Reference Collection

Big impacts, Discovery:

Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A, Nguyen LP, Villacorta R, Amjadi M, Garrigues C, Jovanovich SB, Feldman RA, DeLong EF (2000) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environmental microbiology 2: 516-529

Functional metagenomics:

Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and environmental microbiology 66: 2541-2547

The first environmental genome assemblies (AMD):

Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43

The first big scale metagenomics:

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74

Alternative metagenomics, Metaproteomics:

Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC, 2nd, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308: 1915-1920

Comparative metagenomics:

Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308: 554-557

Soil census:

Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS computational biology 2: e92

Marine census:

Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A 103: 12115-12120

Mesocosm (Sludge metagenomics):

Martin HG, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature biotechnology 24: 1263-1269

Metabolic pathway assemblies in symbionts:

Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443: 950-955

Comparing community diversities:

DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503

Marine virus:

Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368

The first human microbiome metagenomics:

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359

Comparative gut metagenomics:

Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031

Meta-bioinformatics (GOS):

Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol 5: e16

Simulated metagenomes:

Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature methods 4: 495-500

RNA-based metagenomics:

Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, Moran NA, Quan PL, Briese T, Hornig M, Geiser DM, Martinson V, vanEngelsdorp D, Kalkstein AL, Drysdale A, Hui J, Zhai J, Cui L, Hutchison SK, Simons JF, Egholm M, Pettis JS, Lipkin WI (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318: 283-287

Beneficial symbionts, Termite hindgut microbiome:

Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernandez M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P, Leadbetter JR (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450: 560-565

National Academies Press Book, Review

Handelsman J, Tiedje JM, Alvarez-Cohen L, Ashburner M, Cann IKO, Delong EF, Doolittle WF, Fraser-Liggett CM, Godzik A, Gordon JI, Riley M, Schmidt TM (2007) The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, Washington, DC: The National Academies Press.

Incorporating metadata into marine metagenomes:

Lombardot T, Kottmann R, Giuliani G, de Bono A, Addor N, Glockner FO (2007) MetaLook: a 3D visualisation software for marine ecological genomics. BMC bioinformatics [electronic resource] 8: 406

The special issue of Oceanography

The special issue of Oceanography; A Sea of Microbes

The mobile metagenomics

Jones BV, Marchesi JR (2007) Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nature methods 4: 55-61

The first 454-based metagenomic study:

Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M, Peterson DM, Saar MO, Alexander S, Alexander EC, Jr., Rohwer F (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC genomics 7: 57