Phylogenomic diversity

We have been involved in many projects that focus on generating and analyzing microbial genomes to span the diversity of microbes.  Examples are below:

TIGR TOL. 2002-2006.I led the first major project in this area at TIGR (an NSF Tree of Life grant). More on this project can be found here. A few example publications are below.

  • Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb FT Colman AS, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4: e4207. PMID: 19148287. PDF.
  • Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. 2015. Genome sequence of the sulfate-reducing thermophilic bacterium Thermodesulfovibrio yellowstonii DSM 11347T (Phylum Nitrospirae). Genome Announcements 3: e01489-14. doi:10.1128/genomeA.01489-14.
  • Bhatnagar S, Badger JH, Madupu R, Khouri HM, O’Connor EM, Robb FT, Ward NL, Eisen JA. 2015. Genome sequence of a sulfate-reducing thermophilic bacterium, Thermodesulfobacterium commune DSM 2178T (phylum Thermodesulfobacteria). Genome Announcements 3: e01490-14. doi:10.1128/genomeA.01490-14.
  • Holland-Moritz HE, Coil DA, Badger JH, Dmitrov GI, Khouri H, Ward NL, Robb FT, Eisen JA. 2014. Draft genome sequence of the pyridinediol-fermenting bacterium Synergistes jonesii 78-1. Genome Announcements 2: e00833-14.
  • Alexiev A, Coil DA, Badger JH, Enticknap J, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of Coprothermobacter proteolyticus DSM 5265. Genome Announcements 2: e00470-14. PMID: 24831154. PMCID: PMC4022818.
  • Coil DA, Badger JH, Forberger HC, Riggs F, Madupu R, Fedorova N, Ward N, Robb FT, Eisen JA. 2014. Complete genome sequence of the extreme thermophile Dictyoglomus thermophilum H-6-12. Genome Announcements 2: e00109-14. PMCID: PMC3931368.
  • Coil DA, Lo JR, Chen R, Ward N, Robb FT, Eisen JA. 2013. Draft genome sequence of the arsenate respiring bacterium Chrysiogenes arsenatis DSM11915. Genome Announcements 1: e00953-13. PMCID: PMC3828317.

GEBA. 2007-current. I helped launch and coordinate the “Genomic Encyclopedia of Bacteria and Archaea” (aka GEBA) project run at the DOE-JGI where I hold an Adjunct appointment. This in turn led to multiple spin off GEBA projects. More on the original GEBA project can be found here.  Example GEBA related publications are below:

  • Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC. 2017. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35: 676–683. PMID: 28604660.
  • Whitman WB, Woyke T, Klenk HP, Zhou Y, Lilburn TG, Beck BJ, De Vos P, Vandamme P, Eisen JA, Garrity H, Hugenholtz P, Kyrpides NC. 2015. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences 10(1): 26. PMID: 26203337. PMCID: PMC4511459.
  • Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLOS Biology 12: ee1001920. PMID: 25093819. PMCID: PMC4122341.
  • Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. 2013. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences USA 110: 1053-1058. PMID: 23277585. PMCID: PMC3549136. PDF.
  • Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T. 2013. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437. PMID: 23851394.
  • Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060. PMID: 20033048.

Haloarchaeal Phylogenomics. 2009-2012.In collaboration with Marc Facciotti’s lab at UC Davis we ran a haloarchaeal phylogenomics project. More on this project can be found here. Example publications are below.

  • Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. 2014. Phylogenetically driven sequencing of extremely halophilic Archaea reveals strategies for static and dynamic osmo-response. PLOS Genetics 10: e1004784. PMID: 25393412. PMCID: PMC4230888.
  • Lynch EA, Langille MGI, Darling AE, Wilbanks EG, Haltiner C, Shao KSY, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS ONE 7: e41389. PMID: 22848480. PMC3404096. PDF.

Other Sequencing and/or Analysis Efforts. 

We have been involved in many other efforts that were driven largely by the goal of increasing the phylogenetic diversity of available genomes. Example papers on from these projects are below:

  • Castelle C, Hug LA, Wrighton KC, Thgomas, BC, Williams KH, Wu D, Tringe SG, Singer S, Eisen JA, Banfield JF. 2013. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications 4: 2120. PMID: 23979677. PMCID: PMC3903129.
  • Lang JM, Darling AE, Eisen JA. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.PLoS ONE 8: e62510. PMID: 23638103. PMCID: PMC3636077.
  • Wu D, Wu M, Halpern A, Rusch D, Yooseph S, Frazier M, Venter JC, Eisen JA. 2011. Stalking the fourth domain in metagenomic data: searching for and possible discovery of novel deep branches in phylogenetic trees. PLoS ONE 6: e18011. PMID: 21437252. PMCID: PMC3060911. PDF.
  • Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4: e5299. PMID: 19390573. PDF.
  • Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. 2008. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biology 9: R158. PMID: 19000309. PDF.
  • Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E. 2006. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. PLoS Biology 4: e286. PMID: 16933976. PDF.
  • Eisen JA, Nelson KE, Paulsen IT, Heidelberg JF, Wu M, Dodson RJ, Deboy R, Gwinn ML, Nelson WC, Haft DH, Hickey EK, Peterson JD, Durkin AS, Kolonay JL, Yang F, Holt I, Umayam LA, Mason T, Brenner M, Shea TP, Parksey D, Nierman WC, Feldblyum TV, Hansen CL, Craven MB, Radune D, Vamathevan J, Khouri H, White O, Venter JC, Gruber TM, Ketchum KA, Tettelin H, Bryant DA, Fraser CM. 2002. The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proceedings of the National Academy of Sciences USA 99: 9509-9514. PMID: 12093901. PDF.
  • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571-1577. PMID: 10567266. PDF.
  • Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323-329. PMID: 10360571. PDF.
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