Miller, W, and Schuster, SC
| title = Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
| journal = Science
| url =http://www.sciencemag.org/content/311/5759/392
| doi=10.1126/science.1123360
| year = 2006
| issue = 5759
|bibcode = 2006Sci...311..392P | pmid = 16368896
}}
</ref>
<ref name="Edwards2006">
{{chú thích tạp chí
| last = Edwards
| first = RA
| coauthors = Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Rohwer F
| year = 2006
| title = Using pyrosequencing to shed light on deep mine microbial ecology
| journal = BMC Genomics
| volume = 7
| page = 57
| doi = 10.1186/1471-2164-7-57
| pmid = 16549033
| pmc = 1483832}}</ref>
<ref name="Beja2000">
{{chú thích tạp chí
| doi = 10.1046/j.1462-2920.2000.00133.x
| last1 = Beja
| first1 = O.
| last2 = Suzuki
| year = 2000
| first2 = MT
| last3 = Koonin
| first3 = EV
| last4 = Aravind
| first4 = L
| last5 = Hadd
| first5 = A
| last6 = Nguyen
| first6 = LP
| last7 = Villacorta
| first7 = R
| last8 = Amjadi
| first8 = M
| last9 = Garrigues
| first9 = C
| title = Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage
| url =
| journal = Environmental Microbiology
| volume = 2
| issue = 5| pages = 516–29
| pmid = 11233160 | display-authors = 9
}}
</ref>
<ref name="segata2013">
{{chú thích tạp chí
| doi = 10.1038/msb.2013.22
| volume = 9
| issue = 666
| last = Nicola
| first = Segata
| coauthors = Daniela Boernigen, Timothy L Tickle, Xochitl C Morgan, Wendy S Garrett, Curtis Huttenhower
| title = Computational meta’omics for microbial community studies
| journal = Molecular Systems Biology
| year = 2013
| pmid = 23670539
| url = http://www.nature.com/msb/journal/v9/n1/full/msb201322.html
}}
</ref>
<ref name="Allen2005">{{chú thích tạp chí | last = Allen| first = EE |
coauthors = Banfield, JF | year = 2005 | title = Community genomics in microbial ecology and evolution | journal = Nature Reviews Microbiology | volume = 3 |
pages = 489–498 | doi = 10.1038/nrmicro1157 | pmid = 15931167 | issue = 6 }}
</ref>
<ref name="rodrigue2010">{{cite doi |10.1371/journal.pone.0011840}}</ref>
<ref name="schuster2008">{{cite doi |10.1038/nmeth1156}}</ref>
<ref name="nmeth2009">{{cite doi|10.1038/nmeth0909-623}}</ref>
<ref name="wooley2010">
{{Cite doi
| 10.1371/journal.pcbi.1000667
| volume = 6
| issue = 2
| pages = e1000667
| last = Wooley
| first = John C.
| coauthors = Adam Godzik, Iddo Friedberg
| title = A Primer on Metagenomics
| journal = PLoS Comput Biol
| accessdate = 12 December 2011
| date = 26 February 2010
| url = http://dx.doi.org/10.1371/journal.pcbi.1000667
}}
</ref>
<ref name="qin2011">
{{chú thích tạp chí
| issn = 0028-0836
| volume = 464
| issue = 7285
| pages = 59–65
| last = Qin
| first = Junjie
| coauthors = Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R. Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Marcelo Bertalan, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, H. Bjorn Nielsen, Eric Pelletier, Pierre Renault, Thomas Sicheritz-Ponten, Keith Turner, Hongmei Zhu, Chang Yu, Shengting Li, Min Jian, Yan Zhou, Yingrui Li, Xiuqing Zhang, Songgang Li, Nan Qin, Huanming Yang, Jian Wang, Soren Brunak, Joel Dore, Francisco Guarner, Karsten Kristiansen, Oluf Pedersen, Julian Parkhill, Jean Weissenbach, Peer Bork, S. Dusko Ehrlich, Jun Wang
| title = A human gut microbial gene catalogue established by metagenomic sequencing
| journal = Nature
| date = 4 March 2010
| doi = 10.1038/nature08821
| pmid=20203603
|bibcode = 2010Natur.464...59. }}{{subscription required}}</ref>
<ref name="committee2007">
{{chú thích sách
| publisher = The National Academies Press
| isbn = 0-309-10676-1
| last = Committee on Metagenomics: Challenges and Functional Applications, National Research Council
| title = The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
| location = Washington, D.C.
| year = 2007
| url = http://www.nap.edu/catalog/11902.html
}}
</ref>
<ref name='koonin2008'>{{cite doi |10.1128/MMBR.00009-08 }}</ref>
<ref name="MEGAN2011">
{{chú thích tạp chí
| volume = 21
| pages = 1552–1560
| last = Huson
| first = Daniel H
| coauthors = S. Mitra, N. Weber, H. Ruscheweyh and Stephan C. Schuster
| title = Integrative analysis of environmental sequences using MEGAN4
| journal = Genome Research
| url = http://genome.cshlp.org/content/21/9/1552.full
| date = June 2011
| issue=9
| doi = 10.1101/gr.120618.111
| pmid = 21690186
| pmc = 3166839
}}
</ref>
<ref name="Zhu2010">
{{chú thích tạp chí
| doi = 10.1093/nar/gkq275
| volume = 38
| issue = 12
| pages = e132
| last = Zhu
| first = Wenhan
| coauthors = Lomsadze Alex and Borodovsky Mark
| title = Ab initio gene identification in metagenomic sequences
| journal = Nucleic Acids Research
| year = 2010
| pmid = 20403810
| pmc = 2896542
}}
</ref>
<ref name="konopka2008">{{cite doi |10.1038/ismej.2009.88}}</ref>
<ref name="MEGAN2007" >
{{chú thích tạp chí
| volume = 17
| pages = 377–386
| last = Huson
| first = Daniel H
| coauthors = A. Auch, Ji Qi, Stephan C Schuster
| title = MEGAN Analysis of Metagenomic Data
| journal = Genome Research
| url = http://genome.cshlp.org/content/17/3/377.long
| date = January 2007
| pmid = 17255551
| doi = 10.1101/gr.5969107
| issue = 3
| pmc = 1800929
}}
</ref>
<ref name="Venter2004">
{{chú thích tạp chí
| last = Venter
| first = JC
| coauthors = Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y, Smith HO
| year = 2004
| title = Environmental Genome Shotgun Sequencing of the Sargasso Sea
| journal = Science
| volume = 304
| pages = 66–74
| doi = 10.1126/science.1093857
| pmid = 15001713
| issue = 5667
| bibcode=2004Sci...304...66V
}}</ref>
<ref name="pagani2011">
{{chú thích tạp chí
| doi = 10.1093/nar/gkr1100
| issn = 1362-4962
| last = Pagani
| first = Ioanna
| coauthors = Konstantinos Liolios, Jakob Jansson, I-Min A Chen, Tatyana Smirnova, Bahador Nosrat, Victor M Markowitz, Nikos C Kyrpides
| title = The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
| journal = Nucleic Acids Research
| date = 1 December 2011
| volume = 40
| pages = D571–9
| pmid = 22135293
| issue = 1
| pmc=3245063
}}
</ref>
<ref name="yooseph2010">
{{chú thích tạp chí
| issn = 0028-0836
| volume = 468
| issue = 7320
| pages = 60–66
| last = Yooseph
| first = Shibu
| coauthors = Kenneth H. Nealson, Douglas B. Rusch, John P. McCrow, Christopher L. Dupont, Maria Kim, Justin Johnson, Robert Montgomery, Steve Ferriera, Karen Beeson, Shannon J. Williamson, Andrey Tovchigrechko, Andrew E. Allen, Lisa A. Zeigler, Granger Sutton, Eric Eisenstadt, Yu-Hui Rogers, Robert Friedman, Marvin Frazier, J. Craig Venter
| title = Genomic and functional adaptation in surface ocean planktonic prokaryotes
| journal = Nature
| date = 4 November 2010
| doi = 10.1038/nature09530
| pmid = 21048761
|bibcode = 2010Natur.468...60Y }}{{subscription required}}
</ref>
<ref name="Meyer2008">
{{chú thích tạp chí
| last = Meyer| first = F
| coauthors = Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA
| year = 2008
| title =The metagenomics RAST server&nbsp;– a public resource for the automatic phylogenetic and functional analysis of metagenomes
| journal = BMC Bioinformatics
| pmid = 18803844
| volume = 9
| pmc = 2563014
| page = 0
| doi = 10.1186/1471-2105-9-386}}
</ref>
<ref name="markowitz2012">{{Cite pmid|22086953}}</ref>
<ref name="mitra2011">{{chú thích tạp chí
| doi = 10.1186/1471-2105-12-S1-S21
| issn = 1471-2105
| volume = 12 Suppl 1
| pages = S21
| last = Mitra
| first = Suparna
| coauthors = Paul Rupek, Daniel C Richter, Tim Urich, Jack A Gilbert, Folker Meyer, Andreas Wilke, Daniel H Huson
| title = Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
| journal = BMC Bioinformatics
| year = 2011
| pmid=21342551
| pmc = 3044276
}}
</ref>
<ref name='kurokawa2007'>
{{chú thích tạp chí
| doi = 10.1093/dnares/dsm018
| volume = 14
| issue = 4
| pages = 169–181
| last = Kurokawa
| first = Ken
| coauthors = Takehiko Itoh, Tomomi Kuwahara, Kenshiro Oshima, Hidehiro Toh, Atsushi Toyoda, Hideto Takami, Hidetoshi Morita, Vineet K. Sharma, Tulika P. Srivastava, Todd D. Taylor, Hideki Noguchi, Hiroshi Mori, Yoshitoshi Ogura, Dusko S. Ehrlich, Kikuji Itoh, Toshihisa Takagi, Yoshiyuki Sakaki, Tetsuya Hayashi, Masahira Hattori
| title = Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes
| journal = DNA Research
| accessdate = 18 December 2011
| date = 1 January 2007
| url = http://dnaresearch.oxfordjournals.org/content/14/4/169.abstract
| pmid = 17916580
| pmc = 2533590
}}</ref>
<ref name="simon2011">{{Cite doi|10.1128/AEM.02345-10}}
</ref>
<ref name="simon2011">{{cite doi|10.1128/AEM.02345-10}}</ref>
<ref name="mcinerney2009">
{{chú thích tạp chí
| doi = 10.1016/j.copbio.2009.10.001
| issn = 0958-1669
| volume = 20
| issue = 6
| pages = 623–632
| last = McInerney
| first = Michael J.
| coauthors = Jessica R. Sieber, Robert P. Gunsalus
| title = Syntrophy in Anaerobic Global Carbon Cycles
| journal = Current opinion in biotechnology
| date = December 2009
| pmid = 19897353
| pmc = 2790021
}}
</ref>
<ref name="kiltgord2011">{{Cite doi|10.1016/j.copbio.2011.04.018}}</ref>
<ref name="leininger2006">{{cite doi|10.1038/nature04983}}</ref>
<ref name="Charuvaka">{{cite doi |10.1186/1471-2164-12-S2-S8}}</ref>
<ref name= Kristensen>
{{chú thích tạp chí
| last = Kristensen| first = DM
| coauthors = Mushegian AR, Dolja VV, Koonin EV
| year = 2009
| title = New dimensions of the virus world discovered through metagenomics
| journal = Trends in Microbiology
| volume = 18
| pages = 11–19
| doi = 10.1016/j.tim.2009.11.003
| pmid = 19942437
| issue = 1
| pmc = 3293453 }}
</ref>
<ref name="hess2011">
{{chú thích tạp chí
| doi = 10.1126/science.1200387
| issn = 1095-9203
| volume = 331
| issue = 6016
| pages = 463–467
| last = Hess
| first = Matthias
| coauthors = Alexander Sczyrba, Rob Egan, Tae-Wan Kim, Harshal Chokhawala, Gary Schroth, Shujun Luo, Douglas S Clark, Feng Chen, Tao Zhang, Roderick I Mackie, Len A Pennacchio, Susannah G Tringe, Axel Visel, Tanja Woyke, Zhong Wang, Edward M Rubin
| title = Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
| journal = Science
| date = 28 January 2011
| pmid=21273488
|bibcode = 2011Sci...331..463H }}
</ref>
<ref name="zimmer2010">{{chú thích báo|last=Zimmer|first=Carl|title=How Microbes Defend and Define Us|url=http://www.nytimes.com/2010/07/13/science/13micro.html?_r=2&pagewanted=all|accessdate=29 December 2011|newspaper=New York Times|date=13 July 2010}}</ref>
<ref name= NelsonWhite>
{{chú thích sách |author= Nelson KE and White BA |year=2010|chapter=Metagenomics and Its Applications to the Study of the Human Microbiome|title=Metagenomics: Theory, Methods and Applications|publisher=Caister Academic Press|isbn= 978-1-904455-54-7}}
</ref>
<ref name="li2009">
{{chú thích tạp chí
| doi = 10.1186/1754-6834-2-10
| issn = 1754-6834
| volume = 2
| page = 10
| last = Li
| first = Luen-Luen
| coauthors = Sean R McCorkle, Sebastien Monchy, Safiyh Taghavi, Daniel van der Lelie
| title = Bioprospecting metagenomes: glycosyl hydrolases for converting biomass
| journal = Biotechnology for Biofuels
| date = 18 May 2009
}}
</ref>
<ref name="jaenicke2011">
{{chú thích tạp chí
| doi = 10.1371/journal.pone.0014519
| volume = 6
| issue = 1
| pages = e14519
| last = Jaenicke
| first = Sebastian
| coauthors = Christina Ander, Thomas Bekel, Regina Bisdorf, Marcus Dröge, Karl-Heinz Gartemann, Sebastian Jünemann, Olaf Kaiser, Lutz Krause, Felix Tille, Martha Zakrzewski, Alfred Pühler, Andreas Schlüter, Alexander Goesmann
| title = Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing
| journal = PLoS ONE
| date = 26 January 2011
| editor1-last = Aziz
| editor1-first = Ramy K
| pmid = 21297863
| pmc = 3027613
|bibcode = 2011PLoSO...614519J }}
</ref>
<ref name="suen2010">
{{chú thích tạp chí
| issn = 1553-7404
| volume = 6
| issue = 9
| last = Suen
| first = Garret
| coauthors = Jarrod J Scott, Frank O Aylward, Sandra M Adams, Susannah G Tringe, Adrián A Pinto-Tomás, Clifton E Foster, Markus Pauly, Paul J Weimer, Kerrie W Barry, Lynne A Goodwin, Pascal Bouffard, Lewyn Li, Jolene Osterberger, Timothy T Harkins, Steven C Slater, Timothy J Donohue, Cameron R Currie
| title = An insect herbivore microbiome with high plant biomass-degrading capacity
| journal = PLoS Genetics
| date = September 2010
| doi = 10.1371/journal.pgen.1001129
| editor1-last = Sonnenburg
| editor1-first = Justin
| pages = e1001129
| pmid = 20885794
| pmc = 2944797
}}
</ref>
<ref name="george2010">
{{chú thích sách |author= George I|year=2010|chapter=Application of Metagenomics to Bioremediation |title=Metagenomics: Theory, Methods and Applications|publisher=Caister Academic Press|isbn= 978-1-904455-54-7|author-separator= |author2= and others|displayauthors= 1}}
</ref>
<ref name="booklet2007">{{Cite conference | publisher = The National Academies Press | last = Committee on Metagenomics: Challenges and Functional Applications, National Research Council | title = Understanding Our Microbial Planet: The New Science of Metagenomics | year = 2007 | url = http://dels-old.nas.edu/dels/rpt_briefs/metagenomics_final.pdf }}</ref>
<ref name="segata2012">
{{chú thích tạp chí
| doi = 10.1038/nmeth.2066
| volume = 9
| issue = 8
| pages = 811–814
| last = Nicola
| first = Segata
| coauthors = Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower
| title = Metagenomic microbial community profiling using unique clade-specific marker genes
| journal = Nature Methods
| year = 2012
| pmid = 22688413
| url = http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2066.html
}}
</ref>
<ref name="simon2009a">{{cite doi|10.1007/s00253-009-2233-z}}</ref>
<ref name="wong2010">{{chú thích sách
|author= Wong D
|year=2010
|chapter=Applications of Metagenomics for Industrial Bioproducts|title=Metagenomics: Theory, Methods and Applications
|publisher=Caister Academic Press
|isbn= 978-1-904455-54-7}}</ref>
<ref name="schloss2003">
{{chú thích tạp chí
| doi = 10.1016/S0958-1669(03)00067-3
| pmid = 12849784
| issn = 0958-1669
| volume = 14
| issue = 3
| pages = 303–310
| last = Schloss
| first = Patrick D
| coauthors = Jo Handelsman
| title = Biotechnological prospects from metagenomics
| journal = Current Opinion in Biotechnology
| accessdate = 3 January 2012
| date = June 2003
| url = http://handelsmanlab.sites.yale.edu/sites/default/files/Biotechnological%20prospects%20from%20metagenomics.pdf
}}
</ref>
<ref name="kakirde2010">
{{chú thích tạp chí
| doi = 10.1016/j.soilbio.2010.07.021
| issn = 0038-0717
| volume = 42
| issue = 11
| pages = 1911–1923
| last = Kakirde
| first = Kavita S.
| coauthors = Larissa C. Parsley, Mark R. Liles
| title = Size Does Matter: Application-driven Approaches for Soil Metagenomics
| journal = Soil biology & biochemistry
| date = 1 November 2010
}}</ref>
<ref name="parachin2011">
{{chú thích tạp chí
| doi = 10.1186/1754-6834-4-9
| issn = 1754-6834
| volume = 4
| page = 9
| last = Parachin
| first = Nádia Skorupa
| coauthors = Marie F Gorwa-Grauslund
| title = Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library
| journal = Biotechnology for Biofuels
| accessdate = 3 January 2012
| year = 2011
| url = http://www.biotechnologyforbiofuels.com/content/4/1/9
| issue=1
}}
</ref>
<ref name="jansson2011">{{chú thích báo | volume = 6 | issue = 7 | page = 309 | last = Jansson | first = Janet | title = Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes Print E-mail | work = Microbe | year = 2011 | url = http://www.microbemagazine.org/index.php/07-2011-home/3553-towards-tera-terra-terabase-sequencing-of-terrestrial-metagenomes }}</ref>
<ref name="vogel2009">{{cite doi |10.1038/nrmicro2119 }}</ref>
<ref name="terra">{{chú thích web | title = TerraGenome Homepage | work = TerraGenome international sequencing consortium | accessdate = 30 December 2011 | url = http://www.terragenome.org/ }}</ref>
<ref name="charles2010">{{chú thích sách |author= Charles T|year=2010|chapter=The Potential for Investigation of Plant-microbe Interactions Using Metagenomics Methods|title=Metagenomics: Theory, Methods and Applications|publisher=Caister Academic Press|isbn= 978-1-904455-54-7}}</ref>
<ref name="Pace1991">
{{chú thích tạp chí
| last = Pace
| first = NR
| authorlink = Norman R. Pace
| last2 = Delong
| year = 1991
| first2 = EF
| last3 = Pace
| first3 = NR
| title = Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing
| journal = [[Journal of Bacteriology]]
| volume = 173
| issue = 14
| pages = 4371–4378
| pmid=2066334
| pmc = 208098}}</ref>
<ref name="werner2011">
{{chú thích tạp chí
| doi = 10.1073/pnas.1015676108
| issn = 0027-8424
| volume = 108
| issue = 10
| pages = 4158–4163
| last = Werner
| first = Jeffrey J.
| coauthors = Dan Knights, Marcelo L. Garcia, Nicholas B. Scalfone, Samual Smith, Kevin Yarasheski, Theresa A. Cummings, Allen R. Beers, Rob Knight, Largus T. Angenent
| title = Bacterial community structures are unique and resilient in full-scale bioenergy systems
| journal = Proceedings of the National Academy of Sciences of the United States of America
| date = 8 March 2011
| pmid = 21368115
| pmc = 3053989
|bibcode = 2011PNAS..108.4158W }}
</ref>|2}}
 
== Liên kết ngoài ==
Hàng 832 ⟶ 114:
{{Portal bar|Biology|Medicine}}
 
{{Use dmy dates|date=August 2010}}
 
[[Thể loại:Bioinformatics]]
Lấy từ “https://vi.wikipedia.org/wiki/Metagenomics”