メタジェノミクス【metagenomics】
読み方:めたじぇのみくす
メタゲノミクス
(メタジェノミクス から転送)
出典: フリー百科事典『ウィキペディア(Wikipedia)』 (2022/10/28 05:42 UTC 版)
メタゲノミクス(英:Metagenomics)は、環境サンプルから直接回収されたゲノムDNAを扱う微生物学・ウイルス学の研究分野である。広義には環境ゲノミクスやエコゲノミクス、群集ゲノミクスとも呼ばれる[1]。メタゲノム解析(Metagenomic analysis)、あるいは単純にメタゲノム(Metagenome)とも呼称される。従来の微生物のゲノム解析では、単一の菌株を環境サンプルから分離培養する過程を経る必要があったが、メタゲノム解析はこの過程を経ることなく、微生物コミュニティ(細菌叢)から直接ゲノムDNAを抽出し、様々な系統由来のDNAがミックスされた状態でDNAシーケンスを行う。そのため、メタゲノム解析では従来の培養を基本とする方法では困難であった難培養・未培養系統に属する微生物のゲノム情報が入手可能である。一説には、地球上に棲息する細菌の99%以上は単独では培養できない系統であると推察されており[2]、メタゲノム解析は環境中に埋没する膨大な数の未知の細菌、未知の遺伝子を解明できる手法として期待されている。DNAシークエンシングのコストは年々安価になってきており、より大規模で詳細なメタゲノム解析研究が行われることも見込まれる[3]。狭義には、メタゲノム解析はショットガンシーケンスにより得られたゲノム全体の配列情報を解析することを指し、ターゲット遺伝子を絞りPCRを経た増幅シーケンス(16S rRNAタグシーケンスなど)とは区別されるが[4]、後者を広義のメタゲノム解析に含めて扱われることもある[5]。
- ^ 木暮(2011), 「海洋における環境ゲノミクス」『地球環境』 Vol.16 No.1 p,71-79, NAID 40018854028
- ^ 工藤俊章 『難培養微生物の利用技術』 シーエムシー出版、2010年、はじめに
- ^ Eisen, Jonathan A (2007-03-13). Simon Levin. ed. “Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes” (英語). PLoS Biology 5 (3): e82. doi:10.1371/journal.pbio.0050082. ISSN 1545-7885. PMC 1821061. PMID 17355177 .
- ^ Rausch, Philipp; Rühlemann, Malte; Hermes, Britt M.; Doms, Shauni; Dagan, Tal; Dierking, Katja; Domin, Hanna; Fraune, Sebastian et al. (2019-12). “Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms” (英語). Microbiome 7 (1): 133. doi:10.1186/s40168-019-0743-1. ISSN 2049-2618. PMC 6744666. PMID 31521200 .
- ^ “イルミナ「総説:メタゲノム研究」”. 2020年3月23日閲覧。
- ^ 今すぐ始める! メタゲノム解析 実験プロトコール. Hattori, masahira., 服部, 正平. 羊土社. (2016). ISBN 978-4-7581-0197-4. OCLC 1089711913
- ^ a b Handelsman, J.; Rondon, M. R.; Brady, S. F.; Clardy, J.; Goodman, R. M. (1998-10). “Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products”. Chemistry & Biology 5 (10): R245-249. doi:10.1016/s1074-5521(98)90108-9. ISSN 1074-5521. PMID 9818143 .
- ^ Chen, K.; Pachter, L. (2005). "Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities". PLoS Computational Biology 1 (2): e24. doi:10.1371/journal.pcbi.0010024
- ^ Hugenholtz, Philip; Goebel, Brett M.; Pace, Norman R. (1998-09). “Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity”. Journal of Bacteriology 180 (18): 4765-4774. ISSN 0021-9193. PMC 107498. PMID 9733676 .
- ^ Lane, D. J.; Pace, B.; Olsen, G. J.; Stahl, D. A.; Sogin, M. L.; Pace, N. R. (1985-10). “Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses”. Proceedings of the National Academy of Sciences of the United States of America 82 (20): 6955-6959. doi:10.1073/pnas.82.20.6955. ISSN 0027-8424. PMC 391288. PMID 2413450 .
- ^ Pace, Norman R.; Stahl, David A.; Lane, David J.; Olsen, Gary J. (1986). Marshall, K. C.. ed (英語). Advances in Microbial Ecology. Boston, MA: Springer US. pp. 1-55. doi:10.1007/978-1-4757-0611-6_1. ISBN 978-1-4757-0611-6
- ^ Schmidt, T M; DeLong, E F; Pace, N R (1991). “Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.” (英語). Journal of Bacteriology 173 (14): 4371-4378. doi:10.1128/JB.173.14.4371-4378.1991. ISSN 0021-9193. PMC 208098. PMID 2066334 .
- ^ Healy, F. G.; Ray, R. M.; Aldrich, H. C.; Wilkie, A. C.; Ingram, L. O.; Shanmugam, K. T. (1995-09). “Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose” (英語). Applied Microbiology and Biotechnology 43 (4): 667-674. doi:10.1007/BF00164771. ISSN 0175-7598 .
- ^ Stein, J L; Marsh, T L; Wu, K Y; Shizuya, H; DeLong, E F (1996). “Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon.” (英語). Journal of bacteriology 178 (3): 591-599. doi:10.1128/JB.178.3.591-599.1996. ISSN 0021-9193. PMC 177699. PMID 8550487 .
- ^ Breitbart, M.; Salamon, P.; Andresen, B.; Mahaffy, J. M.; Segall, A. M.; Mead, D.; Azam, F.; Rohwer, F. (2002-10-29). “Genomic analysis of uncultured marine viral communities” (英語). Proceedings of the National Academy of Sciences 99 (22): 14250-14255. doi:10.1073/pnas.202488399. ISSN 0027-8424. PMC PMC137870. PMID 12384570 .
- ^ a b Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip; Allen, Eric E.; Ram, Rachna J.; Richardson, Paul M.; Solovyev, Victor V.; Rubin, Edward M. et al. (2004-03). “Community structure and metabolism through reconstruction of microbial genomes from the environment” (英語). Nature 428 (6978): 37-43. doi:10.1038/nature02340. ISSN 0028-0836 .
- ^ Venter, J. C. (2004-04-02). “Environmental Genome Shotgun Sequencing of the Sargasso Sea” (英語). Science 304 (5667): 66-74. doi:10.1126/science.1093857. ISSN 0036-8075 .
- ^ Yooseph, Shibu; Nealson, Kenneth H.; Rusch, Douglas B.; McCrow, John P.; Dupont, Christopher L.; Kim, Maria; Johnson, Justin; Montgomery, Robert et al. (2010-11). “Genomic and functional adaptation in surface ocean planktonic prokaryotes” (英語). Nature 468 (7320): 60-66. doi:10.1038/nature09530. ISSN 0028-0836 .
- ^ a b c Poinar, Hendrik N.; Schwarz, Carsten; Qi, Ji; Shapiro, Beth; MacPhee, Ross D. E.; Buigues, Bernard; Tikhonov, Alexei; Huson, Daniel H. et al. (2006-01-20). “Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA” (英語). Science 311 (5759): 392-394. doi:10.1126/science.1123360. ISSN 0036-8075 .
- ^ Edwards, Robert A; Rodriguez-Brito, Beltran; Wegley, Linda; Haynes, Matthew; Breitbart, Mya; Peterson, Dean M; Saar, Martin O; Alexander, Scott et al. (2006-12). “Using pyrosequencing to shed light on deep mine microbial ecology” (英語). BMC Genomics 7 (1): 57. doi:10.1186/1471-2164-7-57. ISSN 1471-2164. PMC 1483832. PMID 16549033 .
- ^ Jiang, Bai; Song, Kai; Ren, Jie; Deng, Minghua; Sun, Fengzhu; Zhang, Xuegong (2012). “Comparison of metagenomic samples using sequence signatures” (英語). BMC Genomics 13 (1): 730. doi:10.1186/1471-2164-13-730. ISSN 1471-2164. PMC 3549735. PMID 23268604 .
- ^ 服部, 正平; 林, 哲也; 黒川, 顕; 伊藤, 武彦; 桑原, 知巳 (2007) (日本語), ヒト腸内細菌叢のゲノムシークエンス, 公益財団法人 腸内細菌学会, doi:10.11209/jim.21.187 2020年5月25日閲覧。
- ^ Rodrigue, Sébastien; Materna, Arne C.; Timberlake, Sonia C.; Blackburn, Matthew C.; Malmstrom, Rex R.; Alm, Eric J.; Chisholm, Sallie W. (2010-07-28). Gilbert, Jack Anthony. ed. “Unlocking Short Read Sequencing for Metagenomics” (英語). PLoS ONE 5 (7): e11840. doi:10.1371/journal.pone.0011840. ISSN 1932-6203. PMC 2911387. PMID 20676378 .
- ^ Schuster, Stephan C (2008-01). “Next-generation sequencing transforms today's biology” (英語). Nature Methods 5 (1): 16-18. doi:10.1038/nmeth1156. ISSN 1548-7091 .
- ^ “Metagenomics versus Moore's law” (英語). Nature Methods 6 (9): 623-623. (2009-09). doi:10.1038/nmeth0909-623. ISSN 1548-7091 .
- ^ a b Hiraoka, Satoshi; Yang, Ching-chia; Iwasaki, Wataru (2016). “Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond” (英語). Microbes and environments 31 (3): 204-212. doi:10.1264/jsme2.ME16024. ISSN 1342-6311. PMC 5017796. PMID 27383682 .
- ^ Watson, Mick; Roehe, Rainer; Walker, Alan W.; Dewhurst, Richard J.; Snelling, Timothy J.; Ivan Liachko; Langford, Kyle W.; Press, Maximilian O. et al. (28 February 2018). “Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen” (英語). Nature Communications 9 (1): 870. Bibcode: 2018NatCo...9..870S. doi:10.1038/s41467-018-03317-6. ISSN 2041-1723. PMC 5830445. PMID 29491419 .
- ^ Thomas, T.; Gilbert, J.; Meyer, F. (2012). “Metagenomics - a guide from sampling to data analysis”. Microbial Informatics and Experimentation 2 (1): 3. doi:10.1186/2042-5783-2-3. PMC 3351745. PMID 22587947 .
- ^ a b Hess, M.; Sczyrba, A.; Egan, R.; Kim, T.-W.; Chokhawala, H.; Schroth, G.; Luo, S.; Clark, D. S. et al. (2011-01-28). “Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen” (英語). Science 331 (6016): 463-467. doi:10.1126/science.1200387. ISSN 0036-8075 .
- ^ a b MetaHIT Consortium; Qin, Junjie; Li, Ruiqiang; Raes, Jeroen; Arumugam, Manimozhiyan; Burgdorf, Kristoffer Solvsten; Manichanh, Chaysavanh; Nielsen, Trine et al. (2010-03). “A human gut microbial gene catalogue established by metagenomic sequencing” (英語). Nature 464 (7285): 59-65. doi:10.1038/nature08821. ISSN 0028-0836. PMC 3779803. PMID 20203603 .
- ^ Oulas, A; Pavloudi, C; Polymenakou, P; Pavlopoulos, GA; Papanikolaou, N; Kotoulas, G; Arvanitidis, C; Iliopoulos, I (2015). “Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies”. Bioinformatics and Biology Insights 9: 75-88. doi:10.4137/BBI.S12462. PMC 4426941. PMID 25983555 .
- ^ Mende, Daniel R.; Alison S. Waller; Shinichi Sunagawa; Aino I. Järvelin; Michelle M. Chan; Manimozhiyan Arumugam; Jeroen Raes; Peer Bork (23 February 2012). “Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data”. PLoS ONE 7 (2): e31386. Bibcode: 2012PLoSO...731386M. doi:10.1371/journal.pone.0031386. ISSN 1932-6203. PMC 3285633. PMID 22384016 .
- ^ Balzer, S.; Malde, K.; Grohme, M. A.; Jonassen, I. (2013). “Filtering duplicate reads from 454 pyrosequencing data”. Bioinformatics 29 (7): 830-836. doi:10.1093/bioinformatics/btt047. PMC 3605598. PMID 23376350 .
- ^ Mohammed, MH; Sudha Chadaram; Dinakar Komanduri; Tarini Shankar Ghosh; Sharmila S Mande (2011). “Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets”. Journal of Biosciences 36 (4): 709-717. doi:10.1007/s12038-011-9105-2. PMID 21857117.
- ^ R, Schmeider; R Edwards (2011). “Fast identification and removal of sequence contamination from genomic and metagenomic datasets”. PLoS ONE 6 (3): e17288. Bibcode: 2011PLoSO...617288S. doi:10.1371/journal.pone.0017288. PMC 3052304. PMID 21408061 .
- ^ a b c Kunin, V.; Copeland, A.; Lapidus, A.; Mavromatis, K.; Hugenholtz, P. (2008-12-01). “A Bioinformatician's Guide to Metagenomics” (英語). Microbiology and Molecular Biology Reviews 72 (4): 557-578. doi:10.1128/MMBR.00009-08. ISSN 1092-2172. PMC 2593568. PMID 19052320 .
- ^ a b Burton, Joshua N.; Liachko, Ivan; Dunham, Maitreya J.; Shendure, Jay (2014-07). “Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps” (英語). G3: Genes|Genomes|Genetics 4 (7): 1339-1346. doi:10.1534/g3.114.011825. ISSN 2160-1836. PMC 4455782. PMID 24855317 .
- ^ a b c d Wooley, John C.; Godzik, Adam; Friedberg, Iddo (2010-02-26). Bourne, Philip E.. ed. “A Primer on Metagenomics” (英語). PLoS Computational Biology 6 (2): e1000667. doi:10.1371/journal.pcbi.1000667. ISSN 1553-7358. PMC 2829047. PMID 20195499 .
- ^ Zerbino, D. R.; Birney, E. (2008-02-21). “Velvet: Algorithms for de novo short read assembly using de Bruijn graphs” (英語). Genome Research 18 (5): 821-829. doi:10.1101/gr.074492.107. ISSN 1088-9051. PMC 2336801. PMID 18349386 .
- ^ Namiki, Toshiaki; Hachiya, Tsuyoshi; Tanaka, Hideaki; Sakakibara, Yasubumi (2012-11-01). “MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads” (英語). Nucleic Acids Research 40 (20): e155-e155. doi:10.1093/nar/gks678. ISSN 1362-4962. PMC 3488206. PMID 22821567 .
- ^ a b Huson, D. H.; Mitra, S.; Ruscheweyh, H.-J.; Weber, N.; Schuster, S. C. (2011-09-01). “Integrative analysis of environmental sequences using MEGAN4” (英語). Genome Research 21 (9): 1552-1560. doi:10.1101/gr.120618.111. ISSN 1088-9051. PMC 3166839. PMID 21690186 .
- ^ Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark (2010-07). “Ab initio gene identification in metagenomic sequences” (英語). Nucleic Acids Research 38 (12): e132-e132. doi:10.1093/nar/gkq275. ISSN 1362-4962. PMC 2896542. PMID 20403810 .
- ^ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W. et al. (11 April 2016). “A new view of the tree of life”. Nature Microbiology 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
- ^ Konopka, Allan (2009-11). “What is microbial community ecology?” (英語). The ISME Journal 3 (11): 1223-1230. doi:10.1038/ismej.2009.88. ISSN 1751-7362 .
- ^ a b Huson, D. H.; Auch, A. F.; Qi, J.; Schuster, S. C. (2007-02-06). “MEGAN analysis of metagenomic data” (英語). Genome Research 17 (3): 377-386. doi:10.1101/gr.5969107. ISSN 1088-9051. PMC 1800929. PMID 17255551 .
- ^ Segata, Nicola; Waldron, Levi; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, Curtis (2012-08). “Metagenomic microbial community profiling using unique clade-specific marker genes” (英語). Nature Methods 9 (8): 811-814. doi:10.1038/nmeth.2066. ISSN 1548-7091. PMC 3443552. PMID 22688413 .
- ^ Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg; Izquierdo-Carrasco, Fernando; Berger, Simon A; Kultima, Jens Roat; Coelho, Luis Pedro; Arumugam, Manimozhiyan et al. (2013-12). “Metagenomic species profiling using universal phylogenetic marker genes” (英語). Nature Methods 10 (12): 1196-1199. doi:10.1038/nmeth.2693. ISSN 1548-7091 .
- ^ a b Milanese, Alessio; Mende, Daniel R; Paoli, Lucas; Salazar, Guillem; Ruscheweyh, Hans-Joachim; Cuenca, Miguelangel; Hingamp, Pascal; Alves, Renato et al. (2019-12). “Microbial abundance, activity and population genomic profiling with mOTUs2” (英語). Nature Communications 10 (1): 1014. doi:10.1038/s41467-019-08844-4. ISSN 2041-1723. PMC 6399450. PMID 30833550 .
- ^ Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, Mihai (2011). “Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences” (英語). BMC Genomics 12 (Suppl 2): S4. doi:10.1186/1471-2164-12-S2-S4. ISSN 1471-2164. PMC 3194235. PMID 21989143 .
- ^ Dadi, Temesgen Hailemariam; Renard, Bernhard Y.; Wieler, Lothar H.; Semmler, Torsten; Reinert, Knut (2017-03-28). “SLIMM: species level identification of microorganisms from metagenomes” (英語). PeerJ 5: e3138. doi:10.7717/peerj.3138. ISSN 2167-8359. PMC 5372838. PMID 28367376 .
- ^ a b c d e The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: National Academies Press. (2007-05-24). doi:10.17226/11902. ISBN 978-0-309-10676-4
- ^ Pagani, I.; Liolios, K.; Jansson, J.; Chen, I.-M. A.; Smirnova, T.; Nosrat, B.; Markowitz, V. M.; Kyrpides, N. C. (2012-01-01). “The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata” (英語). Nucleic Acids Research 40 (D1): D571-D579. doi:10.1093/nar/gkr1100. ISSN 0305-1048. PMC 3245063. PMID 22135293 .
- ^ Meyer, F; Paarmann, D; D'Souza, M; Olson, R; Glass, Em; Kubal, M; Paczian, T; Rodriguez, A et al. (2008-12). “The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes” (英語). BMC Bioinformatics 9 (1): 386. doi:10.1186/1471-2105-9-386. ISSN 1471-2105. PMC 2563014. PMID 18803844 .
- ^ Markowitz, V. M.; Chen, I.-M. A.; Chu, K.; Szeto, E.; Palaniappan, K.; Grechkin, Y.; Ratner, A.; Jacob, B. et al. (2012-01-01). “IMG/M: the integrated metagenome data management and comparative analysis system” (英語). Nucleic Acids Research 40 (D1): D123-D129. doi:10.1093/nar/gkr975. ISSN 0305-1048. PMC 3245048. PMID 22086953 .
- ^ Mitra, Suparna; Rupek, Paul; Richter, Daniel C; Urich, Tim; Gilbert, Jack A; Meyer, Folker; Wilke, Andreas; Huson, Daniel H (2011-12). “Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG” (英語). BMC Bioinformatics 12 (S1): S21. doi:10.1186/1471-2105-12-S1-S21. ISSN 1471-2105. PMC 3044276. PMID 21342551 .
- ^ Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W. (2012-11-26). “GenBank” (英語). Nucleic Acids Research 41 (D1): D36-D42. doi:10.1093/nar/gks1195. ISSN 0305-1048. PMC 3531190. PMID 23193287 .
- ^ Bazinet, Adam L; Cummings, Michael P (2012-12). “A comparative evaluation of sequence classification programs” (英語). BMC Bioinformatics 13 (1): 92. doi:10.1186/1471-2105-13-92. ISSN 1471-2105. PMC 3428669. PMID 22574964 .
- ^ Ounit, Rachid; Wanamaker, Steve; Close, Timothy J; Lonardi, Stefano (2015-12). “CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers” (英語). BMC Genomics 16 (1): 236. doi:10.1186/s12864-015-1419-2. ISSN 1471-2164. PMC 4428112. PMID 25879410 .
- ^ Pratas, Diogo; Hosseini, Morteza; Grilo, Gonçalo; Pinho, Armando; Silva, Raquel; Caetano, Tânia; Carneiro, João; Pereira, Filipe (2018-09-06). “Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard” (英語). Genes 9 (9): 445. doi:10.3390/genes9090445. ISSN 2073-4425. PMC 6162538. PMID 30200636 .
- ^ Kurokawa, Ken; Itoh, Takehiko; Kuwahara, Tomomi; Oshima, Kenshiro; Toh, Hidehiro; Toyoda, Atsushi; Takami, Hideto; Morita, Hidetoshi et al. (2007). “Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes” (英語). DNA Research 14 (4): 169-181. doi:10.1093/dnares/dsm018. ISSN 1756-1663. PMC 2533590. PMID 17916580 .
- ^ a b c d e Simon, Carola; Daniel, Rolf (2011-02-15). “Metagenomic Analyses: Past and Future Trends” (英語). Applied and Environmental Microbiology 77 (4): 1153-1161. doi:10.1128/AEM.02345-10. ISSN 0099-2240. PMC 3067235. PMID 21169428 .
- ^ Willner, D; RV Thurber; F Rohwer (2009). “Metagenomic signatures of 86 microbial and viral metagenomes.”. Environmental Microbiology 11 (7): 1752-66. doi:10.1111/j.1462-2920.2009.01901.x. PMID 19302541.
- ^ Ghosh, Tarini Shankar; Monzoorul Haque Mohammed; Hannah Rajasingh; Sudha Chadaram; Sharmila S Mande (2011). “HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences.”. BMC Bioinformatics 12 (Supplement 13): S9. doi:10.1186/1471-2105-12-s13-s9. PMC 3278849. PMID 22373355 .
- ^ Fimereli, Danai; Detours, Vincent; Konopka, Tomasz (2013-04-01). “TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data” (英語). Nucleic Acids Research 41 (7): e86-e86. doi:10.1093/nar/gkt094. ISSN 1362-4962. PMC 3627586. PMID 23408855 .
- ^ Maillet, Nicolas; Lemaitre, Claire; Chikhi, Rayan; Lavenier, Dominique; Peterlongo, Pierre (2012-12). “Compareads: comparing huge metagenomic experiments” (英語). BMC Bioinformatics 13 (S19): S10. doi:10.1186/1471-2105-13-S19-S10. ISSN 1471-2105. PMC 3526429. PMID 23282463 .
- ^ Paulson, Joseph N; Stine, O Colin; Bravo, Héctor Corrada; Pop, Mihai (2013-12). “Differential abundance analysis for microbial marker-gene surveys” (英語). Nature Methods 10 (12): 1200-1202. doi:10.1038/nmeth.2658. ISSN 1548-7091. PMC 4010126. PMID 24076764 .
- ^ Bhusan, Kuntal Kumar; Tarini Shankar Ghosh; Sharmila S Mande (2013). “Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes”. Genomics 102 (4): 409-418. doi:10.1016/j.ygeno.2013.08.004. PMID 23978768.
- ^ Werner, J. J.; Knights, D.; Garcia, M. L.; Scalfone, N. B.; Smith, S.; Yarasheski, K.; Cummings, T. A.; Beers, A. R. et al. (2011-03-08). “Bacterial community structures are unique and resilient in full-scale bioenergy systems” (英語). Proceedings of the National Academy of Sciences 108 (10): 4158-4163. doi:10.1073/pnas.1015676108. ISSN 0027-8424. PMC 3053989. PMID 21368115 .
- ^ McInerney, Michael J; Sieber, Jessica R; Gunsalus, Robert P (2009-12). “Syntrophy in anaerobic global carbon cycles” (英語). Current Opinion in Biotechnology 20 (6): 623-632. doi:10.1016/j.copbio.2009.10.001. PMC 2790021. PMID 19897353 .
- ^ Klitgord, Niels; Segrè, Daniel (2011-08). “Ecosystems biology of microbial metabolism” (英語). Current Opinion in Biotechnology 22 (4): 541-546. doi:10.1016/j.copbio.2011.04.018 .
- ^ Leininger, S.; Urich, T.; Schloter, M.; Schwark, L.; Qi, J.; Nicol, G. W.; Prosser, J. I.; Schuster, S. C. et al. (2006-08). “Archaea predominate among ammonia-oxidizing prokaryotes in soils” (英語). Nature 442 (7104): 806-809. doi:10.1038/nature04983. ISSN 0028-0836 .
- ^ “Uncovering Earth's virome”. Nature 536 (7617): 425-30. (August 2016). Bibcode: 2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034 .
- ^ “IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses”. Nucleic Acids Research 45 (D1): D457-D465. (January 2017). doi:10.1093/nar/gkw1030. PMC 5210529. PMID 27799466 .
- ^ “IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes”. Nucleic Acids Research 47 (D1): D678-D686. (January 2019). doi:10.1093/nar/gky1127. PMC 6323928. PMID 30407573 .
- ^ Paez-Espino, David; Pavlopoulos, Georgios A; Ivanova, Natalia N; Kyrpides, Nikos C (2017-08). “Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data” (英語). Nature Protocols 12 (8): 1673-1682. doi:10.1038/nprot.2017.063. ISSN 1754-2189 .
- ^ Kristensen, David M.; Mushegian, Arcady R.; Dolja, Valerian V.; Koonin, Eugene V. (2010-01). “New dimensions of the virus world discovered through metagenomics” (英語). Trends in Microbiology 18 (1): 11-19. doi:10.1016/j.tim.2009.11.003. PMC 3293453. PMID 19942437 .
- ^ “Giant viruses of the Kutch Desert”. Archives of Virology 161 (3): 721-4. (March 2016). arXiv:1410.1278. doi:10.1007/s00705-015-2720-8. PMID 26666442.
- ^ “The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys”. Archives of Virology 162 (6): 1671-1676. (June 2017). arXiv:1503.05575. doi:10.1007/s00705-017-3286-4. PMID 28247094.
- ^ “The World Within Us”. Healthcare Journal of New Orleans: 21-26. (Sep-Oct 2017) .
- ^ 楠本憲一「メタゲノム解析」『日本食品科学工学会誌』第58巻第3号、2011年、 136-136頁、 doi:10.3136/nskkk.58.136、 ISSN 1341-027X。
- ^ Jansson, Janet (2011-01-01). “Towards “Tera-Terra”: Terabase Sequencing of Terrestrial Metagenomes: Microbial ecologists are taking a metagenomics approach to analyze complex and diverse soil microbial communities” (英語). Microbe Magazine 6 (7): 309-315. doi:10.1128/microbe.6.309.1. ISSN 1558-7452 .
- ^ Vogel, Timothy M.; Simonet, Pascal; Jansson, Janet K.; Hirsch, Penny R.; Tiedje, James M.; van Elsas, Jan Dirk; Bailey, Mark J.; Nalin, Renaud et al. (2009-04). “TerraGenome: a consortium for the sequencing of a soil metagenome” (英語). Nature Reviews Microbiology 7 (4): 252-252. doi:10.1038/nrmicro2119. ISSN 1740-1526 .
- ^ a b c d Metagenomics : theory, methods, and applications. Marco, Diana.. Wymondham: Caister Academic Press. (2010). ISBN 978-1-904455-54-7. OCLC 351318426
- ^ “Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics”. Frontiers in Microbiology 6: 486. (22 May 2015). doi:10.3389/fmicb.2015.00486. PMC 4440916. PMID 26052316 .
- ^ Li, Luen-Luen; McCorkle, Sean R; Monchy, Sebastien; Taghavi, Safiyh; van der Lelie, Daniel (2009). “Bioprospecting metagenomes: glycosyl hydrolases for converting biomass” (英語). Biotechnology for Biofuels 2 (1): 10. doi:10.1186/1754-6834-2-10. ISSN 1754-6834. PMC 2694162. PMID 19450243 .
- ^ Jaenicke, Sebastian; Ander, Christina; Bekel, Thomas; Bisdorf, Regina; Dröge, Marcus; Gartemann, Karl-Heinz; Jünemann, Sebastian; Kaiser, Olaf et al. (2011-01-26). Aziz, Ramy K.. ed. “Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing” (英語). PLoS ONE 6 (1): e14519. doi:10.1371/journal.pone.0014519. ISSN 1932-6203. PMC 3027613. PMID 21297863 .
- ^ Suen, Garret; Scott, Jarrod J.; Aylward, Frank O.; Adams, Sandra M.; Tringe, Susannah G.; Pinto-Tomás, Adrián A.; Foster, Clifton E.; Pauly, Markus et al. (2010-09-23). Sonnenburg, Justin. ed. “An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity” (英語). PLoS Genetics 6 (9): e1001129. doi:10.1371/journal.pgen.1001129. ISSN 1553-7404. PMC 2944797. PMID 20885794 .
- ^ Simon, Carola; Daniel, Rolf (2009-11). “Achievements and new knowledge unraveled by metagenomic approaches” (英語). Applied Microbiology and Biotechnology 85 (2): 265-276. doi:10.1007/s00253-009-2233-z. ISSN 0175-7598. PMC 2773367. PMID 19760178 .
- ^ a b Schloss, Patrick D; Handelsman, Jo (2003-06). “Biotechnological prospects from metagenomics” (英語). Current Opinion in Biotechnology 14 (3): 303-310. doi:10.1016/S0958-1669(03)00067-3 .
- ^ a b c Kakirde, Kavita S.; Parsley, Larissa C.; Liles, Mark R. (2010-11). “Size does matter: Application-driven approaches for soil metagenomics” (英語). Soil Biology and Biochemistry 42 (11): 1911-1923. doi:10.1016/j.soilbio.2010.07.021. PMC 2976544. PMID 21076656 .
- ^ Parachin, Nádia; Gorwa-Grauslund, Marie F (2011). “Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library” (英語). Biotechnology for Biofuels 4 (1): 9. doi:10.1186/1754-6834-4-9. ISSN 1754-6834. PMC 3113934. PMID 21545702 .
- ^ “Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens”. Nature Microbiology 3 (4): 415-422. (April 2018). doi:10.1038/s41564-018-0110-1. PMC 5874163. PMID 29434326 .
- ^ “Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data”. Molecular Systems Biology 7: 473. (March 2011). doi:10.1038/msb.2011.6. PMC 3094067. PMID 21407210 .
- ^ “High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces”. PloS One 7 (5): e36478. (2012). Bibcode: 2012PLoSO...736478L. doi:10.1371/journal.pone.0036478. PMC 3350522. PMID 22606263 .
- ^ Miller, Ruth R; Montoya, Vincent; Gardy, Jennifer L; Patrick, David M; Tang, Patrick (2013). “Metagenomics for pathogen detection in public health” (英語). Genome Medicine 5 (9): 81. doi:10.1186/gm485. ISSN 1756-994X. PMC 3978900. PMID 24050114 .
- ^ Ren, Li-Li; Wang, Ye-Ming; Wu, Zhi-Qiang; Xiang, Zi-Chun; Guo, Li; Xu, Teng; Jiang, Yong-Zhong; Xiong, Yan et al. (2020-05). “Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study” (英語). Chinese Medical Journal 133 (9): 1015-1024. doi:10.1097/CM9.0000000000000722. ISSN 0366-6999. PMC 7147275. PMID 32004165 .
- メタジェノミクスのページへのリンク