Metagenomics: Facts and artifacts, and computational challenges

Journal of Computer Science and Technology

Volumn 25, Issue 1, 2010, Pages 71-81

  Wooley, John C ^a   Ye, Yuzhen ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Comparative metagenomics; Metagenomics; Next generation sequencing (NGS); Statistical approaches; Taxonomic functional profiling

Indexed keywords

BACTERIA; DATA HANDLING; FREQUENCY ESTIMATION; INFORMATION ANALYSIS; STATISTICAL MECHANICS;

COMPUTATIONAL APPROACH; COMPUTATIONAL CHALLENGES; ENVIRONMENTAL MICROBES; EXPERIMENTAL PROTOCOLS; METAGENOMICS; NEXT-GENERATION SEQUENCING; STATISTICAL APPROACH; TAXONOMIC/FUNCTIONAL PROFILING;

ENVIRONMENTAL MICROBIOLOGY;

EID: 75749135218     PISSN: 10009000     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11390-010-9306-4     Document Type: Article

References (91)

1. J Handelsman MR Rondon SF Brady J Clardy RM Goodman 1998 Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products Chemistry & Biology 5 10 245 249 10.1016/S1074-5521(98) 90108-9
2. E Mardis 2006 Anticipating the 1,000 dollar genome Genome Biol. 7 7 112 10.1186/gb-2006-7-7-112 (Pubitemid 44848830)
3. G Tyson J Chapman P Hugenholtz E Allen R Ram P Richardson V Solovyev E Rubin D Rokhsar J Banfield 2004 Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 428 6978 37 43 10.1038/nature02340 (Pubitemid 38332350)
4. J Venter K Remington J Heidelberg, et al. 2004 Environmental genome shotgun sequencing of the Sargasso Sea Science 304 5667 66 74 10.1126/science.1093857 (Pubitemid 38451457)
5. EA Dinsdale O Pantos S Smriga RA Edwards, et al. 2008 Microbial ecology of four coral atolls in the Northern Line Islands PLoS ONE 3 2 1584 10.1371/journal.pone.0001584 (Pubitemid 351877715)
6. P Lorenz J Eck 2005 Metagenomics and industrial applications Nat. Rev. Microbiol. 3 6 510 516 10.1038/nrmicro1161 (Pubitemid 40716178)
7. PJ Turnbaugh M Hamady T Yatsunenko, et al. 2009 A core gut microbiome in obese and lean twins Nature 457 7228 480 484 10.1038/nature07540
8. PJ Turnbaugh RE Ley M Hamady CM Fraser-Liggett R Knight JI Gordon 2007 The human microbiome project Nature 449 7164 804 810 10.1038/nature06244 (Pubitemid 47598620)
9. M Hamady JJ Walker JK Harris NJ Gold R Knight 2008 Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex Nat. Methods 5 3 235 237 10.1038/nmeth.1184 (Pubitemid 351325646)
10. L Li S McCorkle S Monchy S Taghavi D van der Lelie 2009 Bioprospecting metagenomes: Glycosyl hydrolases for converting biomass Biotechnol. Biofuels 2 10 10.1186/1754-6834-2-10
11. J Brulc D Antonopoulos M Miller, et al. 2009 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases Proc. Natl. Acad. Sci. USA 106 6 1948 1953 10.1073/pnas.0806191105
12. B Jones M Begley C Hill C Gahan J Marchesi 2008 Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome Proc. Natl. Acad. Sci. USA 105 36 13580 13585 10.1073/pnas.0804437105
13. T Mori S Mizuta H Suenaga K Miyazaki 2008 Metagenomic screening for bleomycin resistance genes Appl. Environ. Microbiol. 74 21 6803 6805 10.1128/AEM.00873-08
14. H Steele K Jaeger R Daniel W Streit 2009 Advances in recovery of novel biocatalysts from metagenomes J Mol. Microbiol. Biotechnol. 16 1/2 25 37 10.1159/000142892
15. Handelsman J, Tiedje J M, Alvarez-Cohen L et al. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. The National Academies Press, 2007.
16. S Tringe C von Mering A Kobayashi, et al. 2005 Comparative metagenomics of microbial communities Science 308 5721 554 557 10.1126/science.1107851 (Pubitemid 40570586)
17. PJ Turnbaugh RE Ley MA Mahowald V Magrini ER Mardis JI Gordon 2006 An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 7122 1027 1131 10.1038/nature05414 (Pubitemid 46018515)
18. SD Hooper J Raes KU Foerstner ED Harrington D Dalevi P Bork 2008 A molecular study of microbe transfer between distant environments PLoS ONE 3 7 2607 10.1371/journal.pone.0002607
19. J Raes KU Foerstner P Bork 2007 Get the most out of your metagenome: Computational analysis of environmental sequence data Curr. Opin. Microbiol. 10 5 490 498 10.1016/j.mib.2007.09.001 (Pubitemid 350052690)
20. V Kunin A Copeland A Lapidus K Mavromatis P Hugenholtz 2008 A bioinformatician's guide to metagenomics Microbiol. Mol. Biol. Rev. 72 4 557 578 10.1128/MMBR.00009-08
21. M Hamady R Knight 2009 Microbial community profiling for human microbiome projects: Tools, techniques, and challenges Genome Res. 19 7 1141 1152 10.1101/gr.085464.108
22. M Galperin 2004 Metagenomics: From acid mine to shining sea Environ. Microbiol. 6 6 543 545 10.1111/j.1462-2920.2004.00652.x (Pubitemid 38708688)
23. D Hernandez P Francois L Farinelli M Osteras J Schrenzel 2008 De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer Genome Res. 18 5 802 809 10.1101/gr.072033.107 (Pubitemid 351645070)
24. J Butler I MacCallum M Kleber IA Shlyakhter MK Belmonte ES Lander C Nusbaum DB Jaffe 2008 ALLPATHS: De novo assembly of whole-genome shotgun microreads Genome Res. 18 5 810 820 10.1101/gr.7337908 (Pubitemid 351645071)
25. MJ Chaisson PA Pevzner 2008 Short read fragment assembly of bacterial genomes Genome Res. 18 2 324 330 10.1101/gr.7088808 (Pubitemid 351240742)
26. M Pop 2009 Genome assembly reborn: Recent computational challenges Brief Bioinform. 10 4 354 366 10.1093/bib/bbp026
27. H Noguchi J Park T Takagi 2006 MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences Nucleic Acids Res. 34 19 5623 5630 10.1093/nar/gkl723 (Pubitemid 44742449)
28. KJ Hoff M Tech T Lingner R Daniel B Morgenstern P Meinicke 2008 Gene prediction in metagenomic fragments: A large scale machine learning approach BMC Bioinformatics 9 217 10.1186/1471-2105-9-217 (Pubitemid 351785135)
29. KJ Hoff T Lingner P Meinicke M Tech 2009 Orphelia: Predicting genes in metagenomic sequencing reads Nucleic Acids Res. 37 Web Server Issue 101 105 10.1093/nar/gkp327
30. L Krause NN Diaz D Bartels RA Edwards A Puhler F Rohwer F Meyer J Stoye 2006 Finding novel genes in bacterial communities isolated from the environment Bioinformatics 22 14 281 289 10.1093/bioinformatics/btl247 (Pubitemid 44288297)
31. Y Ye H Tang 2009 An orfome assembly approach to metagenomics sequences analysis J. Bioinform. Comput. Biol. 7 3 455 471 10.1142/S0219720009004151
32. E Cardenas J Tiedje 2008 New tools for discovering and characterizing microbial diversity Curr. Opin. Biotechnol. 19 6 544 549 10.1016/j.copbio.2008. 10.010
33. DH Huson AF Auch J Qi SC Schuster 2007 MEGAN analysis of metagenomic data Genome Res. 17 3 377 386 10.1101/gr.5969107 (Pubitemid 46376747)
34. S Chakravorty D Helb M Burday N Connell D Alland 2007 A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria J. Microbiol. Methods 69 2 330 339 10.1016/j.mimet.2007.02.005 (Pubitemid 46566457)
35. A Monier JM Claverie H Ogata 2008 Taxonomic distribution of large DNA viruses in the sea Genome Biol. 9 7 106 10.1186/gb-2008-9-7-r106
36. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork 2006 Toward automatic reconstruction of a highly resolved tree of life Science 311 5765 1283 1287 10.1126/science.1123061 (Pubitemid 43334717)
37. C von Mering P Hugenholtz J Raes SG Tringe T Doerks LJ Jensen N Ward P Bork 2007 Quantitative phylogenetic assessment of microbial communities in diverse environments Science 315 5815 1126 1130 10.1126/science.1133420 (Pubitemid 46328023)
38. M Wu JA Eisen 2008 A simple, fast, and accurate method of phylogenomic inference Genome Biol. 9 10 151 10.1186/gb-2008-9-10-r151
39. L Krause NN Diaz A Goesmann S Kelley TW Nattkemper F Rohwer RA Edwards J Stoye 2008 Phylogenetic classification of short environmental DNA fragments Nucleic Acids Res. 36 7 2230 2239 10.1093/nar/gkn038 (Pubitemid 351566997)
40. RD Finn J Mistry B Schuster-Bockler, et al. 2006 Pfam: Clans, Web tools and services Nucleic Acids Res. 34 Database Issue 247 251 10.1093/nar/gkj149
41. SD Bentley J Parkhill 2004 Comparative genomic structure of prokaryotes Annu. Rev. Genet. 38 771 792 10.1146/annurev.genet.38.072902.094318 (Pubitemid 40013745)
42. H Teeling J Waldmann T Lombardot M Bauer FO Glockner 2004 TETRA: A Web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences BMC Bioinformatics 5 163 10.1186/1471-2105-5-163 (Pubitemid 40195345)
43. T Woyke H Teeling NN Ivanova, et al. 2006 Symbiosis insights through metagenomic analysis of a microbial consortium Nature 443 7114 950 955 10.1038/nature05192 (Pubitemid 44646166)
44. Chatterji S, Yamazaki I, Bai Z, Eisen J. CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads. In Proc. the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008), Singapore, March 30-April 2, 2008, pp.17-28.
45. F Zhou V Olman Y Xu 2008 Barcodes for genomes and applications BMC Bioinformatics 9 546 10.1186/1471-2105-9-546
46. A Brady SL Salzberg 2009 Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models Nat. Methods 6 9 673 676 10.1038/nmeth.1358
47. JA Gilbert D Field Y Huang R Edwards W Li P Gilna I Joint 2008 Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities PLoS One 3 8 3042 10.1371/journal.pone.0003042
48. M Kanehisa S Goto 2000 KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 1 27 30 10.1093/nar/28.1.27
49. R Overbeek T Begley RM Butler, et al. 2005 The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res. 33 7 5691 5702 10.1093/nar/gki866 (Pubitemid 41548835)
50. EA Dinsdale RA Edwards D Hall, et al. 2008 Functional metagenomic profiling of nine biomes Nature 452 7187 629 632 10.1038/nature06810
51. F Meyer D Paarmann M D'Souza, et al. 2008 The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinformatics 9 386 10.1186/1471-2105-9-386
52. S Yooseph G Sutton DB Rusch, et al. 2007 The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families PLoS Biol. 5 3 16 10.1371/journal.pbio.0050016 (Pubitemid 46422966)
53. W Li JC Wooley A Godzik 2008 Probing metagenomics by rapid cluster analysis of very large datasets PLoS One 3 10 3375 10.1371/journal.pone.0003375
54. W Li L Jaroszewski A Godzik 2001 Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 17 3 282 283 10.1093/bioinformatics/17.3.282
55. EM Marcotte 2000 Computational genetics: Finding protein function by nonhomology methods Curr. Opin. Struct. Biol. 10 3 359 365 10.1016/S0959- 440X(00)00097-X 1774780 (Pubitemid 30333108)
56. SG Tringe C von Mering A Kobayashi, et al. 2005 Comparative metagenomics of microbial communities Science 308 5721 554 557 10.1126/science.1107851 (Pubitemid 40570586)
57. KU Foerstner C von Mering SD Hooper P Bork 2005 Environments shape the nucleotide composition of genomes EMBO Rep. 6 12 1208 1213 10.1038/sj.embor. 7400538 (Pubitemid 41741707)
58. J Raes JO Korbel MJ Lercher C von Mering P Bork 2007 Prediction of effective genome size in metagenomic samples Genome Biol. 8 1 10 10.1186/gb-2007-8-1-r10 (Pubitemid 351910992)
59. TA Gianoulis J Raes PV Patel, et al. 2009 Quantifying environmental adaptation of metabolic pathways in metagenomics Proc. Natl. Acad. Sci. USA 106 5 1374 1379 10.1073/pnas.0808022106
60. C Lozupone R Knight 2005 UniFrac: A new phylogenetic method for comparing microbial communities Appl. Environ. Microbiol. 71 12 8228 8235 10.1128/AEM.71.12.8228-8235.2005 (Pubitemid 41803949)
61. DH Huson DC Richter S Mitra AF Auch SC Schuster 2009 Methods for comparative metagenomics BMC Bioinformatics 10 Suppl 1 12 10.1186/1471-2105-10- S1-S12
62. S Mitra B Klar DH Huson 2009 Visual and statistical comparison of metagenomes Bioinformatics 25 15 1849 1855 10.1093/bioinformatics/btp341
63. PD Schloss J Handelsman 2008 A statistical toolbox for metagenomics: Assessing functional diversity in microbial communities BMC Bioinformatics 9 34 10.1186/1471-2105-9-34 (Pubitemid 351234738)
64. KE Wommack J Bhavsar J Ravel 2008 Metagenomics: Read length matters Appl. Environ. Microbiol. 74 5 1453 1463 10.1128/AEM.02181-07 (Pubitemid 351358441)
65. JB Hughes JJ Hellmann TH Ricketts BJ Bohannan 2001 Counting the uncountable: Statistical approaches to estimating microbial diversity Appl. Environ. Microbiol. 67 10 4399 4406 10.1128/AEM.67.10.4399-4406.2001 (Pubitemid 33646064)
66. M Breitbart P Salamon B Andresen JM Mahaffy AM Segall D Mead F Azam F Rohwer 2002 Genomic analysis of uncultured marine viral communities Proc. Natl. Acad. Sci. USA 99 22 14250 14255 10.1073/pnas.202488399 (Pubitemid 35257658)
67. PD Schloss J Handelsman 2005 Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness Appl. Environ. Microbiol. 71 3 1501 1506 10.1128/AEM.71.3.1501-1506.2005 (Pubitemid 40396689)
68. F Angly B Rodriguez-Brito D Bangor P McNairnie M Breitbart P Salamon B Felts J Nulton J Mahaffy F Rohwer 2005 PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information BMC Bioinformatics 6 41 10.1186/1471-2105-6-41 (Pubitemid 41357973)
69. PD Schloss 2008 Evaluating different approaches that test whether microbial communities have the same structure ISME J 2 3 265 275 10.1038/ismej.2008.5 (Pubitemid 351334275)
70. PD Schloss J Handelsman 2006 Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures Appl. Environ. Microbiol. 72 10 6773 6779 10.1128/AEM.00474-06 (Pubitemid 44582921)
71. J White N Nagarajan M Pop 2009 Statistical methods for detecting differentially abundant features in clinical metagenomic samples PLoS Comput. Biol. 5 4 1000352 10.1371/journal.pcbi.1000352
72. J Zaneveld PJ Turnbaugh C Lozupone RE Ley M Hamady JI Gordon R Knight 2008 Host-bacterial coevolution and the search for new drug targets Curr. Opin. Chem. Biol. 12 1 109 114 10.1016/j.cbpa.2008.01.015
73. RE Ley M Hamady C Lozupone PJ Turnbaugh RR Ramey JS Bircher ML Schlegel TA Tucker MD Schrenzel R Knight JI Gordon 2008 Evolution of mammals and their gut microbes Science 320 5883 1647 1651 10.1126/science.1155725 (Pubitemid 351931256)
74. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker 2003 Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res. 13 11 2498 2504 10.1101/gr.1239303 (Pubitemid 37428274)
75. DB Rusch AL Halpern G Sutton, et al. 2007 The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific PLoS Biol. 5 3 77 10.1371/journal.pbio.0050077 (Pubitemid 46422965)
76. KE Ashelford NA Chuzhanova JC Fry AJ Jones AJ Weightman 2005 At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies Appl. Environ. Microbiol. 71 12 7724 7736 10.1128/AEM.71.12.7724-7736.2005 (Pubitemid 41803890)
77. R Williams S Peisajovich O Miller S Magdassi D Tawfik A Griffiths 2006 Amplification of complex gene libraries by emulsion PCR Nat. Methods 3 7 545 550 10.1038/nmeth896 (Pubitemid 43941773)
78. T Huber G Faulkner P Hugenholz 2004 Bellerophon: A program to detect chimeric sequences in multiple sequence alignments Bioinformatics 20 14 2317 2319 10.1093/bioinformatics/bth226 (Pubitemid 39341624)
79. KE Ashelford NA Chuzhanova JC Fry AJ Jones AJ Weightman 2006 New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras Appl. Environ. Microbiol. 72 9 5734 5741 10.1128/AEM.00556-06 (Pubitemid 44414595)
80. V Gomez-Alvarez T Teal T Schmidt 2009 Systematic artifacts in metagenomes from complex microbial communities ISME J 3 11 1314 1317 10.1038/ismej.2009.72
81. Sharon I, Pati A, Markowitz V M, Pintter R Y. A statistical framework for the functional analysis of metagenomes. In Proc. RECOMB 2009, Tucson, USA, May 18-21, 2009, pp.496-511.
82. E Lander 1988 S Waterman M S. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2 231 239
83. Y Ye TG Doak 2009 A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes PLoS Comput. Biol. 5 8 1000465 10.1371/journal.pcbi.1000465
84. S Okuda T Yamada M Hamajima M Itoh T Katayama P Bork S Goto M Kanehisa 2008 KEGG Atlas mapping for global analysis of metabolic pathways Nucleic Acids Res. 36 Web Server Issue 423 426 10.1093/nar/gkn282
85. FM Rosin N Watanabe E Lam 2005 Moonlighting vacuolar protease: Multiple jobs for a busy protein Trends Plant Sci. 10 11 516 518 10.1016/j.tplants.2005. 09.002 (Pubitemid 41566272)
86. R Seshadri SA Kravitz L Smarr P Gilna M Frazier 2007 CAMERA: A community resource for metagenomics PLoS Biol. 5 3 75 10.1371/journal.pbio.0050075 (Pubitemid 46422964)
87. MN Price PS Dehal AP Arkin 2008 FastBLAST: Homology relationships for millions of proteins PLoS One 3 10 3589 10.1371/journal.pone.0003589
88. Y Sun Y Cai L Liu F Yu ML Farrell W McKendree W Farmerie 2009 ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences Nucleic Acids Res. 37 10 76 10.1093/nar/gkp285
89. Y Shi GW Tyson EF DeLong 2009 Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column Nature 459 7244 266 269 10.1038/nature08055
90. NC Verberkmoes AL Russell M Shah A Godzik M Rosenquist J Halfvarson MG Lefsrud J Apajalahti C Tysk RL Hettich JK Jansson 2009 Shotgun metaproteomics of the human distal gut microbiota ISME J 3 2 179 189 10.1038/ismej.2008.108
91. J Frias-Lopez Y Shi GW Tyson ML Coleman SC Schuster SW Chisholm EF Delong 2008 Microbial community gene expression in ocean surface waters Proc. Natl. Acad. Sci. USA 105 10 3805 3810 10.1073/pnas.0708897105 (Pubitemid 351723480)