Metagenomics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Metagenomics" in English language version.

refsWebsite

Global rank English rank

160nih.gov

4^th place

98doi.org

2^nd place

38harvard.edu

18^th place

17^th place

18worldcat.org

5^th place

16semanticscholar.org

11^th place

8^th place

3nature.com

234^th place

397^th place

3web.archive.org

1^st place

2escholarship.org

1,523^rd place

976^th place

2arxiv.org

69^th place

59^th place

1sciencedirect.com

149^th place

178^th place

1handle.net

102^nd place

76^th place

1oup.com

485^th place

440^th place

1springer.com

274^th place

309^th place

1psu.edu

207^th place

136^th place

1bbc.co.uk

8^th place

10^th place

1nap.edu

2,128^th place

1,553^rd place

1claudiacopeland.com

low place

1microbemagazine.org

low place

1terragenome.org

low place

1nas.edu

low place

1yale.edu

565^th place

460^th place

1npr.org

92^nd place

72^nd place

1pensoft.net

5,291^st place

4,808^th place

1nytimes.com

7^th place

arxiv.org

Kerepesi C, Grolmusz V (March 2016). "Giant viruses of the Kutch Desert". Archives of Virology. 161 (3): 721–4. arXiv:1410.1278. doi:10.1007/s00705-015-2720-8. PMID 26666442. S2CID 13145926.
Kerepesi C, Grolmusz V (June 2017). "The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys". Archives of Virology. 162 (6): 1671–1676. arXiv:1503.05575. doi:10.1007/s00705-017-3286-4. PMID 28247094. S2CID 1925728.

bbc.co.uk

Walsh, Fergus (30 April 2025). "Metagenomics test saves woman's sight after mystery infection". BBC News.

claudiacopeland.com

Copeland CS (September–October 2017). "The World Within Us" (PDF). Healthcare Journal of New Orleans: 21–26.

doi.org

Wooley JC, Godzik A, Friedberg I (February 2010). Bourne PE (ed.). "A primer on metagenomics". PLOS Computational Biology. 6 (2): e1000667. Bibcode:2010PLSCB...6E0667W. doi:10.1371/journal.pcbi.1000667. PMC 2829047. PMID 20195499.
Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio (November 2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. ISSN 1476-4687. PMC 6192678. PMID 29088705.
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, HarshaVardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J. (October 2018). "Temporal development of the gut microbiome in early childhood from the TEDDY study". Nature. 562 (7728): 583–588. Bibcode:2018Natur.562..583S. doi:10.1038/s41586-018-0617-x. ISSN 1476-4687. PMC 6415775. PMID 30356187.
Carlino, Niccolò; Blanco-Míguez, Aitor; Punčochář, Michal; Mengoni, Claudia; Pinto, Federica; Tatti, Alessia; Manghi, Paolo; Armanini, Federica; Avagliano, Michele; Barcenilla, Coral; Breselge, Samuel; Cabrera-Rubio, Raul; Calvete-Torre, Inés; Coakley, Mairéad; Cobo-Díaz, José F. (3 October 2024). "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome". Cell. 187 (20): 5775–5795.e15. doi:10.1016/j.cell.2024.07.039. hdl:10261/373917. ISSN 0092-8674.
Eisen JA (March 2007). "Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes". PLOS Biology. 5 (3): e82. doi:10.1371/journal.pbio.0050082. PMC 1821061. PMID 17355177.
Chen, Liang; Zhao, Na; Cao, Jiabao; Liu, Xiaolin; Xu, Jiayue; Ma, Yue; Yu, Ying; Zhang, Xuan; Zhang, Wenhui; Guan, Xiangyu; Yu, Xiaotong; Liu, Zhipeng; Fan, Yanqun; Wang, Yang; Liang, Fan (8 June 2022). "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes". Nature Communications. 13 (1): 3175. Bibcode:2022NatCo..13.3175C. doi:10.1038/s41467-022-30857-9. ISSN 2041-1723. PMC 9177567. PMID 35676264.
Zepeda Mendoza, Marie Lisandra; Sicheritz-Pontén, Thomas; Gilbert, M. Thomas P. (1 September 2015). "Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses". Briefings in Bioinformatics. 16 (5): 745–758. doi:10.1093/bib/bbv001. ISSN 1467-5463. PMC 4570204. PMID 25673291.
Rieder, Jessica; Kapopoulou, Adamandia; Bank, Claudia; Adrian-Kalchhauser, Irene (14 February 2023). "Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems". Environmental Microbiome. 18 (1): 8. Bibcode:2023EMicb..18....8R. doi:10.1186/s40793-023-00459-z. ISSN 2524-6372. PMC 9930364. PMID 36788626.
Semenov, M. V. (1 January 2021). "Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects". Biology Bulletin Reviews. 11 (1): 40–53. Bibcode:2021BioBR..11...40S. doi:10.1134/S2079086421010084. ISSN 2079-0872.
Hugenholtz P, Goebel BM, Pace NR (September 1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". Journal of Bacteriology. 180 (18): 4765–74. doi:10.1128/JB.180.18.4765-4774.1998. PMC 107498. PMID 9733676.
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (October 1998). "Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products". Chemistry & Biology. 5 (10): R245-9. doi:10.1016/S1074-5521(98)90108-9. PMID 9818143..
Chen K, Pachter L (July 2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLOS Computational Biology. 1 (2): 106–12. Bibcode:2005PLSCB...1...24C. doi:10.1371/journal.pcbi.0010024. PMC 1185649. PMID 16110337.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (October 1985). "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): 6955–9. Bibcode:1985PNAS...82.6955L. doi:10.1073/pnas.82.20.6955. PMC 391288. PMID 2413450.
Pace NR, Stahl DA, Lane DJ, Olsen GJ (1986). "The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences". In Marshall KC (ed.). Advances in Microbial Ecology. Vol. 9. Springer US. pp. 1–55. doi:10.1007/978-1-4757-0611-6_1. ISBN 978-1-4757-0611-6.
Schmidt TM, DeLong EF, Pace NR (July 1991). "Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing". Journal of Bacteriology. 173 (14): 4371–8. doi:10.1128/jb.173.14.4371-4378.1991. PMC 208098. PMID 2066334.
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". Applied Microbiology and Biotechnology. 43 (4): 667–74. doi:10.1007/BF00164771. PMID 7546604. S2CID 31384119.
Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (February 1996). "Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon". Journal of Bacteriology. 178 (3): 591–9. doi:10.1128/jb.178.3.591-599.1996. PMC 177699. PMID 8550487.
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (October 2002). "Genomic analysis of uncultured marine viral communities". Proceedings of the National Academy of Sciences of the United States of America. 99 (22): 14250–5. Bibcode:2002PNAS...9914250B. doi:10.1073/pnas.202488399. PMC 137870. PMID 12384570.
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". Nature. 428 (6978): 37–43. Bibcode:2004Natur.428...37T. doi:10.1038/nature02340. PMID 14961025. S2CID 4420754.(subscription required)
Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, et al. (November 2010). "Genomic and functional adaptation in surface ocean planktonic prokaryotes". Nature. 468 (7320): 60–6. Bibcode:2010Natur.468...60Y. doi:10.1038/nature09530. PMID 21048761.(subscription required)
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". Science. 311 (5759): 392–4. Bibcode:2006Sci...311..392P. doi:10.1126/science.1123360. PMID 16368896. S2CID 11238470.
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, et al. (March 2006). "Using pyrosequencing to shed light on deep mine microbial ecology". BMC Genomics. 7: 57. doi:10.1186/1471-2164-7-57. PMC 1483832. PMID 16549033.
Thomas T, Gilbert J, Meyer F (February 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.
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". Environmental Microbiology. 2 (5): 516–29. Bibcode:2000EnvMi...2..516B. doi:10.1046/j.1462-2920.2000.00133.x. PMID 11233160. S2CID 8267748.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (May 2013). "Computational meta'omics for microbial community studies". Molecular Systems Biology. 9 (666): 666. doi:10.1038/msb.2013.22. PMC 4039370. PMID 23670539.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW (July 2010). Gilbert JA (ed.). "Unlocking short read sequencing for metagenomics". PLOS ONE. 5 (7): e11840. Bibcode:2010PLoSO...511840R. doi:10.1371/journal.pone.0011840. PMC 2911387. PMID 20676378.
Schuster SC (January 2008). "Next-generation sequencing transforms today's biology". Nature Methods. 5 (1): 16–8. doi:10.1038/nmeth1156. PMID 18165802. S2CID 1465786.
"Metagenomics versus Moore's law". Nature Methods. 6 (9): 623. 2009. doi:10.1038/nmeth0909-623.
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. (February 2018). "Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen". Nature Communications. 9 (1): 870. Bibcode:2018NatCo...9..870S. doi:10.1038/s41467-018-03317-6. PMC 5830445. PMID 29491419.
Hiraoka S, Yang CC, Iwasaki W (September 2016). "Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond". Microbes and Environments. 31 (3): 204–12. doi:10.1264/jsme2.ME16024. PMC 5017796. PMID 27383682.
Carter, Matthew M.; Olm, Matthew R.; Merrill, Bryan D.; Dahan, Dylan; Tripathi, Surya; Spencer, Sean P.; Yu, Feiqiao B.; Jain, Sunit; Neff, Norma; Jha, Aashish R.; Sonnenburg, Erica D.; Sonnenburg, Justin L. (6 July 2023). "Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes". Cell. 186 (14): 3111–3124.e13. doi:10.1016/j.cell.2023.05.046. ISSN 0092-8674. PMC 10330870. PMID 37348505.
Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R.; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E.; Morley, Paul S.; McAllister, Tim A. (12 April 2018). "Impact of sequencing depth on the characterization of the microbiome and resistome". Scientific Reports. 8 (1): 5890. Bibcode:2018NatSR...8.5890Z. doi:10.1038/s41598-018-24280-8. ISSN 2045-2322. PMC 5897366. PMID 29651035.
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C (2020). "Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses". Microbial Genomics. 6 (8). doi:10.1099/mgen.0.000409. PMC 7641418. PMID 32706331.
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". Science. 331 (6016): 463–7. Bibcode:2011Sci...331..463H. doi:10.1126/science.1200387. PMID 21273488. S2CID 36572885.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.(subscription required)
Paulson JN, Stine OC, Bravo HC, Pop M (December 2013). "Differential abundance analysis for microbial marker-gene surveys". Nature Methods. 10 (12): 1200–2. doi:10.1038/nmeth.2658. PMC 4010126. PMID 24076764.
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: The National Academies Press. doi:10.17226/11902. ISBN 978-0-309-10676-4. PMID 21678629.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, et al. (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 DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, et al. (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. PMC 3285633. PMID 22384016.
Balzer S, Malde K, Grohme MA, Jonassen I (April 2013). "Filtering duplicate reads from 454 pyrosequencing data". Bioinformatics. 29 (7): 830–6. doi:10.1093/bioinformatics/btt047. PMC 3605598. PMID 23376350.
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS (September 2011). "Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets". Journal of Biosciences. 36 (4): 709–17. doi:10.1007/s12038-011-9105-2. PMID 21857117. S2CID 25857874.
Schmieder R, Edwards R (March 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.
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (December 2008). "A bioinformatician's guide to metagenomics". Microbiology and Molecular Biology Reviews. 72 (4): 557–78, Table of Contents. doi:10.1128/MMBR.00009-08. PMC 2593568. PMID 19052320.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y (November 2012). "MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads". Nucleic Acids Research. 40 (20): e155. doi:10.1093/nar/gks678. PMC 3488206. PMID 22821567.
Zerbino DR, Birney E (May 2008). "Velvet: algorithms for de novo short read assembly using de Bruijn graphs". Genome Research. 18 (5): 821–9. doi:10.1101/gr.074492.107. PMC 2336801. PMID 18349386.
Burton JN, Liachko I, Dunham MJ, Shendure J (May 2014). "Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps". G3. 4 (7): 1339–46. doi:10.1534/g3.114.011825. PMC 4455782. PMID 24855317.
Konopka A (November 2009). "What is microbial community ecology?". The ISME Journal. 3 (11): 1223–30. Bibcode:2009ISMEJ...3.1223K. doi:10.1038/ismej.2009.88. PMID 19657372.
Huson DH, Auch AF, Qi J, Schuster SC (March 2007). "MEGAN analysis of metagenomic data". Genome Research. 17 (3): 377–86. doi:10.1101/gr.5969107. PMC 1800929. PMID 17255551.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (June 2012). "Metagenomic microbial community profiling using unique clade-specific marker genes". Nature Methods. 9 (8): 811–4. doi:10.1038/nmeth.2066. PMC 3443552. PMID 22688413.
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". Nature Methods. 10 (12): 1196–9. doi:10.1038/nmeth.2693. PMID 24141494. S2CID 7728395.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, et al. (March 2019). "Microbial abundance, activity and population genomic profiling with mOTUs2". Nature Communications. 10 (1): 1014. Bibcode:2019NatCo..10.1014M. doi:10.1038/s41467-019-08844-4. PMC 6399450. PMID 30833550.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M (2011). "Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences". BMC Genomics. 12 (Suppl 2): S4. doi:10.1186/1471-2164-12-S2-S4. PMC 3194235. PMID 21989143.
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K (2017). "SLIMM: species level identification of microorganisms from metagenomes". PeerJ. 5: e3138. doi:10.7717/peerj.3138. PMC 5372838. PMID 28367376.
Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Murat Eren, A; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja (August 2017). "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea". Nature Biotechnology. 35 (8): 725–731. doi:10.1038/nbt.3893. PMC 6436528. PMID 28787424.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (September 2011). "Integrative analysis of environmental sequences using MEGAN4". Genome Research. 21 (9): 1552–60. doi:10.1101/gr.120618.111. PMC 3166839. PMID 21690186.
Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542. PMID 20403810.
Liu, Shaopeng; Rodriguez, Judith S.; Munteanu, Viorel; Ronkowski, Cynthia; Sharma, Nitesh Kumar; Alser, Mohammed; Andreace, Francesco; Blekhman, Ran; Błaszczyk, Dagmara; Chikhi, Rayan; Crandall, Keith A.; Della Libera, Katja; Francis, Dallace; Frolova, Alina; Gancz, Abigail Shahar (23 January 2025). "Analysis of metagenomic data". Nature Reviews Methods Primers. 5 (1): 1–28. doi:10.1038/s43586-024-00376-6. ISSN 2662-8449.
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. (August 2007). "Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes". DNA Research. 14 (4): 169–81. doi:10.1093/dnares/dsm018. PMC 2533590. PMID 17916580.
Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. (November 2014). "Estimating coverage in metagenomic data sets and why it matters". The ISME Journal. 8 (11): 2349–2351. Bibcode:2014ISMEJ...8.2349R. doi:10.1038/ismej.2014.76. ISSN 1751-7370. PMC 4992084. PMID 24824669.
Beghini, Francesco; McIver, Lauren J.; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis (4 May 2021). "Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3". eLife. 10: e65088. doi:10.7554/eLife.65088. ISSN 2050-084X. PMC 8096432. PMID 33944776.
Pascal Andreu, Victòria; Augustijn, Hannah E.; Chen, Lianmin; Zhernakova, Alexandra; Fu, Jingyuan; Fischbach, Michael A.; Dodd, Dylan; Medema, Marnix H. (October 2023). "gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota". Nature Biotechnology. 41 (10): 1416–1423. doi:10.1038/s41587-023-01675-1. ISSN 1546-1696. PMC 10423304. PMID 36782070.
Simon C, Daniel R (February 2011). "Metagenomic analyses: past and future trends". Applied and Environmental Microbiology. 77 (4): 1153–61. Bibcode:2011ApEnM..77.1153S. doi:10.1128/AEM.02345-10. PMC 3067235. PMID 21169428.
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, et al. (March 2011). "Bacterial community structures are unique and resilient in full-scale bioenergy systems". Proceedings of the National Academy of Sciences of the United States of America. 108 (10): 4158–63. Bibcode:2011PNAS..108.4158W. doi:10.1073/pnas.1015676108. PMC 3053989. PMID 21368115.
McInerney MJ, Sieber JR, Gunsalus RP (December 2009). "Syntrophy in anaerobic global carbon cycles". Current Opinion in Biotechnology. 20 (6): 623–32. doi:10.1016/j.copbio.2009.10.001. PMC 2790021. PMID 19897353.
Klitgord N, Segrè D (August 2011). "Ecosystems biology of microbial metabolism". Current Opinion in Biotechnology. 22 (4): 541–6. Bibcode:2011COBt...22..541K. doi:10.1016/j.copbio.2011.04.018. PMID 21592777.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–9. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID 16915287. S2CID 4380804.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016). "Uncovering Earth's virome". Nature. 536 (7617): 425–30. Bibcode:2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034. S2CID 4466854.
Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. (January 2017). "IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses". Nucleic Acids Research. 45 (D1): D457 – D465. doi:10.1093/nar/gkw1030. PMC 5210529. PMID 27799466.
Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. (January 2019). "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. doi:10.1093/nar/gky1127. PMC 6323928. PMID 30407573.
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC (August 2017). "Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data" (PDF). Nature Protocols. 12 (8): 1673–1682. doi:10.1038/nprot.2017.063. PMID 28749930. S2CID 2127494.
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV (January 2010). "New dimensions of the virus world discovered through metagenomics". Trends in Microbiology. 18 (1): 11–9. doi:10.1016/j.tim.2009.11.003. PMC 3293453. PMID 19942437.
Kerepesi C, Grolmusz V (March 2016). "Giant viruses of the Kutch Desert". Archives of Virology. 161 (3): 721–4. arXiv:1410.1278. doi:10.1007/s00705-015-2720-8. PMID 26666442. S2CID 13145926.
Kerepesi C, Grolmusz V (June 2017). "The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys". Archives of Virology. 162 (6): 1671–1676. arXiv:1503.05575. doi:10.1007/s00705-017-3286-4. PMID 28247094. S2CID 1925728.
Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, Van Elsas JD, Bailey MJ, Nalin R, Philippot L (2009). "TerraGenome: A consortium for the sequencing of a soil metagenome". Nature Reviews Microbiology. 7 (4): 252. doi:10.1038/nrmicro2119.
Bringel F, Couée I (22 May 2015). "Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics". Frontiers in Microbiology. 6: 486. doi:10.3389/fmicb.2015.00486. PMC 4440916. PMID 26052316.
Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (May 2009). "Bioprospecting metagenomes: glycosyl hydrolases for converting biomass". Biotechnology for Biofuels. 2 (1): 10. Bibcode:2009BB......2...10L. doi:10.1186/1754-6834-2-10. PMC 2694162. PMID 19450243.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, et al. (January 2011). Aziz RK (ed.). "Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing". PLOS ONE. 6 (1): e14519. Bibcode:2011PLoSO...614519J. doi:10.1371/journal.pone.0014519. PMC 3027613. PMID 21297863.
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, et al. (September 2010). Sonnenburg J (ed.). "An insect herbivore microbiome with high plant biomass-degrading capacity". PLOS Genetics. 6 (9): e1001129. doi:10.1371/journal.pgen.1001129. PMC 2944797. PMID 20885794.
Simon C, Daniel R (November 2009). "Achievements and new knowledge unraveled by metagenomic approaches". Applied Microbiology and Biotechnology. 85 (2): 265–76. doi:10.1007/s00253-009-2233-z. PMC 2773367. PMID 19760178.
Schloss PD, Handelsman J (June 2003). "Biotechnological prospects from metagenomics" (PDF). Current Opinion in Biotechnology. 14 (3): 303–10. doi:10.1016/S0958-1669(03)00067-3. PMID 12849784. Archived from the original (PDF) on 4 March 2016. Retrieved 20 January 2012.
Kakirde KS, Parsley LC, Liles MR (November 2010). "Size Does Matter: Application-driven Approaches for Soil Metagenomics". Soil Biology & Biochemistry. 42 (11): 1911–1923. Bibcode:2010SBiBi..42.1911K. doi:10.1016/j.soilbio.2010.07.021. PMC 2976544. PMID 21076656.
Parachin NS, Gorwa-Grauslund MF (May 2011). "Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library". Biotechnology for Biofuels. 4 (1): 9. Bibcode:2011BB......4....9P. doi:10.1186/1754-6834-4-9. PMC 3113934. PMID 21545702.
Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, et al. (April 2018). "Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens". Nature Microbiology. 3 (4): 415–422. doi:10.1038/s41564-018-0110-1. PMC 5874163. PMID 29434326.
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (March 2011). "Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data". Molecular Systems Biology. 7: 473. doi:10.1038/msb.2011.6. PMC 3094067. PMID 21407210.
Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012). Steinke D (ed.). "High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces". PLOS ONE. 7 (5): e36478. Bibcode:2012PLoSO...736478L. doi:10.1371/journal.pone.0036478. PMC 3350522. PMID 22606263.
Chua, Physilia Y. S.; Crampton-Platt, Alex; Lammers, Youri; Alsos, Inger G.; Boessenkool, Sanne; Bohmann, Kristine (25 May 2021). "Metagenomics: A viable tool for reconstructing herbivore diet". Molecular Ecology Resources. 21 (7): 1755–0998.13425. Bibcode:2021MolER..21.2249C. doi:10.1111/1755-0998.13425. PMC 8518049. PMID 33971086.
Chua, Physilia Y. S.; Carøe, Christian; Crampton-Platt, Alex; Reyes-Avila, Claudia S.; Jones, Gareth; Streicker, Daniel G.; Bohmann, Kristine (4 July 2022). "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)". Metabarcoding and Metagenomics. 6: e78756. doi:10.3897/mbmg.6.78756. ISSN 2534-9708. S2CID 248041252.
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). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. ISSN 1476-4687. PMC 3779803. PMID 20203603.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
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; Huttenhower, Curtis (2012). "PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome". PLOS Computational Biology. 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. doi:10.1371/journal.pcbi.1002358. PMC 3374609. PMID 22719234.
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022). "Taking metagenomics under the wings". Nature Reviews Microbiology. 20 (8): 447. doi:10.1038/s41579-022-00746-5. ISSN 1740-1534. PMID 35546350. S2CID 248739527.
Chiu, Charles Y.; Miller, Steven A. (2019). "Clinical metagenomics". Nature Reviews Genetics. 20 (6): 341–355. doi:10.1038/s41576-019-0113-7. ISSN 1471-0064. PMC 6858796. PMID 30918369.
Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ (23 May 2019). "Exploiting the Legacy of the Arbovirus Hunters". Viruses. 11 (5): 471. doi:10.3390/v11050471. PMC 6563318. PMID 31126128.
Gajurel K, Dhakal R, Deresinski S (15 November 2024). "Arbovirus in Solid Organ Transplants: A Narrative Review of the Literature". Viruses. 16 (11): 1778. doi:10.3390/v16111778. PMC 11599096. PMID 39599892.
Patiño L, Benítez AD, Carrazco-Montalvo A, Regato-Arrata M (August 2024). "Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories". Viruses. 16 (8): 1242. doi:10.3390/v16081242. PMC 11360194. PMID 39205216.
Diener, Christian; Holscher, Hannah D.; Filek, Klara; Corbin, Karen D.; Moissl-Eichinger, Christine; Gibbons, Sean M. (March 2025). "Metagenomic estimation of dietary intake from human stool". Nature Metabolism. 7 (3): 617–630. doi:10.1038/s42255-025-01220-1. ISSN 2522-5812. PMC 11949708. PMID 39966520.

escholarship.org

Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016). "Uncovering Earth's virome". Nature. 536 (7617): 425–30. Bibcode:2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034. S2CID 4466854.
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC (August 2017). "Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data" (PDF). Nature Protocols. 12 (8): 1673–1682. doi:10.1038/nprot.2017.063. PMID 28749930. S2CID 2127494.

handle.net

hdl.handle.net

Carlino, Niccolò; Blanco-Míguez, Aitor; Punčochář, Michal; Mengoni, Claudia; Pinto, Federica; Tatti, Alessia; Manghi, Paolo; Armanini, Federica; Avagliano, Michele; Barcenilla, Coral; Breselge, Samuel; Cabrera-Rubio, Raul; Calvete-Torre, Inés; Coakley, Mairéad; Cobo-Díaz, José F. (3 October 2024). "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome". Cell. 187 (20): 5775–5795.e15. doi:10.1016/j.cell.2024.07.039. hdl:10261/373917. ISSN 0092-8674.

harvard.edu

ui.adsabs.harvard.edu

Wooley JC, Godzik A, Friedberg I (February 2010). Bourne PE (ed.). "A primer on metagenomics". PLOS Computational Biology. 6 (2): e1000667. Bibcode:2010PLSCB...6E0667W. doi:10.1371/journal.pcbi.1000667. PMC 2829047. PMID 20195499.
Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio (November 2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. ISSN 1476-4687. PMC 6192678. PMID 29088705.
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, HarshaVardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J. (October 2018). "Temporal development of the gut microbiome in early childhood from the TEDDY study". Nature. 562 (7728): 583–588. Bibcode:2018Natur.562..583S. doi:10.1038/s41586-018-0617-x. ISSN 1476-4687. PMC 6415775. PMID 30356187.
Chen, Liang; Zhao, Na; Cao, Jiabao; Liu, Xiaolin; Xu, Jiayue; Ma, Yue; Yu, Ying; Zhang, Xuan; Zhang, Wenhui; Guan, Xiangyu; Yu, Xiaotong; Liu, Zhipeng; Fan, Yanqun; Wang, Yang; Liang, Fan (8 June 2022). "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes". Nature Communications. 13 (1): 3175. Bibcode:2022NatCo..13.3175C. doi:10.1038/s41467-022-30857-9. ISSN 2041-1723. PMC 9177567. PMID 35676264.
Rieder, Jessica; Kapopoulou, Adamandia; Bank, Claudia; Adrian-Kalchhauser, Irene (14 February 2023). "Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems". Environmental Microbiome. 18 (1): 8. Bibcode:2023EMicb..18....8R. doi:10.1186/s40793-023-00459-z. ISSN 2524-6372. PMC 9930364. PMID 36788626.
Semenov, M. V. (1 January 2021). "Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects". Biology Bulletin Reviews. 11 (1): 40–53. Bibcode:2021BioBR..11...40S. doi:10.1134/S2079086421010084. ISSN 2079-0872.
Chen K, Pachter L (July 2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLOS Computational Biology. 1 (2): 106–12. Bibcode:2005PLSCB...1...24C. doi:10.1371/journal.pcbi.0010024. PMC 1185649. PMID 16110337.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (October 1985). "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): 6955–9. Bibcode:1985PNAS...82.6955L. doi:10.1073/pnas.82.20.6955. PMC 391288. PMID 2413450.
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (October 2002). "Genomic analysis of uncultured marine viral communities". Proceedings of the National Academy of Sciences of the United States of America. 99 (22): 14250–5. Bibcode:2002PNAS...9914250B. doi:10.1073/pnas.202488399. PMC 137870. PMID 12384570.
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". Nature. 428 (6978): 37–43. Bibcode:2004Natur.428...37T. doi:10.1038/nature02340. PMID 14961025. S2CID 4420754.(subscription required)
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, et al. (November 2010). "Genomic and functional adaptation in surface ocean planktonic prokaryotes". Nature. 468 (7320): 60–6. Bibcode:2010Natur.468...60Y. doi:10.1038/nature09530. PMID 21048761.(subscription required)
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". Science. 311 (5759): 392–4. Bibcode:2006Sci...311..392P. doi:10.1126/science.1123360. PMID 16368896. S2CID 11238470.
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". Environmental Microbiology. 2 (5): 516–29. Bibcode:2000EnvMi...2..516B. doi:10.1046/j.1462-2920.2000.00133.x. PMID 11233160. S2CID 8267748.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW (July 2010). Gilbert JA (ed.). "Unlocking short read sequencing for metagenomics". PLOS ONE. 5 (7): e11840. Bibcode:2010PLoSO...511840R. doi:10.1371/journal.pone.0011840. PMC 2911387. PMID 20676378.
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. (February 2018). "Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen". Nature Communications. 9 (1): 870. Bibcode:2018NatCo...9..870S. doi:10.1038/s41467-018-03317-6. PMC 5830445. PMID 29491419.
Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R.; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E.; Morley, Paul S.; McAllister, Tim A. (12 April 2018). "Impact of sequencing depth on the characterization of the microbiome and resistome". Scientific Reports. 8 (1): 5890. Bibcode:2018NatSR...8.5890Z. doi:10.1038/s41598-018-24280-8. ISSN 2045-2322. PMC 5897366. PMID 29651035.
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". Science. 331 (6016): 463–7. Bibcode:2011Sci...331..463H. doi:10.1126/science.1200387. PMID 21273488. S2CID 36572885.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.(subscription required)
Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, et al. (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. PMC 3285633. PMID 22384016.
Schmieder R, Edwards R (March 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.
Konopka A (November 2009). "What is microbial community ecology?". The ISME Journal. 3 (11): 1223–30. Bibcode:2009ISMEJ...3.1223K. doi:10.1038/ismej.2009.88. PMID 19657372.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, et al. (March 2019). "Microbial abundance, activity and population genomic profiling with mOTUs2". Nature Communications. 10 (1): 1014. Bibcode:2019NatCo..10.1014M. doi:10.1038/s41467-019-08844-4. PMC 6399450. PMID 30833550.
Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. (November 2014). "Estimating coverage in metagenomic data sets and why it matters". The ISME Journal. 8 (11): 2349–2351. Bibcode:2014ISMEJ...8.2349R. doi:10.1038/ismej.2014.76. ISSN 1751-7370. PMC 4992084. PMID 24824669.
Simon C, Daniel R (February 2011). "Metagenomic analyses: past and future trends". Applied and Environmental Microbiology. 77 (4): 1153–61. Bibcode:2011ApEnM..77.1153S. doi:10.1128/AEM.02345-10. PMC 3067235. PMID 21169428.
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, et al. (March 2011). "Bacterial community structures are unique and resilient in full-scale bioenergy systems". Proceedings of the National Academy of Sciences of the United States of America. 108 (10): 4158–63. Bibcode:2011PNAS..108.4158W. doi:10.1073/pnas.1015676108. PMC 3053989. PMID 21368115.
Klitgord N, Segrè D (August 2011). "Ecosystems biology of microbial metabolism". Current Opinion in Biotechnology. 22 (4): 541–6. Bibcode:2011COBt...22..541K. doi:10.1016/j.copbio.2011.04.018. PMID 21592777.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–9. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID 16915287. S2CID 4380804.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016). "Uncovering Earth's virome". Nature. 536 (7617): 425–30. Bibcode:2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034. S2CID 4466854.
Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (May 2009). "Bioprospecting metagenomes: glycosyl hydrolases for converting biomass". Biotechnology for Biofuels. 2 (1): 10. Bibcode:2009BB......2...10L. doi:10.1186/1754-6834-2-10. PMC 2694162. PMID 19450243.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, et al. (January 2011). Aziz RK (ed.). "Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing". PLOS ONE. 6 (1): e14519. Bibcode:2011PLoSO...614519J. doi:10.1371/journal.pone.0014519. PMC 3027613. PMID 21297863.
Kakirde KS, Parsley LC, Liles MR (November 2010). "Size Does Matter: Application-driven Approaches for Soil Metagenomics". Soil Biology & Biochemistry. 42 (11): 1911–1923. Bibcode:2010SBiBi..42.1911K. doi:10.1016/j.soilbio.2010.07.021. PMC 2976544. PMID 21076656.
Parachin NS, Gorwa-Grauslund MF (May 2011). "Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library". Biotechnology for Biofuels. 4 (1): 9. Bibcode:2011BB......4....9P. doi:10.1186/1754-6834-4-9. PMC 3113934. PMID 21545702.
Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012). Steinke D (ed.). "High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces". PLOS ONE. 7 (5): e36478. Bibcode:2012PLoSO...736478L. doi:10.1371/journal.pone.0036478. PMC 3350522. PMID 22606263.
Chua, Physilia Y. S.; Crampton-Platt, Alex; Lammers, Youri; Alsos, Inger G.; Boessenkool, Sanne; Bohmann, Kristine (25 May 2021). "Metagenomics: A viable tool for reconstructing herbivore diet". Molecular Ecology Resources. 21 (7): 1755–0998.13425. Bibcode:2021MolER..21.2249C. doi:10.1111/1755-0998.13425. PMC 8518049. PMID 33971086.
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). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. ISSN 1476-4687. PMC 3779803. PMID 20203603.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
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; Huttenhower, Curtis (2012). "PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome". PLOS Computational Biology. 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. doi:10.1371/journal.pcbi.1002358. PMC 3374609. PMID 22719234.

microbemagazine.org

Jansson J (2011). "Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes Print E-mail". Microbe. Vol. 6, no. 7. p. 309. Archived from the original on 31 March 2012.

nap.edu

Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: The National Academies Press. doi:10.17226/11902. ISBN 978-0-309-10676-4. PMID 21678629.

nas.edu

dels-old.nas.edu

Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). Understanding Our Microbial Planet: The New Science of Metagenomics (PDF). The National Academies Press. Archived from the original (PDF) on 30 October 2012. Retrieved 30 December 2011.

nature.com

Liu, Shaopeng; Rodriguez, Judith S.; Munteanu, Viorel; Ronkowski, Cynthia; Sharma, Nitesh Kumar; Alser, Mohammed; Andreace, Francesco; Blekhman, Ran; Błaszczyk, Dagmara; Chikhi, Rayan; Crandall, Keith A.; Della Libera, Katja; Francis, Dallace; Frolova, Alina; Gancz, Abigail Shahar (23 January 2025). "Analysis of metagenomic data". Nature Reviews Methods Primers. 5 (1): 1–28. doi:10.1038/s43586-024-00376-6. ISSN 2662-8449.
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022). "Taking metagenomics under the wings". Nature Reviews Microbiology. 20 (8): 447. doi:10.1038/s41579-022-00746-5. ISSN 1740-1534. PMID 35546350. S2CID 248739527.
Diener, Christian; Holscher, Hannah D.; Filek, Klara; Corbin, Karen D.; Moissl-Eichinger, Christine; Gibbons, Sean M. (March 2025). "Metagenomic estimation of dietary intake from human stool". Nature Metabolism. 7 (3): 617–630. doi:10.1038/s42255-025-01220-1. ISSN 2522-5812. PMC 11949708. PMID 39966520.

nih.gov

pubmed.ncbi.nlm.nih.gov

Wooley JC, Godzik A, Friedberg I (February 2010). Bourne PE (ed.). "A primer on metagenomics". PLOS Computational Biology. 6 (2): e1000667. Bibcode:2010PLSCB...6E0667W. doi:10.1371/journal.pcbi.1000667. PMC 2829047. PMID 20195499.
Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio (November 2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. ISSN 1476-4687. PMC 6192678. PMID 29088705.
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, HarshaVardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J. (October 2018). "Temporal development of the gut microbiome in early childhood from the TEDDY study". Nature. 562 (7728): 583–588. Bibcode:2018Natur.562..583S. doi:10.1038/s41586-018-0617-x. ISSN 1476-4687. PMC 6415775. PMID 30356187.
Eisen JA (March 2007). "Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes". PLOS Biology. 5 (3): e82. doi:10.1371/journal.pbio.0050082. PMC 1821061. PMID 17355177.
Chen, Liang; Zhao, Na; Cao, Jiabao; Liu, Xiaolin; Xu, Jiayue; Ma, Yue; Yu, Ying; Zhang, Xuan; Zhang, Wenhui; Guan, Xiangyu; Yu, Xiaotong; Liu, Zhipeng; Fan, Yanqun; Wang, Yang; Liang, Fan (8 June 2022). "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes". Nature Communications. 13 (1): 3175. Bibcode:2022NatCo..13.3175C. doi:10.1038/s41467-022-30857-9. ISSN 2041-1723. PMC 9177567. PMID 35676264.
Zepeda Mendoza, Marie Lisandra; Sicheritz-Pontén, Thomas; Gilbert, M. Thomas P. (1 September 2015). "Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses". Briefings in Bioinformatics. 16 (5): 745–758. doi:10.1093/bib/bbv001. ISSN 1467-5463. PMC 4570204. PMID 25673291.
Rieder, Jessica; Kapopoulou, Adamandia; Bank, Claudia; Adrian-Kalchhauser, Irene (14 February 2023). "Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems". Environmental Microbiome. 18 (1): 8. Bibcode:2023EMicb..18....8R. doi:10.1186/s40793-023-00459-z. ISSN 2524-6372. PMC 9930364. PMID 36788626.
Hugenholtz P, Goebel BM, Pace NR (September 1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". Journal of Bacteriology. 180 (18): 4765–74. doi:10.1128/JB.180.18.4765-4774.1998. PMC 107498. PMID 9733676.
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (October 1998). "Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products". Chemistry & Biology. 5 (10): R245-9. doi:10.1016/S1074-5521(98)90108-9. PMID 9818143..
Chen K, Pachter L (July 2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLOS Computational Biology. 1 (2): 106–12. Bibcode:2005PLSCB...1...24C. doi:10.1371/journal.pcbi.0010024. PMC 1185649. PMID 16110337.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (October 1985). "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): 6955–9. Bibcode:1985PNAS...82.6955L. doi:10.1073/pnas.82.20.6955. PMC 391288. PMID 2413450.
Schmidt TM, DeLong EF, Pace NR (July 1991). "Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing". Journal of Bacteriology. 173 (14): 4371–8. doi:10.1128/jb.173.14.4371-4378.1991. PMC 208098. PMID 2066334.
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". Applied Microbiology and Biotechnology. 43 (4): 667–74. doi:10.1007/BF00164771. PMID 7546604. S2CID 31384119.
Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (February 1996). "Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon". Journal of Bacteriology. 178 (3): 591–9. doi:10.1128/jb.178.3.591-599.1996. PMC 177699. PMID 8550487.
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (October 2002). "Genomic analysis of uncultured marine viral communities". Proceedings of the National Academy of Sciences of the United States of America. 99 (22): 14250–5. Bibcode:2002PNAS...9914250B. doi:10.1073/pnas.202488399. PMC 137870. PMID 12384570.
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". Nature. 428 (6978): 37–43. Bibcode:2004Natur.428...37T. doi:10.1038/nature02340. PMID 14961025. S2CID 4420754.(subscription required)
Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.
Yooseph S, Nealson KH, Rusch DB, McCrow JP, Dupont CL, Kim M, et al. (November 2010). "Genomic and functional adaptation in surface ocean planktonic prokaryotes". Nature. 468 (7320): 60–6. Bibcode:2010Natur.468...60Y. doi:10.1038/nature09530. PMID 21048761.(subscription required)
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". Science. 311 (5759): 392–4. Bibcode:2006Sci...311..392P. doi:10.1126/science.1123360. PMID 16368896. S2CID 11238470.
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, et al. (March 2006). "Using pyrosequencing to shed light on deep mine microbial ecology". BMC Genomics. 7: 57. doi:10.1186/1471-2164-7-57. PMC 1483832. PMID 16549033.
Thomas T, Gilbert J, Meyer F (February 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.
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". Environmental Microbiology. 2 (5): 516–29. Bibcode:2000EnvMi...2..516B. doi:10.1046/j.1462-2920.2000.00133.x. PMID 11233160. S2CID 8267748.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (May 2013). "Computational meta'omics for microbial community studies". Molecular Systems Biology. 9 (666): 666. doi:10.1038/msb.2013.22. PMC 4039370. PMID 23670539.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW (July 2010). Gilbert JA (ed.). "Unlocking short read sequencing for metagenomics". PLOS ONE. 5 (7): e11840. Bibcode:2010PLoSO...511840R. doi:10.1371/journal.pone.0011840. PMC 2911387. PMID 20676378.
Schuster SC (January 2008). "Next-generation sequencing transforms today's biology". Nature Methods. 5 (1): 16–8. doi:10.1038/nmeth1156. PMID 18165802. S2CID 1465786.
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. (February 2018). "Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen". Nature Communications. 9 (1): 870. Bibcode:2018NatCo...9..870S. doi:10.1038/s41467-018-03317-6. PMC 5830445. PMID 29491419.
Hiraoka S, Yang CC, Iwasaki W (September 2016). "Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond". Microbes and Environments. 31 (3): 204–12. doi:10.1264/jsme2.ME16024. PMC 5017796. PMID 27383682.
Carter, Matthew M.; Olm, Matthew R.; Merrill, Bryan D.; Dahan, Dylan; Tripathi, Surya; Spencer, Sean P.; Yu, Feiqiao B.; Jain, Sunit; Neff, Norma; Jha, Aashish R.; Sonnenburg, Erica D.; Sonnenburg, Justin L. (6 July 2023). "Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes". Cell. 186 (14): 3111–3124.e13. doi:10.1016/j.cell.2023.05.046. ISSN 0092-8674. PMC 10330870. PMID 37348505.
Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R.; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E.; Morley, Paul S.; McAllister, Tim A. (12 April 2018). "Impact of sequencing depth on the characterization of the microbiome and resistome". Scientific Reports. 8 (1): 5890. Bibcode:2018NatSR...8.5890Z. doi:10.1038/s41598-018-24280-8. ISSN 2045-2322. PMC 5897366. PMID 29651035.
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C (2020). "Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses". Microbial Genomics. 6 (8). doi:10.1099/mgen.0.000409. PMC 7641418. PMID 32706331.
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". Science. 331 (6016): 463–7. Bibcode:2011Sci...331..463H. doi:10.1126/science.1200387. PMID 21273488. S2CID 36572885.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.(subscription required)
Paulson JN, Stine OC, Bravo HC, Pop M (December 2013). "Differential abundance analysis for microbial marker-gene surveys". Nature Methods. 10 (12): 1200–2. doi:10.1038/nmeth.2658. PMC 4010126. PMID 24076764.
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: The National Academies Press. doi:10.17226/11902. ISBN 978-0-309-10676-4. PMID 21678629.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, et al. (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 DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, et al. (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. PMC 3285633. PMID 22384016.
Balzer S, Malde K, Grohme MA, Jonassen I (April 2013). "Filtering duplicate reads from 454 pyrosequencing data". Bioinformatics. 29 (7): 830–6. doi:10.1093/bioinformatics/btt047. PMC 3605598. PMID 23376350.
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS (September 2011). "Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets". Journal of Biosciences. 36 (4): 709–17. doi:10.1007/s12038-011-9105-2. PMID 21857117. S2CID 25857874.
Schmieder R, Edwards R (March 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.
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (December 2008). "A bioinformatician's guide to metagenomics". Microbiology and Molecular Biology Reviews. 72 (4): 557–78, Table of Contents. doi:10.1128/MMBR.00009-08. PMC 2593568. PMID 19052320.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y (November 2012). "MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads". Nucleic Acids Research. 40 (20): e155. doi:10.1093/nar/gks678. PMC 3488206. PMID 22821567.
Zerbino DR, Birney E (May 2008). "Velvet: algorithms for de novo short read assembly using de Bruijn graphs". Genome Research. 18 (5): 821–9. doi:10.1101/gr.074492.107. PMC 2336801. PMID 18349386.
Burton JN, Liachko I, Dunham MJ, Shendure J (May 2014). "Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps". G3. 4 (7): 1339–46. doi:10.1534/g3.114.011825. PMC 4455782. PMID 24855317.
Konopka A (November 2009). "What is microbial community ecology?". The ISME Journal. 3 (11): 1223–30. Bibcode:2009ISMEJ...3.1223K. doi:10.1038/ismej.2009.88. PMID 19657372.
Huson DH, Auch AF, Qi J, Schuster SC (March 2007). "MEGAN analysis of metagenomic data". Genome Research. 17 (3): 377–86. doi:10.1101/gr.5969107. PMC 1800929. PMID 17255551.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (June 2012). "Metagenomic microbial community profiling using unique clade-specific marker genes". Nature Methods. 9 (8): 811–4. doi:10.1038/nmeth.2066. PMC 3443552. PMID 22688413.
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". Nature Methods. 10 (12): 1196–9. doi:10.1038/nmeth.2693. PMID 24141494. S2CID 7728395.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, et al. (March 2019). "Microbial abundance, activity and population genomic profiling with mOTUs2". Nature Communications. 10 (1): 1014. Bibcode:2019NatCo..10.1014M. doi:10.1038/s41467-019-08844-4. PMC 6399450. PMID 30833550.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M (2011). "Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences". BMC Genomics. 12 (Suppl 2): S4. doi:10.1186/1471-2164-12-S2-S4. PMC 3194235. PMID 21989143.
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K (2017). "SLIMM: species level identification of microorganisms from metagenomes". PeerJ. 5: e3138. doi:10.7717/peerj.3138. PMC 5372838. PMID 28367376.
Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Murat Eren, A; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja (August 2017). "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea". Nature Biotechnology. 35 (8): 725–731. doi:10.1038/nbt.3893. PMC 6436528. PMID 28787424.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (September 2011). "Integrative analysis of environmental sequences using MEGAN4". Genome Research. 21 (9): 1552–60. doi:10.1101/gr.120618.111. PMC 3166839. PMID 21690186.
Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542. PMID 20403810.
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. (August 2007). "Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes". DNA Research. 14 (4): 169–81. doi:10.1093/dnares/dsm018. PMC 2533590. PMID 17916580.
Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. (November 2014). "Estimating coverage in metagenomic data sets and why it matters". The ISME Journal. 8 (11): 2349–2351. Bibcode:2014ISMEJ...8.2349R. doi:10.1038/ismej.2014.76. ISSN 1751-7370. PMC 4992084. PMID 24824669.
Beghini, Francesco; McIver, Lauren J.; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis (4 May 2021). "Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3". eLife. 10: e65088. doi:10.7554/eLife.65088. ISSN 2050-084X. PMC 8096432. PMID 33944776.
Pascal Andreu, Victòria; Augustijn, Hannah E.; Chen, Lianmin; Zhernakova, Alexandra; Fu, Jingyuan; Fischbach, Michael A.; Dodd, Dylan; Medema, Marnix H. (October 2023). "gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota". Nature Biotechnology. 41 (10): 1416–1423. doi:10.1038/s41587-023-01675-1. ISSN 1546-1696. PMC 10423304. PMID 36782070.
Simon C, Daniel R (February 2011). "Metagenomic analyses: past and future trends". Applied and Environmental Microbiology. 77 (4): 1153–61. Bibcode:2011ApEnM..77.1153S. doi:10.1128/AEM.02345-10. PMC 3067235. PMID 21169428.
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, et al. (March 2011). "Bacterial community structures are unique and resilient in full-scale bioenergy systems". Proceedings of the National Academy of Sciences of the United States of America. 108 (10): 4158–63. Bibcode:2011PNAS..108.4158W. doi:10.1073/pnas.1015676108. PMC 3053989. PMID 21368115.
McInerney MJ, Sieber JR, Gunsalus RP (December 2009). "Syntrophy in anaerobic global carbon cycles". Current Opinion in Biotechnology. 20 (6): 623–32. doi:10.1016/j.copbio.2009.10.001. PMC 2790021. PMID 19897353.
Klitgord N, Segrè D (August 2011). "Ecosystems biology of microbial metabolism". Current Opinion in Biotechnology. 22 (4): 541–6. Bibcode:2011COBt...22..541K. doi:10.1016/j.copbio.2011.04.018. PMID 21592777.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–9. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID 16915287. S2CID 4380804.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016). "Uncovering Earth's virome". Nature. 536 (7617): 425–30. Bibcode:2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034. S2CID 4466854.
Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. (January 2017). "IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses". Nucleic Acids Research. 45 (D1): D457 – D465. doi:10.1093/nar/gkw1030. PMC 5210529. PMID 27799466.
Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. (January 2019). "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. doi:10.1093/nar/gky1127. PMC 6323928. PMID 30407573.
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC (August 2017). "Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data" (PDF). Nature Protocols. 12 (8): 1673–1682. doi:10.1038/nprot.2017.063. PMID 28749930. S2CID 2127494.
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV (January 2010). "New dimensions of the virus world discovered through metagenomics". Trends in Microbiology. 18 (1): 11–9. doi:10.1016/j.tim.2009.11.003. PMC 3293453. PMID 19942437.
Kerepesi C, Grolmusz V (March 2016). "Giant viruses of the Kutch Desert". Archives of Virology. 161 (3): 721–4. arXiv:1410.1278. doi:10.1007/s00705-015-2720-8. PMID 26666442. S2CID 13145926.
Kerepesi C, Grolmusz V (June 2017). "The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys". Archives of Virology. 162 (6): 1671–1676. arXiv:1503.05575. doi:10.1007/s00705-017-3286-4. PMID 28247094. S2CID 1925728.
Bringel F, Couée I (22 May 2015). "Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics". Frontiers in Microbiology. 6: 486. doi:10.3389/fmicb.2015.00486. PMC 4440916. PMID 26052316.
Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (May 2009). "Bioprospecting metagenomes: glycosyl hydrolases for converting biomass". Biotechnology for Biofuels. 2 (1): 10. Bibcode:2009BB......2...10L. doi:10.1186/1754-6834-2-10. PMC 2694162. PMID 19450243.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, et al. (January 2011). Aziz RK (ed.). "Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing". PLOS ONE. 6 (1): e14519. Bibcode:2011PLoSO...614519J. doi:10.1371/journal.pone.0014519. PMC 3027613. PMID 21297863.
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, et al. (September 2010). Sonnenburg J (ed.). "An insect herbivore microbiome with high plant biomass-degrading capacity". PLOS Genetics. 6 (9): e1001129. doi:10.1371/journal.pgen.1001129. PMC 2944797. PMID 20885794.
Simon C, Daniel R (November 2009). "Achievements and new knowledge unraveled by metagenomic approaches". Applied Microbiology and Biotechnology. 85 (2): 265–76. doi:10.1007/s00253-009-2233-z. PMC 2773367. PMID 19760178.
Schloss PD, Handelsman J (June 2003). "Biotechnological prospects from metagenomics" (PDF). Current Opinion in Biotechnology. 14 (3): 303–10. doi:10.1016/S0958-1669(03)00067-3. PMID 12849784. Archived from the original (PDF) on 4 March 2016. Retrieved 20 January 2012.
Kakirde KS, Parsley LC, Liles MR (November 2010). "Size Does Matter: Application-driven Approaches for Soil Metagenomics". Soil Biology & Biochemistry. 42 (11): 1911–1923. Bibcode:2010SBiBi..42.1911K. doi:10.1016/j.soilbio.2010.07.021. PMC 2976544. PMID 21076656.
Parachin NS, Gorwa-Grauslund MF (May 2011). "Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library". Biotechnology for Biofuels. 4 (1): 9. Bibcode:2011BB......4....9P. doi:10.1186/1754-6834-4-9. PMC 3113934. PMID 21545702.
Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, et al. (April 2018). "Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens". Nature Microbiology. 3 (4): 415–422. doi:10.1038/s41564-018-0110-1. PMC 5874163. PMID 29434326.
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (March 2011). "Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data". Molecular Systems Biology. 7: 473. doi:10.1038/msb.2011.6. PMC 3094067. PMID 21407210.
Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012). Steinke D (ed.). "High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces". PLOS ONE. 7 (5): e36478. Bibcode:2012PLoSO...736478L. doi:10.1371/journal.pone.0036478. PMC 3350522. PMID 22606263.
Chua, Physilia Y. S.; Crampton-Platt, Alex; Lammers, Youri; Alsos, Inger G.; Boessenkool, Sanne; Bohmann, Kristine (25 May 2021). "Metagenomics: A viable tool for reconstructing herbivore diet". Molecular Ecology Resources. 21 (7): 1755–0998.13425. Bibcode:2021MolER..21.2249C. doi:10.1111/1755-0998.13425. PMC 8518049. PMID 33971086.
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). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. ISSN 1476-4687. PMC 3779803. PMID 20203603.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
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; Huttenhower, Curtis (2012). "PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome". PLOS Computational Biology. 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. doi:10.1371/journal.pcbi.1002358. PMC 3374609. PMID 22719234.
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022). "Taking metagenomics under the wings". Nature Reviews Microbiology. 20 (8): 447. doi:10.1038/s41579-022-00746-5. ISSN 1740-1534. PMID 35546350. S2CID 248739527.
Chiu, Charles Y.; Miller, Steven A. (2019). "Clinical metagenomics". Nature Reviews Genetics. 20 (6): 341–355. doi:10.1038/s41576-019-0113-7. ISSN 1471-0064. PMC 6858796. PMID 30918369.
Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ (23 May 2019). "Exploiting the Legacy of the Arbovirus Hunters". Viruses. 11 (5): 471. doi:10.3390/v11050471. PMC 6563318. PMID 31126128.
Gajurel K, Dhakal R, Deresinski S (15 November 2024). "Arbovirus in Solid Organ Transplants: A Narrative Review of the Literature". Viruses. 16 (11): 1778. doi:10.3390/v16111778. PMC 11599096. PMID 39599892.
Patiño L, Benítez AD, Carrazco-Montalvo A, Regato-Arrata M (August 2024). "Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories". Viruses. 16 (8): 1242. doi:10.3390/v16081242. PMC 11360194. PMID 39205216.
Diener, Christian; Holscher, Hannah D.; Filek, Klara; Corbin, Karen D.; Moissl-Eichinger, Christine; Gibbons, Sean M. (March 2025). "Metagenomic estimation of dietary intake from human stool". Nature Metabolism. 7 (3): 617–630. doi:10.1038/s42255-025-01220-1. ISSN 2522-5812. PMC 11949708. PMID 39966520.

ncbi.nlm.nih.gov

Wooley JC, Godzik A, Friedberg I (February 2010). Bourne PE (ed.). "A primer on metagenomics". PLOS Computational Biology. 6 (2): e1000667. Bibcode:2010PLSCB...6E0667W. doi:10.1371/journal.pcbi.1000667. PMC 2829047. PMID 20195499.
Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio (November 2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. ISSN 1476-4687. PMC 6192678. PMID 29088705.
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, HarshaVardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J. (October 2018). "Temporal development of the gut microbiome in early childhood from the TEDDY study". Nature. 562 (7728): 583–588. Bibcode:2018Natur.562..583S. doi:10.1038/s41586-018-0617-x. ISSN 1476-4687. PMC 6415775. PMID 30356187.
Eisen JA (March 2007). "Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes". PLOS Biology. 5 (3): e82. doi:10.1371/journal.pbio.0050082. PMC 1821061. PMID 17355177.
Chen, Liang; Zhao, Na; Cao, Jiabao; Liu, Xiaolin; Xu, Jiayue; Ma, Yue; Yu, Ying; Zhang, Xuan; Zhang, Wenhui; Guan, Xiangyu; Yu, Xiaotong; Liu, Zhipeng; Fan, Yanqun; Wang, Yang; Liang, Fan (8 June 2022). "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes". Nature Communications. 13 (1): 3175. Bibcode:2022NatCo..13.3175C. doi:10.1038/s41467-022-30857-9. ISSN 2041-1723. PMC 9177567. PMID 35676264.
Zepeda Mendoza, Marie Lisandra; Sicheritz-Pontén, Thomas; Gilbert, M. Thomas P. (1 September 2015). "Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses". Briefings in Bioinformatics. 16 (5): 745–758. doi:10.1093/bib/bbv001. ISSN 1467-5463. PMC 4570204. PMID 25673291.
Rieder, Jessica; Kapopoulou, Adamandia; Bank, Claudia; Adrian-Kalchhauser, Irene (14 February 2023). "Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems". Environmental Microbiome. 18 (1): 8. Bibcode:2023EMicb..18....8R. doi:10.1186/s40793-023-00459-z. ISSN 2524-6372. PMC 9930364. PMID 36788626.
Hugenholtz P, Goebel BM, Pace NR (September 1998). "Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity". Journal of Bacteriology. 180 (18): 4765–74. doi:10.1128/JB.180.18.4765-4774.1998. PMC 107498. PMID 9733676.
Chen K, Pachter L (July 2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities". PLOS Computational Biology. 1 (2): 106–12. Bibcode:2005PLSCB...1...24C. doi:10.1371/journal.pcbi.0010024. PMC 1185649. PMID 16110337.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (October 1985). "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): 6955–9. Bibcode:1985PNAS...82.6955L. doi:10.1073/pnas.82.20.6955. PMC 391288. PMID 2413450.
Schmidt TM, DeLong EF, Pace NR (July 1991). "Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing". Journal of Bacteriology. 173 (14): 4371–8. doi:10.1128/jb.173.14.4371-4378.1991. PMC 208098. PMID 2066334.
Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF (February 1996). "Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon". Journal of Bacteriology. 178 (3): 591–9. doi:10.1128/jb.178.3.591-599.1996. PMC 177699. PMID 8550487.
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, et al. (October 2002). "Genomic analysis of uncultured marine viral communities". Proceedings of the National Academy of Sciences of the United States of America. 99 (22): 14250–5. Bibcode:2002PNAS...9914250B. doi:10.1073/pnas.202488399. PMC 137870. PMID 12384570.
Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC 139013. PMID 11864374.
Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, et al. (March 2006). "Using pyrosequencing to shed light on deep mine microbial ecology". BMC Genomics. 7: 57. doi:10.1186/1471-2164-7-57. PMC 1483832. PMID 16549033.
Thomas T, Gilbert J, Meyer F (February 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.
Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C (May 2013). "Computational meta'omics for microbial community studies". Molecular Systems Biology. 9 (666): 666. doi:10.1038/msb.2013.22. PMC 4039370. PMID 23670539.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW (July 2010). Gilbert JA (ed.). "Unlocking short read sequencing for metagenomics". PLOS ONE. 5 (7): e11840. Bibcode:2010PLoSO...511840R. doi:10.1371/journal.pone.0011840. PMC 2911387. PMID 20676378.
Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, et al. (February 2018). "Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen". Nature Communications. 9 (1): 870. Bibcode:2018NatCo...9..870S. doi:10.1038/s41467-018-03317-6. PMC 5830445. PMID 29491419.
Hiraoka S, Yang CC, Iwasaki W (September 2016). "Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond". Microbes and Environments. 31 (3): 204–12. doi:10.1264/jsme2.ME16024. PMC 5017796. PMID 27383682.
Carter, Matthew M.; Olm, Matthew R.; Merrill, Bryan D.; Dahan, Dylan; Tripathi, Surya; Spencer, Sean P.; Yu, Feiqiao B.; Jain, Sunit; Neff, Norma; Jha, Aashish R.; Sonnenburg, Erica D.; Sonnenburg, Justin L. (6 July 2023). "Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes". Cell. 186 (14): 3111–3124.e13. doi:10.1016/j.cell.2023.05.046. ISSN 0092-8674. PMC 10330870. PMID 37348505.
Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R.; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E.; Morley, Paul S.; McAllister, Tim A. (12 April 2018). "Impact of sequencing depth on the characterization of the microbiome and resistome". Scientific Reports. 8 (1): 5890. Bibcode:2018NatSR...8.5890Z. doi:10.1038/s41598-018-24280-8. ISSN 2045-2322. PMC 5897366. PMID 29651035.
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C (2020). "Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses". Microbial Genomics. 6 (8). doi:10.1099/mgen.0.000409. PMC 7641418. PMID 32706331.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.(subscription required)
Paulson JN, Stine OC, Bravo HC, Pop M (December 2013). "Differential abundance analysis for microbial marker-gene surveys". Nature Methods. 10 (12): 1200–2. doi:10.1038/nmeth.2658. PMC 4010126. PMID 24076764.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, et al. (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 DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, et al. (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. PMC 3285633. PMID 22384016.
Balzer S, Malde K, Grohme MA, Jonassen I (April 2013). "Filtering duplicate reads from 454 pyrosequencing data". Bioinformatics. 29 (7): 830–6. doi:10.1093/bioinformatics/btt047. PMC 3605598. PMID 23376350.
Schmieder R, Edwards R (March 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.
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (December 2008). "A bioinformatician's guide to metagenomics". Microbiology and Molecular Biology Reviews. 72 (4): 557–78, Table of Contents. doi:10.1128/MMBR.00009-08. PMC 2593568. PMID 19052320.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y (November 2012). "MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads". Nucleic Acids Research. 40 (20): e155. doi:10.1093/nar/gks678. PMC 3488206. PMID 22821567.
Zerbino DR, Birney E (May 2008). "Velvet: algorithms for de novo short read assembly using de Bruijn graphs". Genome Research. 18 (5): 821–9. doi:10.1101/gr.074492.107. PMC 2336801. PMID 18349386.
Burton JN, Liachko I, Dunham MJ, Shendure J (May 2014). "Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps". G3. 4 (7): 1339–46. doi:10.1534/g3.114.011825. PMC 4455782. PMID 24855317.
Huson DH, Auch AF, Qi J, Schuster SC (March 2007). "MEGAN analysis of metagenomic data". Genome Research. 17 (3): 377–86. doi:10.1101/gr.5969107. PMC 1800929. PMID 17255551.
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C (June 2012). "Metagenomic microbial community profiling using unique clade-specific marker genes". Nature Methods. 9 (8): 811–4. doi:10.1038/nmeth.2066. PMC 3443552. PMID 22688413.
Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, et al. (March 2019). "Microbial abundance, activity and population genomic profiling with mOTUs2". Nature Communications. 10 (1): 1014. Bibcode:2019NatCo..10.1014M. doi:10.1038/s41467-019-08844-4. PMC 6399450. PMID 30833550.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M (2011). "Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences". BMC Genomics. 12 (Suppl 2): S4. doi:10.1186/1471-2164-12-S2-S4. PMC 3194235. PMID 21989143.
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K (2017). "SLIMM: species level identification of microorganisms from metagenomes". PeerJ. 5: e3138. doi:10.7717/peerj.3138. PMC 5372838. PMID 28367376.
Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Murat Eren, A; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja (August 2017). "Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea". Nature Biotechnology. 35 (8): 725–731. doi:10.1038/nbt.3893. PMC 6436528. PMID 28787424.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (September 2011). "Integrative analysis of environmental sequences using MEGAN4". Genome Research. 21 (9): 1552–60. doi:10.1101/gr.120618.111. PMC 3166839. PMID 21690186.
Zhu W, Lomsadze A, Borodovsky M (July 2010). "Ab initio gene identification in metagenomic sequences". Nucleic Acids Research. 38 (12): e132. doi:10.1093/nar/gkq275. PMC 2896542. PMID 20403810.
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, et al. (August 2007). "Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes". DNA Research. 14 (4): 169–81. doi:10.1093/dnares/dsm018. PMC 2533590. PMID 17916580.
Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. (November 2014). "Estimating coverage in metagenomic data sets and why it matters". The ISME Journal. 8 (11): 2349–2351. Bibcode:2014ISMEJ...8.2349R. doi:10.1038/ismej.2014.76. ISSN 1751-7370. PMC 4992084. PMID 24824669.
Beghini, Francesco; McIver, Lauren J.; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis (4 May 2021). "Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3". eLife. 10: e65088. doi:10.7554/eLife.65088. ISSN 2050-084X. PMC 8096432. PMID 33944776.
Pascal Andreu, Victòria; Augustijn, Hannah E.; Chen, Lianmin; Zhernakova, Alexandra; Fu, Jingyuan; Fischbach, Michael A.; Dodd, Dylan; Medema, Marnix H. (October 2023). "gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota". Nature Biotechnology. 41 (10): 1416–1423. doi:10.1038/s41587-023-01675-1. ISSN 1546-1696. PMC 10423304. PMID 36782070.
Simon C, Daniel R (February 2011). "Metagenomic analyses: past and future trends". Applied and Environmental Microbiology. 77 (4): 1153–61. Bibcode:2011ApEnM..77.1153S. doi:10.1128/AEM.02345-10. PMC 3067235. PMID 21169428.
Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, et al. (March 2011). "Bacterial community structures are unique and resilient in full-scale bioenergy systems". Proceedings of the National Academy of Sciences of the United States of America. 108 (10): 4158–63. Bibcode:2011PNAS..108.4158W. doi:10.1073/pnas.1015676108. PMC 3053989. PMID 21368115.
McInerney MJ, Sieber JR, Gunsalus RP (December 2009). "Syntrophy in anaerobic global carbon cycles". Current Opinion in Biotechnology. 20 (6): 623–32. doi:10.1016/j.copbio.2009.10.001. PMC 2790021. PMID 19897353.
Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. (January 2017). "IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses". Nucleic Acids Research. 45 (D1): D457 – D465. doi:10.1093/nar/gkw1030. PMC 5210529. PMID 27799466.
Paez-Espino D, Roux S, Chen IA, Palaniappan K, Ratner A, Chu K, et al. (January 2019). "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. doi:10.1093/nar/gky1127. PMC 6323928. PMID 30407573.
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV (January 2010). "New dimensions of the virus world discovered through metagenomics". Trends in Microbiology. 18 (1): 11–9. doi:10.1016/j.tim.2009.11.003. PMC 3293453. PMID 19942437.
Bringel F, Couée I (22 May 2015). "Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics". Frontiers in Microbiology. 6: 486. doi:10.3389/fmicb.2015.00486. PMC 4440916. PMID 26052316.
Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D (May 2009). "Bioprospecting metagenomes: glycosyl hydrolases for converting biomass". Biotechnology for Biofuels. 2 (1): 10. Bibcode:2009BB......2...10L. doi:10.1186/1754-6834-2-10. PMC 2694162. PMID 19450243.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, et al. (January 2011). Aziz RK (ed.). "Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing". PLOS ONE. 6 (1): e14519. Bibcode:2011PLoSO...614519J. doi:10.1371/journal.pone.0014519. PMC 3027613. PMID 21297863.
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, et al. (September 2010). Sonnenburg J (ed.). "An insect herbivore microbiome with high plant biomass-degrading capacity". PLOS Genetics. 6 (9): e1001129. doi:10.1371/journal.pgen.1001129. PMC 2944797. PMID 20885794.
Simon C, Daniel R (November 2009). "Achievements and new knowledge unraveled by metagenomic approaches". Applied Microbiology and Biotechnology. 85 (2): 265–76. doi:10.1007/s00253-009-2233-z. PMC 2773367. PMID 19760178.
Kakirde KS, Parsley LC, Liles MR (November 2010). "Size Does Matter: Application-driven Approaches for Soil Metagenomics". Soil Biology & Biochemistry. 42 (11): 1911–1923. Bibcode:2010SBiBi..42.1911K. doi:10.1016/j.soilbio.2010.07.021. PMC 2976544. PMID 21076656.
Parachin NS, Gorwa-Grauslund MF (May 2011). "Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library". Biotechnology for Biofuels. 4 (1): 9. Bibcode:2011BB......4....9P. doi:10.1186/1754-6834-4-9. PMC 3113934. PMID 21545702.
Hover BM, Kim SH, Katz M, Charlop-Powers Z, Owen JG, Ternei MA, et al. (April 2018). "Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens". Nature Microbiology. 3 (4): 415–422. doi:10.1038/s41564-018-0110-1. PMC 5874163. PMID 29434326.
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (March 2011). "Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data". Molecular Systems Biology. 7: 473. doi:10.1038/msb.2011.6. PMC 3094067. PMID 21407210.
Lavery TJ, Roudnew B, Seymour J, Mitchell JG, Jeffries T (2012). Steinke D (ed.). "High nutrient transport and cycling potential revealed in the microbial metagenome of Australian sea lion (Neophoca cinerea) faeces". PLOS ONE. 7 (5): e36478. Bibcode:2012PLoSO...736478L. doi:10.1371/journal.pone.0036478. PMC 3350522. PMID 22606263.
Chua, Physilia Y. S.; Crampton-Platt, Alex; Lammers, Youri; Alsos, Inger G.; Boessenkool, Sanne; Bohmann, Kristine (25 May 2021). "Metagenomics: A viable tool for reconstructing herbivore diet". Molecular Ecology Resources. 21 (7): 1755–0998.13425. Bibcode:2021MolER..21.2249C. doi:10.1111/1755-0998.13425. PMC 8518049. PMID 33971086.
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). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. ISSN 1476-4687. PMC 3779803. PMID 20203603.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. (March 2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. PMC 3779803. PMID 20203603.
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; Huttenhower, Curtis (2012). "PLOS Computational Biology: Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome". PLOS Computational Biology. 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. doi:10.1371/journal.pcbi.1002358. PMC 3374609. PMID 22719234.
Chiu, Charles Y.; Miller, Steven A. (2019). "Clinical metagenomics". Nature Reviews Genetics. 20 (6): 341–355. doi:10.1038/s41576-019-0113-7. ISSN 1471-0064. PMC 6858796. PMID 30918369.
Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ (23 May 2019). "Exploiting the Legacy of the Arbovirus Hunters". Viruses. 11 (5): 471. doi:10.3390/v11050471. PMC 6563318. PMID 31126128.
Gajurel K, Dhakal R, Deresinski S (15 November 2024). "Arbovirus in Solid Organ Transplants: A Narrative Review of the Literature". Viruses. 16 (11): 1778. doi:10.3390/v16111778. PMC 11599096. PMID 39599892.
Patiño L, Benítez AD, Carrazco-Montalvo A, Regato-Arrata M (August 2024). "Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories". Viruses. 16 (8): 1242. doi:10.3390/v16081242. PMC 11360194. PMID 39205216.

npr.org

"What's Swimming in the River? Just Look For DNA". NPR.org. 24 July 2013. Retrieved 10 October 2014.

nytimes.com

Zimmer C (13 July 2010). "How Microbes Defend and Define Us". New York Times. Retrieved 29 December 2011.

oup.com

academic.oup.com

Zepeda Mendoza, Marie Lisandra; Sicheritz-Pontén, Thomas; Gilbert, M. Thomas P. (1 September 2015). "Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses". Briefings in Bioinformatics. 16 (5): 745–758. doi:10.1093/bib/bbv001. ISSN 1467-5463. PMC 4570204. PMID 25673291.

pensoft.net

mbmg.pensoft.net

Chua, Physilia Y. S.; Carøe, Christian; Crampton-Platt, Alex; Reyes-Avila, Claudia S.; Jones, Gareth; Streicker, Daniel G.; Bohmann, Kristine (4 July 2022). "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)". Metabarcoding and Metagenomics. 6: e78756. doi:10.3897/mbmg.6.78756. ISSN 2534-9708. S2CID 248041252.

psu.edu

citeseerx.ist.psu.edu

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.

sciencedirect.com

Carlino, Niccolò; Blanco-Míguez, Aitor; Punčochář, Michal; Mengoni, Claudia; Pinto, Federica; Tatti, Alessia; Manghi, Paolo; Armanini, Federica; Avagliano, Michele; Barcenilla, Coral; Breselge, Samuel; Cabrera-Rubio, Raul; Calvete-Torre, Inés; Coakley, Mairéad; Cobo-Díaz, José F. (3 October 2024). "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome". Cell. 187 (20): 5775–5795.e15. doi:10.1016/j.cell.2024.07.039. hdl:10261/373917. ISSN 0092-8674.

semanticscholar.org

api.semanticscholar.org

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". Applied Microbiology and Biotechnology. 43 (4): 667–74. doi:10.1007/BF00164771. PMID 7546604. S2CID 31384119.
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". Nature. 428 (6978): 37–43. Bibcode:2004Natur.428...37T. doi:10.1038/nature02340. PMID 14961025. S2CID 4420754.(subscription required)
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. (April 2004). "Environmental genome shotgun sequencing of the Sargasso Sea". Science. 304 (5667): 66–74. Bibcode:2004Sci...304...66V. CiteSeerX 10.1.1.124.1840. doi:10.1126/science.1093857. PMID 15001713. S2CID 1454587.
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". Science. 311 (5759): 392–4. Bibcode:2006Sci...311..392P. doi:10.1126/science.1123360. PMID 16368896. S2CID 11238470.
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". Environmental Microbiology. 2 (5): 516–29. Bibcode:2000EnvMi...2..516B. doi:10.1046/j.1462-2920.2000.00133.x. PMID 11233160. S2CID 8267748.
Schuster SC (January 2008). "Next-generation sequencing transforms today's biology". Nature Methods. 5 (1): 16–8. doi:10.1038/nmeth1156. PMID 18165802. S2CID 1465786.
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". Science. 331 (6016): 463–7. Bibcode:2011Sci...331..463H. doi:10.1126/science.1200387. PMID 21273488. S2CID 36572885.
Mohammed MH, Chadaram S, Komanduri D, Ghosh TS, Mande SS (September 2011). "Eu-Detect: an algorithm for detecting eukaryotic sequences in metagenomic data sets". Journal of Biosciences. 36 (4): 709–17. doi:10.1007/s12038-011-9105-2. PMID 21857117. S2CID 25857874.
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". Nature Methods. 10 (12): 1196–9. doi:10.1038/nmeth.2693. PMID 24141494. S2CID 7728395.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, et al. (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–9. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID 16915287. S2CID 4380804.
Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, et al. (August 2016). "Uncovering Earth's virome". Nature. 536 (7617): 425–30. Bibcode:2016Natur.536..425P. doi:10.1038/nature19094. PMID 27533034. S2CID 4466854.
Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC (August 2017). "Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data" (PDF). Nature Protocols. 12 (8): 1673–1682. doi:10.1038/nprot.2017.063. PMID 28749930. S2CID 2127494.
Kerepesi C, Grolmusz V (March 2016). "Giant viruses of the Kutch Desert". Archives of Virology. 161 (3): 721–4. arXiv:1410.1278. doi:10.1007/s00705-015-2720-8. PMID 26666442. S2CID 13145926.
Kerepesi C, Grolmusz V (June 2017). "The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys". Archives of Virology. 162 (6): 1671–1676. arXiv:1503.05575. doi:10.1007/s00705-017-3286-4. PMID 28247094. S2CID 1925728.
Chua, Physilia Y. S.; Carøe, Christian; Crampton-Platt, Alex; Reyes-Avila, Claudia S.; Jones, Gareth; Streicker, Daniel G.; Bohmann, Kristine (4 July 2022). "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)". Metabarcoding and Metagenomics. 6: e78756. doi:10.3897/mbmg.6.78756. ISSN 2534-9708. S2CID 248041252.
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022). "Taking metagenomics under the wings". Nature Reviews Microbiology. 20 (8): 447. doi:10.1038/s41579-022-00746-5. ISSN 1740-1534. PMID 35546350. S2CID 248739527.

springer.com

link.springer.com

Semenov, M. V. (1 January 2021). "Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects". Biology Bulletin Reviews. 11 (1): 40–53. Bibcode:2021BioBR..11...40S. doi:10.1134/S2079086421010084. ISSN 2079-0872.

terragenome.org

"TerraGenome Homepage". TerraGenome international sequencing consortium. Retrieved 30 December 2011.

web.archive.org

Jansson J (2011). "Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes Print E-mail". Microbe. Vol. 6, no. 7. p. 309. Archived from the original on 31 March 2012.
Committee on Metagenomics: Challenges and Functional Applications, National Research Council (2007). Understanding Our Microbial Planet: The New Science of Metagenomics (PDF). The National Academies Press. Archived from the original (PDF) on 30 October 2012. Retrieved 30 December 2011.
Schloss PD, Handelsman J (June 2003). "Biotechnological prospects from metagenomics" (PDF). Current Opinion in Biotechnology. 14 (3): 303–10. doi:10.1016/S0958-1669(03)00067-3. PMID 12849784. Archived from the original (PDF) on 4 March 2016. Retrieved 20 January 2012.

worldcat.org

search.worldcat.org

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio (November 2017). "A communal catalogue reveals Earth's multiscale microbial diversity". Nature. 551 (7681): 457–463. Bibcode:2017Natur.551..457T. doi:10.1038/nature24621. ISSN 1476-4687. PMC 6192678. PMID 29088705.
Stewart, Christopher J.; Ajami, Nadim J.; O’Brien, Jacqueline L.; Hutchinson, Diane S.; Smith, Daniel P.; Wong, Matthew C.; Ross, Matthew C.; Lloyd, Richard E.; Doddapaneni, HarshaVardhan; Metcalf, Ginger A.; Muzny, Donna; Gibbs, Richard A.; Vatanen, Tommi; Huttenhower, Curtis; Xavier, Ramnik J. (October 2018). "Temporal development of the gut microbiome in early childhood from the TEDDY study". Nature. 562 (7728): 583–588. Bibcode:2018Natur.562..583S. doi:10.1038/s41586-018-0617-x. ISSN 1476-4687. PMC 6415775. PMID 30356187.
Carlino, Niccolò; Blanco-Míguez, Aitor; Punčochář, Michal; Mengoni, Claudia; Pinto, Federica; Tatti, Alessia; Manghi, Paolo; Armanini, Federica; Avagliano, Michele; Barcenilla, Coral; Breselge, Samuel; Cabrera-Rubio, Raul; Calvete-Torre, Inés; Coakley, Mairéad; Cobo-Díaz, José F. (3 October 2024). "Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome". Cell. 187 (20): 5775–5795.e15. doi:10.1016/j.cell.2024.07.039. hdl:10261/373917. ISSN 0092-8674.
Chen, Liang; Zhao, Na; Cao, Jiabao; Liu, Xiaolin; Xu, Jiayue; Ma, Yue; Yu, Ying; Zhang, Xuan; Zhang, Wenhui; Guan, Xiangyu; Yu, Xiaotong; Liu, Zhipeng; Fan, Yanqun; Wang, Yang; Liang, Fan (8 June 2022). "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes". Nature Communications. 13 (1): 3175. Bibcode:2022NatCo..13.3175C. doi:10.1038/s41467-022-30857-9. ISSN 2041-1723. PMC 9177567. PMID 35676264.
Zepeda Mendoza, Marie Lisandra; Sicheritz-Pontén, Thomas; Gilbert, M. Thomas P. (1 September 2015). "Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses". Briefings in Bioinformatics. 16 (5): 745–758. doi:10.1093/bib/bbv001. ISSN 1467-5463. PMC 4570204. PMID 25673291.
Rieder, Jessica; Kapopoulou, Adamandia; Bank, Claudia; Adrian-Kalchhauser, Irene (14 February 2023). "Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems". Environmental Microbiome. 18 (1): 8. Bibcode:2023EMicb..18....8R. doi:10.1186/s40793-023-00459-z. ISSN 2524-6372. PMC 9930364. PMID 36788626.
Semenov, M. V. (1 January 2021). "Metabarcoding and Metagenomics in Soil Ecology Research: Achievements, Challenges, and Prospects". Biology Bulletin Reviews. 11 (1): 40–53. Bibcode:2021BioBR..11...40S. doi:10.1134/S2079086421010084. ISSN 2079-0872.
Carter, Matthew M.; Olm, Matthew R.; Merrill, Bryan D.; Dahan, Dylan; Tripathi, Surya; Spencer, Sean P.; Yu, Feiqiao B.; Jain, Sunit; Neff, Norma; Jha, Aashish R.; Sonnenburg, Erica D.; Sonnenburg, Justin L. (6 July 2023). "Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes". Cell. 186 (14): 3111–3124.e13. doi:10.1016/j.cell.2023.05.046. ISSN 0092-8674. PMC 10330870. PMID 37348505.
Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R.; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E.; Morley, Paul S.; McAllister, Tim A. (12 April 2018). "Impact of sequencing depth on the characterization of the microbiome and resistome". Scientific Reports. 8 (1): 5890. Bibcode:2018NatSR...8.5890Z. doi:10.1038/s41598-018-24280-8. ISSN 2045-2322. PMC 5897366. PMID 29651035.
Liu, Shaopeng; Rodriguez, Judith S.; Munteanu, Viorel; Ronkowski, Cynthia; Sharma, Nitesh Kumar; Alser, Mohammed; Andreace, Francesco; Blekhman, Ran; Błaszczyk, Dagmara; Chikhi, Rayan; Crandall, Keith A.; Della Libera, Katja; Francis, Dallace; Frolova, Alina; Gancz, Abigail Shahar (23 January 2025). "Analysis of metagenomic data". Nature Reviews Methods Primers. 5 (1): 1–28. doi:10.1038/s43586-024-00376-6. ISSN 2662-8449.
Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T. (November 2014). "Estimating coverage in metagenomic data sets and why it matters". The ISME Journal. 8 (11): 2349–2351. Bibcode:2014ISMEJ...8.2349R. doi:10.1038/ismej.2014.76. ISSN 1751-7370. PMC 4992084. PMID 24824669.
Beghini, Francesco; McIver, Lauren J.; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis (4 May 2021). "Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3". eLife. 10: e65088. doi:10.7554/eLife.65088. ISSN 2050-084X. PMC 8096432. PMID 33944776.
Pascal Andreu, Victòria; Augustijn, Hannah E.; Chen, Lianmin; Zhernakova, Alexandra; Fu, Jingyuan; Fischbach, Michael A.; Dodd, Dylan; Medema, Marnix H. (October 2023). "gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota". Nature Biotechnology. 41 (10): 1416–1423. doi:10.1038/s41587-023-01675-1. ISSN 1546-1696. PMC 10423304. PMID 36782070.
Chua, Physilia Y. S.; Carøe, Christian; Crampton-Platt, Alex; Reyes-Avila, Claudia S.; Jones, Gareth; Streicker, Daniel G.; Bohmann, Kristine (4 July 2022). "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)". Metabarcoding and Metagenomics. 6: e78756. doi:10.3897/mbmg.6.78756. ISSN 2534-9708. S2CID 248041252.
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). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature. 464 (7285): 59–65. Bibcode:2010Natur.464...59.. doi:10.1038/nature08821. ISSN 1476-4687. PMC 3779803. PMID 20203603.
Chua, Physilia Ying Shi; Rasmussen, Jacob Agerbo (11 May 2022). "Taking metagenomics under the wings". Nature Reviews Microbiology. 20 (8): 447. doi:10.1038/s41579-022-00746-5. ISSN 1740-1534. PMID 35546350. S2CID 248739527.
Chiu, Charles Y.; Miller, Steven A. (2019). "Clinical metagenomics". Nature Reviews Genetics. 20 (6): 341–355. doi:10.1038/s41576-019-0113-7. ISSN 1471-0064. PMC 6858796. PMID 30918369.
Diener, Christian; Holscher, Hannah D.; Filek, Klara; Corbin, Karen D.; Moissl-Eichinger, Christine; Gibbons, Sean M. (March 2025). "Metagenomic estimation of dietary intake from human stool". Nature Metabolism. 7 (3): 617–630. doi:10.1038/s42255-025-01220-1. ISSN 2522-5812. PMC 11949708. PMID 39966520.

yale.edu

handelsmanlab.sites.yale.edu

Schloss PD, Handelsman J (June 2003). "Biotechnological prospects from metagenomics" (PDF). Current Opinion in Biotechnology. 14 (3): 303–10. doi:10.1016/S0958-1669(03)00067-3. PMID 12849784. Archived from the original (PDF) on 4 March 2016. Retrieved 20 January 2012.