Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology

Environmental Science and Technology

Volumn 49, Issue 21, 2015, Pages 12628-12640

  Ju, Feng ^a   Zhang, Tong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BIOHAZARDS; BIOINFORMATICS; BIOREMEDIATION; DNA SEQUENCES; ENVIRONMENTAL ENGINEERING; ENZYMES; GENE ENCODING; MICROORGANISMS; STATISTICS; WASTEWATER TREATMENT;

ANTIBIOTIC RESISTANCE GENES; BIOENERGY PRODUCTIONS; BIOINFORMATICS ANALYSIS; BIOTECHNOLOGICAL APPLICATIONS; ENVIRONMENTAL SCIENCE; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY STRUCTURES; MULTIPLE DISCIPLINES;

BIOTECHNOLOGY;

ANTIBIOTICS; BIOENERGY; BIOINFORMATICS; BIOREMEDIATION; BIOTECHNOLOGY; DATABASE; ENZYME ACTIVITY; EXPERIMENTAL DESIGN; MICROBIAL COMMUNITY; PATHOGEN; WASTEWATER; WATER TREATMENT;

ARTICLE; BIOENERGY; BIOINFORMATICS; BIOREMEDIATION; BIOSAFETY; BIOTECHNOLOGY; COMMUNITY STRUCTURE; DATA MINING; EXPERIMENTAL DESIGN; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; WASTE WATER MANAGEMENT; BIOLOGY; DNA SEQUENCE; ECOLOGY; GENETICS; GENOME; METHODOLOGY; MICROBIAL CONSORTIUM; ORGANISMAL INTERACTION; PROCEDURES; SEWAGE;

BIOFUEL;

BIODEGRADATION, ENVIRONMENTAL; BIOFUELS; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; ECOLOGY; GENOME; METAGENOMICS; MICROBIAL CONSORTIA; MICROBIAL INTERACTIONS; RESEARCH DESIGN; SEQUENCE ANALYSIS, DNA; WASTE DISPOSAL, FLUID;

EID: 84946594583     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/acs.est.5b03719     Document Type: Article

References (167)

1. Fang, H. H. P.; Zhang, T., Eds. Anaerobic Biotechnology: Environmental Protection and Resource Recovery; Imperial College Press: London, 2015.
2. Grady Jr, C. L.; Daigger, G. T.; Love, N. G.; Filipe, C. D.; Leslie Grady, C. Biological Wastewater Treatment; IWA Publishing: London, U.K. 2011.
3. Lovley, D. R. Cleaning up with genomics: applying molecular biology to bioremediation Nat. Rev. Microbiol. 2003, 1 (1) 35-44 10.1038/nrmicro731
4. Sieber, J. R.; McInerney, M. J.; Gunsalus, R. P. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation Annu. Rev. Microbiol. 2012, 66 (1) 429-452 10.1146/annurev-micro-090110-102844
5. van Dijk, E. L.; Auger, H.; Jaszczyszyn, Y.; Thermes, C. Ten years of next-generation sequencing technology Trends Genet. 2014, 30 (9) 418-426 10.1016/j.tig.2014.07.001
6. Pernthaler, A.; Dekas, A. E.; Brown, C. T.; Goffredi, S. K.; Embaye, T.; Orphan, V. J. Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (19) 7052-7057 10.1073/pnas.0711303105
7. Frias-Lopez, J.; Shi, Y.; Tyson, G. W.; Coleman, M. L.; Schuster, S. C.; Chisholm, S. W.; DeLong, E. F. Microbial community gene expression in ocean surface waters Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (10) 3805-3810 10.1073/pnas.0708897105
8. Mason, O. U.; Hazen, T. C.; Borglin, S.; Chain, P. S. G.; Dubinsky, E. A.; Fortney, J. L.; Han, J.; Holman, H. Y. N.; Hultman, J.; Lamendella, R. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill ISME J. 2012, 6 (9) 1715-1727 10.1038/ismej.2012.59
9. Shi, Y.; Tyson, G. W.; Eppley, J. M.; DeLong, E. F. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean ISME J. 2011, 5 (6) 999-1013 10.1038/ismej.2010.189
10. Tyson, G. W.; Chapman, J.; Hugenholtz, P.; Allen, E. E.; Ram, R. J.; Richardson, P. M.; Solovyev, V. V.; Rubin, E. M.; Rokhsar, D. S.; Banfield, J. F. Community structure and metabolism through reconstruction of microbial genomes from the environment Nature 2004, 428 (6978) 37-43 10.1038/nature02340
11. Tringe, S. G.; Von Mering, C.; Kobayashi, A.; Salamov, A. A.; Chen, K.; Chang, H. W.; Podar, M.; Short, J. M.; Mathur, E. J.; Detter, J. C. Comparative metagenomics of microbial communities Science 2005, 308 (5721) 554-557 10.1126/science.1107851
12. Ju, F.; Guo, F.; Ye, L.; Xia, Y.; Zhang, T. Metagenomic analysis on seasonal microbial variations of activated sludge from a full-scale wastewater treatment plant over 4 years Environ. Microbiol. Rep. 2014, 6 (1) 80-89 10.1111/1758-2229.12110
13. Xia, Y.; Wang, Y.; Fang, H. H.; Jin, T.; Zhong, H.; Zhang, T. Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis Sci. Rep. 2014, 4, 6708-6716 10.1038/srep06708
14. Xia, Y.; Ju, F.; Fang, H. H.; Zhang, T. Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortium by metagenomics PLoS One 2013, 8 (1) e53779 10.1371/journal.pone.0053779
15. Wexler, M.; Bond, P. L.; Richardson, D. J.; Johnston, A. W. A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase Environ. Microbiol. 2005, 7 (12) 1917-1926 10.1111/j.1462-2920.2005.00854.x
16. Martín, H. G.; Ivanova, N.; Kunin, V.; Warnecke, F.; Barry, K. W.; McHardy, A. C.; Yeates, C.; He, S.; Salamov, A. A.; Szeto, E. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities Nat. Biotechnol. 2006, 24 (10) 1263-1269 10.1038/nbt1247
17. Krause, L.; Diaz, N. N.; Edwards, R. A.; Gartemann, K. H.; Krömeke, H.; Neuweger, H.; Pühler, A.; Runte, K. J.; Schlüter, A.; Stoye, J. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor J. Biotechnol. 2008, 136 (1) 91-101 10.1016/j.jbiotec.2008.06.003
18. Guermazi, S.; Daegelen, P.; Dauga, C.; Rivière, D.; Bouchez, T.; Godon, J. J.; Gyapay, G.; Sghir, A.; Pelletier, E.; Weissenbach, J. Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach Environ. Microbiol. 2008, 10 (8) 2111-2123 10.1111/j.1462-2920.2008.01632.x
19. Rinke, C.; Schwientek, P.; Sczyrba, A.; Ivanova, N. N.; Anderson, I. J.; Cheng, J. F.; Darling, A.; Malfatti, S.; Swan, B. K.; Gies, E. A. Insights into the phylogeny and coding potential of microbial dark matter Nature 2013, 499 (7459) 431-437 10.1038/nature12352
20. Albertsen, M.; Hugenholtz, P.; Skarshewski, A.; Nielsen, K. L.; Tyson, G. W.; Nielsen, P. H. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Nat. Biotechnol. 2013, 31 (6) 533-538 10.1038/nbt.2579
21. Wrighton, K. C.; Thomas, B. C.; Sharon, I.; Miller, C. S.; Castelle, C. J.; VerBerkmoes, N. C.; Wilkins, M. J.; Hettich, R. L.; Lipton, M. S.; Williams, K. H. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla Science 2012, 337 (6102) 1661-1665 10.1126/science.1224041
22. Mao, Y.; Yu, K.; Xia, Y.; Chao, Y.; Zhang, T. Genome Reconstruction and Gene Expression of "Candidatus Accumulibacter phosphatis Clade IB Performing Biological Phosphorus Removal Environ. Sci. Technol. 2014, 48 (17) 10363-10371 10.1021/es502642b
23. Meyerdierks, A.; Kube, M.; Kostadinov, I.; Teeling, H.; Glöckner, F. O.; Reinhardt, R.; Amann, R. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group Environ. Microbiol. 2010, 12 (2) 422-439 10.1111/j.1462-2920.2009.02083.x
24. Yu, K.; Zhang, T. Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge PLoS One 2012, 7 (5) e38183 10.1371/journal.pone.0038183
25. Thomas, T.; Gilbert, J.; Meyer, F. Metagenomics-a guide from sampling to data analysis Microb. Inf. Exp. 2012, 2 (3) 1-12 10.1186/2042-5783-2-3
26. Howe, A. C.; Jansson, J. K.; Malfatti, S. A.; Tringe, S. G.; Tiedje, J. M.; Brown, C. T. Tackling soil diversity with the assembly of large, complex metagenomes Proc. Natl. Acad. Sci. U. S. A. 2014, 111 (13) 4904-4909 10.1073/pnas.1402564111
27. Desai, N.; Antonopoulos, D.; Gilbert, J. A.; Glass, E. M.; Meyer, F. From genomics to metagenomics Curr. Opin. Biotechnol. 2012, 23 (1) 72-76 10.1016/j.copbio.2011.12.017
28. Knight, R.; Jansson, J.; Field, D.; Fierer, N.; Desai, N.; Fuhrman, J. A.; Hugenholtz, P.; van der Lelie, D.; Meyer, F.; Stevens, R. Unlocking the potential of metagenomics through replicated experimental design Nat. Biotechnol. 2012, 30 (6) 513-520 10.1038/nbt.2235
29. Goodrich, J. K.; Di Rienzi, S. C.; Poole, A. C.; Koren, O.; Walters, W. A.; Caporaso, J. G.; Knight, R.; Ley, R. E. Conducting a Microbiome Study Cell 2014, 158 (2) 250-262 10.1016/j.cell.2014.06.037
30. Scholz, M. B.; Lo, C. C.; Chain, P. S. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis Curr. Opin. Biotechnol. 2012, 23 (1) 9-15 10.1016/j.copbio.2011.11.013
31. Zhou, J.; He, Z.; Yang, Y.; Deng, Y.; Tringe, S. G.; Alvarez-Cohen, L. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats mBio 2015, 6 (1) e02288-14 10.1128/mBio.02288-14
32. Kunin, V.; Copeland, A.; Lapidus, A.; Mavromatis, K.; Hugenholtz, P. A bioinformaticians guide to metagenomics Microbiol. Mol. Biol. Rev. 2008, 72 (4) 557-578 10.1128/MMBR.00009-08
33. Zhang, T.; Shao, M. F.; Ye, L. 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants ISME J. 2012, 6 (6) 1137-1147 10.1038/ismej.2011.188
34. Riesgo, A.; PPéREZ-PORRO, A. R.; Carmona, S.; Leys, S. P.; Giribet, G. Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing Mol. Ecol. Resour. 2012, 12 (2) 312-322 10.1111/j.1755-0998.2011.03097.x
35. Kucuktas, H.; Liu, Z. J. Library construction for next generation sequencing. In Next Generation Sequencing and Whole Genome Selection in Aquaculture; Liu, Z. J., Ed; Blackwell Publishing Ltd.: Oxford, U.K., 2010; pp 57-67.
36. Head, S. R.; Komori, H. K.; LaMere, S. A.; Whisenant, T.; Van Nieuwerburgh, F.; Salomon, D. R.; Ordoukhanian, P. Library construction for next-generation sequencing: overviews and challenges BioTechniques 2013, 56 (2) 61-64 10.1002/9780470958964.ch4
37. Peng, Y.; Leung, H. C.; Yiu, S. M.; Chin, F. Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth Bioinformatics 2012, 28 (11) 1420-1428 10.1093/bioinformatics/bts174
38. Masella, A. P.; Bartram, A. K.; Truszkowski, J. M.; Brown, D. G.; Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences BMC Bioinf. 2012, 13 (1) 31 10.1186/1471-2105-13-31
39. Imelfort, M.; Parks, D.; Woodcroft, B. J.; Dennis, P.; Hugenholtz, P.; Tyson, G. W. GroopM: an automated tool for the recovery of population genomes from related metagenomes PeerJ 2014, 2, e603 10.7717/peerj.603
40. Prjibelski, A. D.; Vasilinetc, I.; Bankevich, A.; Gurevich, A.; Krivosheeva, T.; Nurk, S.; Pham, S.; Korobeynikov, A.; Lapidus, A.; Pevzner, P. A. ExSPAnder: a universal repeat resolver for DNA fragment assembly Bioinformatics 2014, 30 (12) 293-301 10.1093/bioinformatics/btu266
41. Koren, S.; Schatz, M. C.; Walenz, B. P.; Martin, J.; Howard, J. T.; Ganapathy, G.; Wang, Z.; Rasko, D. A.; McCombie, W. R.; Jarvis, E. D. Hybrid error correction and de novo assembly of single-molecule sequencing reads Nat. Biotechnol. 2012, 30 (7) 693-700 10.1038/nbt.2280
42. Roesch, L. F.; Fulthorpe, R. R.; Riva, A.; Casella, G.; Hadwin, A. K.; Kent, A. D.; Daroub, S. H.; Camargo, F. A.; Farmerie, W. G.; Triplett, E. W. Pyrosequencing enumerates and contrasts soil microbial diversity ISME J. 2007, 1 (4) 283-290 10.1038/ismej.2007.53
43. Wang, Y.; Sheng, H. F.; He, Y.; Wu, J. Y.; Jiang, Y. X.; Tam, N. F. Y.; Zhou, H. W. Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags Appl. Environ. Microbiol. 2012, 78 (23) 8264-8271 10.1128/AEM.01821-12
44. Ju, F.; Zhang, T. Novel microbial populations in ambient and mesophilic biogas-producing and phenol-degrading consortia unraveled by high-throughput sequencing Microb. Ecol. 2014, 68 (2) 235-246 10.1007/s00248-014-0405-6
45. Ye, L.; Zhang, T. Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing Appl. Microbiol. Biotechnol. 2013, 97 (6) 2681-2690 10.1007/s00253-012-4082-4
46. Ju, F.; Zhang, T. 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions Appl. Microbiol. Biotechnol. 2015, 99 (10) 4119-4129 10.1007/s00253-015-6536-y
47. Ye, L.; Zhang, T.; Wang, T.; Fang, Z. Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing Environ. Sci. Technol. 2012, 46 (24) 13244-13252 10.1021/es303454k
48. Ufarté, L.; Potocki-Véronèse, G.; Laville, E. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology Front. Microbiol. 2015, 6, 563-572 10.3389/fmicb.2015.00563
49. Meyer, F.; Paarmann, D.; DSouza, M.; Olson, R.; Glass, E. M.; Kubal, M.; Paczian, T.; Rodriguez, A.; Stevens, R.; Wilke, A. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes BMC Bioinf. 2008, 9 (1) 386-393 10.1186/1471-2105-9-386
50. Torres-García, W.; Zheng, S.; Sivachenko, A.; Vegesna, R.; Wang, Q.; Yao, R.; Berger, M. F.; Weinstein, J. N.; Getz, G.; Verhaak, R. G. PRADA: pipeline for RNA sequencing data analysis Bioinformatics 2014, 30 (15) 2224-2226 10.1093/bioinformatics/btu169
51. Schmieder, R.; Edwards, R. Quality control and preprocessing of metagenomic datasets Bioinformatics 2011, 27 (6) 863-864 10.1093/bioinformatics/btr026
52. Patel, R. K.; Jain, M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data PLoS One 2012, 7 (2) e30619 10.1371/journal.pone.0030619
53. Schmieder, R.; Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets PLoS One 2011, 6 (3) e17288 10.1371/journal.pone.0017288
54. Wang, L.; Wang, S.; Li, W. RSeQC: quality control of RNA-seq experiments Bioinformatics 2012, 28 (16) 2184-2185 10.1093/bioinformatics/bts356
55. DeLuca, D. S.; Levin, J. Z.; Sivachenko, A.; Fennell, T.; Nazaire, M. D.; Williams, C.; Reich, M.; Winckler, W.; Getz, G. RNA-SeQC: RNA-seq metrics for quality control and process optimization Bioinformatics 2012, 28 (11) 1530-1532 10.1093/bioinformatics/bts196
56. Niu, B.; Fu, L.; Sun, S.; Li, W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data BMC Bioinf. 2010, 11 (1) 187-197 10.1186/1471-2105-11-187
57. Schloss, P. D.; Westcott, S. L.; Ryabin, T.; Hall, J. R.; Hartmann, M.; Hollister, E. B.; Lesniewski, R. A.; Oakley, B. B.; Parks, D. H.; Robinson, C. J. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl. Environ. Microbiol. 2009, 75 (23) 7537-7541 10.1128/AEM.01541-09
58. Caporaso, J. G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F. D.; Costello, E. K.; Fierer, N.; Peña, A. G.; Goodrich, J. K.; Gordon, J. I. QIIME allows analysis of high-throughput community sequencing data Nat. Methods 2010, 7 (5) 335-336 10.1038/nmeth.f.303
59. Magoč, T.; Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies Bioinformatics 2011, 27 (21) 2957-2963 10.1093/bioinformatics/btr507
60. Langille, M. G.; Hsiao, W. W.; Brinkman, F. S. Detecting genomic islands using bioinformatics approaches Nat. Rev. Microbiol. 2010, 8 (5) 373-382 10.1038/nrmicro2350
61. Zerbino, D. R.; Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs Genome Res. 2008, 18 (5) 821-829 10.1101/gr.074492.107
62. Simpson, J. T.; Wong, K.; Jackman, S. D.; Schein, J. E.; Jones, S. J.; Birol, I. ABySS: a parallel assembler for short read sequence data Genome Res. 2009, 19 (6) 1117-1123 10.1101/gr.089532.108
63. Luo, R.; Liu, B.; Xie, Y.; Li, Z.; Huang, W.; Yuan, J.; He, G.; Chen, Y.; Pan, Q.; Liu, Y. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Bioinformatics 2012, 1 (1) 18-23 10.1093/bioinformatics/btu077
64. Peng, Y.; Leung, H. C.; Yiu, S. M.; Chin, F. Y. Meta-IDBA: a de Novo assembler for metagenomic data Bioinformatics 2011, 27 (13) 94-101 10.1093/bioinformatics/btr216
65. Namiki, T.; Hachiya, T.; Tanaka, H.; Sakakibara, Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads Nucleic Acids Res. 2012, 40 (20) 155-155 10.1093/nar/gks678
66. Boisvert, S.; Raymond, F.; Godzaridis, é.; Laviolette, F.; Corbeil, J. Ray Meta: scalable de novo metagenome assembly and profiling Genome Biol. 2012, 13 (12) 122-134 10.1186/gb-2012-13-12-r122
67. Haider, B.; Ahn, T. H.; Bushnell, B.; Chai, J.; Copeland, A.; Pan, C. Omega: an Overlap-graph de novo Assembler for Metagenomics Bioinformatics 2014, 30 (19) 2717-2722 10.1093/bioinformatics/btu395
68. Li, D.; Liu, C. M.; Luo, R.; Sadakane, K.; Lam, T. W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Bioinformatics 2015, 31 (10) 1674-1676 10.1093/bioinformatics/btv033
69. Martin, J. A.; Wang, Z. Next-generation transcriptome assembly Nat. Rev. Genet. 2011, 12 (10) 671-682 10.1038/nrg3068
70. Grabherr, M. G.; Haas, B. J.; Yassour, M.; Levin, J. Z.; Thompson, D. A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q. Full-length transcriptome assembly from RNA-Seq data without a reference genome Nat. Biotechnol. 2011, 29 (7) 644-652 10.1038/nbt.1883
71. Schulz, M. H.; Zerbino, D. R.; Vingron, M.; Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels Bioinformatics 2012, 28 (8) 1086-1092 10.1093/bioinformatics/bts094
72. Birol, I.; Jackman, S. D.; Nielsen, C. B.; Qian, J. Q.; Varhol, R.; Stazyk, G.; Morin, R. D.; Zhao, Y.; Hirst, M.; Schein, J. E. De novo transcriptome assembly with ABySS Bioinformatics 2009, 25 (21) 2872-2877 10.1093/bioinformatics/btp367
73. Xie, Y.; Wu, G.; Tang, J.; Luo, R.; Patterson, J.; Liu, S.; Huang, W.; He, G.; Gu, S.; Li, S. SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads Bioinformatics 2014, 30 (12) 1660-1666 10.1093/bioinformatics/btu077
74. Pertea, M.; Pertea, G. M.; Antonescu, C. M.; Chang, T. C.; Mendell, J. T.; Salzberg, S. L. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nat. Biotechnol. 2015, 33 (3) 290-295 10.1038/nbt.3122
75. Guttman, M.; Garber, M.; Levin, J. Z.; Donaghey, J.; Robinson, J.; Adiconis, X.; Fan, L.; Koziol, M. J.; Gnirke, A.; Nusbaum, C. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Nat. Biotechnol. 2010, 28 (5) 503-510 10.1038/nbt.1633
76. Yang, Y.; Smith, S. A. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics BMC Genomics 2013, 14 (1) 328-338 10.1186/1471-2164-14-328
77. Li, B.; Fillmore, N.; Bai, Y.; Collins, M.; Thomson, J. A.; Stewart, R.; Dewey, C. Evaluation of de novo transcriptome assemblies from RNA-Seq data Genome Biol. 2014, 15 (12) 553-273 10.1186/s13059-014-0553-5
78. Surget-Groba, Y.; Montoya-Burgos, J. I. Optimization of de novo transcriptome assembly from next-generation sequencing data Genome Res. 2010, 20 (10) 1432-1440 10.1101/gr.103846.109
79. Zhao, Q. Y.; Wang, Y.; Kong, Y. M.; Luo, D.; Li, X.; Hao, P. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study BMC Bioinf. 2011, 12 (14) 1-12 10.1186/1471-2105-12-S14-S2
80. Leung, H. C.; Yiu, S. M.; Parkinson, J.; Chin, F. Y. IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology J. Comput. Biol. 2013, 20 (7) 540-550 10.1089/cmb.2013.0042
81. Leung, H. C.; Yiu, S. M.; Chin, F. Y. IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information, Research in Computational Molecular Biology 2014; Springer, 2014; pp 160-172.
82. Sharon, I.; Morowitz, M. J.; Thomas, B. C.; Costello, E. K.; Relman, D. A.; Banfield, J. F. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization Genome Res. 2013, 23 (1) 111-120 10.1101/gr.142315.112
83. Segata, N.; Waldron, L.; Ballarini, A.; Narasimhan, V.; Jousson, O.; Huttenhower, C. Metagenomic microbial community profiling using unique clade-specific marker genes Nat. Methods 2012, 9 (8) 811-814 10.1038/nmeth.2066
84. Liu, B.; Gibbons, T.; Ghodsi, M.; Pop, M. MetaPhyler: Taxonomic profiling for metagenomic sequences, Bioinformatics and Biomedicine (BIBM). In 2010 IEEE International Conference; IEEE: 2010; pp 95-100.
85. Gerlach, W.; Stoye, J. Taxonomic classification of metagenomic shotgun sequences with CARMA3 Nucleic Acids Res. 2011, 39 (14) e91 10.1093/nar/gkr225
86. Teeling, H.; Waldmann, J.; Lombardot, T.; Bauer, M.; Glöckner, F. O. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences BMC Bioinf. 2004, 5 (1) 163-169 10.1186/1471-2105-5-163
87. McHardy, A. C.; Martín, H. G.; Tsirigos, A.; Hugenholtz, P.; Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments Nat. Methods 2007, 4 (1) 63-72 10.1038/nmeth976
88. Chatterji, S.; Yamazaki, I.; Bai, Z.; Eisen, J. A. CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads, Research in Computational Molecular Biology, 2008; Springer: 2008; pp 17-28.
89. Diaz, N. N.; Krause, L.; Goesmann, A.; Niehaus, K.; Nattkemper, T. W. TACOA-Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach BMC Bioinf. 2009, 10 (1) 56-71 10.1186/1471-2105-10-56
90. Brady, A.; Salzberg, S. L. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models Nat. Methods 2009, 6 (9) 673-676 10.1038/nmeth.1358
91. Wang, Y.; Leung, H. C.; Yiu, S. M.; Chin, F. Y. MetaCluster 4.0: a novel binning algorithm for NGS reads and huge number of species J. Comput. Biol. 2012, 19 (2) 241-249 10.1089/cmb.2011.0276
92. Dick, G. J.; Andersson, A. F.; Baker, B. J.; Simmons, S. L.; Thomas, B. C.; Yelton, A. P.; Banfield, J. F. Community-wide analysis of microbial genome sequence signatures Genome Biol. 2009, 10 (8) R85-R100 10.1186/gb-2009-10-8-r85
93. Sheik, C. S.; Jain, S.; Dick, G. J. Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics Environ. Microbiol. 2014, 16 (1) 304-317 10.1111/1462-2920.12165
94. Karlsson, F. H.; Tremaroli, V.; Nookaew, I.; Bergström, G.; Behre, C. J.; Fagerberg, B.; Nielsen, J.; Bäckhed, F. Gut metagenome in European women with normal, impaired and diabetic glucose control Nature 2013, 498 (7452) 99-103 10.1038/nature12198
95. Alneberg, J.; Bjarnason, B. S.; de Bruijn, I.; Schirmer, M.; Quick, J.; Ijaz, U. Z.; Lahti, L.; Loman, N. J.; Andersson, A. F.; Quince, C. Binning metagenomic contigs by coverage and composition Nat. Methods 2014, 11 (11) 1144-1146 10.1038/nmeth.3103
96. Wu, Y. W.; Tang, Y. H.; Tringe, S. G.; Simmons, B. A.; Singer, S. W. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm Microbiome 2014, 2 (1) 1-18 10.1186/2049-2618-2-26
97. Kang, D. D.; Froula, J.; Egan, R.; Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities PeerJ 2015, 3, e1165 10.7717/peerj.1165
98. Dupont, C. L.; Rusch, D. B.; Yooseph, S.; Lombardo, M. J.; Richter, R. A.; Valas, R.; Novotny, M.; Yee-Greenbaum, J.; Selengut, J. D.; Haft, D. H. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage ISME J. 2012, 6 (6) 1186-1199 10.1038/ismej.2011.189
99. Raes, J.; Korbel, J. O.; Lercher, M. J.; von Mering, C.; Bork, P. Prediction of effective genome size in metagenomic samples Genome Biol. 2007, 8 (1) 10-20 10.1186/gb-2007-8-1-r10
100. Parks, D. H.; Imelfort, M.; Skennerton, C. T.; Hugenholtz, P.; Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Res. 2015, 25, 1043 10.1101/gr.186072.114
101. Kanehisa, M.; Goto, S. KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 2000, 28 (1) 27-30 10.1093/nar/28.1.27
102. Overbeek, R.; Begley, T.; Butler, R. M.; Choudhuri, J. V.; Chuang, H. Y.; Cohoon, M.; de Crécy-Lagard, V.; Diaz, N.; Disz, T.; Edwards, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes Nucleic Acids Res. 2005, 33 (17) 5691-5702 10.1093/nar/gki866
103. Yang, Y.; Li, B.; Ju, F.; Zhang, T. Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach Environ. Sci. Technol. 2013, 47 (18) 10197-10205 10.1021/es4017365
104. Li, B.; Yang, Y.; Ma, L.; Ju, F.; Guo, F.; Tiedje, J. M.; Zhang, T. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes ISME J. 2015, 10.1038/ismej.2015.59
105. Gomez-Alvarez, V.; Revetta, R. P.; Santo Domingo, J. W. Metagenomic analyses of drinking water receiving different disinfection treatments Appl. Environ. Microbiol. 2012, 78 (17) 6095-6102 10.1128/AEM.01018-12
106. Li, B.; Ju, F.; Cai, L.; Zhang, T. Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-throughput metagenomic approach Environ. Sci. Technol. 2015, 49 (17) 10492-10502 10.1021/acs.est.5b02345
107. Bibby, K.; Peccia, J. Identification of viral pathogen diversity in sewage sludge by metagenome analysis Environ. Sci. Technol. 2013, 47 (4) 1945-1951 10.1021/es305181x
108. Tamaki, H.; Zhang, R.; Angly, F. E.; Nakamura, S.; Hong, P. Y.; Yasunaga, T.; Kamagata, Y.; Liu, W. T. Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate Environ. Microbiol. 2012, 14 (2) 441-452 10.1111/j.1462-2920.2011.02630.x
109. Francis, O. E.; Bendall, M.; Manimaran, S.; Hong, C.; Clement, N. L.; Castro-Nallar, E.; Snell, Q.; Schaalje, G. B.; Clement, M. J.; Crandall, K. A. Pathoscope: Species identification and strain attribution with unassembled sequencing data Genome Res. 2013, 23 (10) 1721-1729 10.1101/gr.150151.112
110. Ahn, T. H.; Chai, J.; Pan, C. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance Bioinformatics 2015, 31 (2) 170-177 10.1093/bioinformatics/btu641
111. Consortium, H. M. P. Structure, function and diversity of the healthy human microbiome Nature 2012, 486 (7402) 207-214 10.1038/nature11234
112. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST Bioinformatics 2010, 26 (19) 2460-2461 10.1093/bioinformatics/btq461
113. Kent, W. J. BLAT-the BLAST-like alignment tool Genome Res. 2002, 12 (4) 656-664 10.1101/gr.229202
114. Zhao, Y.; Tang, H.; Ye, Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data Bioinformatics 2012, 28 (1) 125-126 10.1093/bioinformatics/btr595
115. Buchfink, B.; Xie, C.; Huson, D. H. Fast and sensitive protein alignment using DIAMOND Nat. Methods 2015, 12 (1) 59-60 10.1038/nmeth.3176
116. Yang, Y.; Jiang, X. T.; Zhang, T. Evaluation of a hybrid approach using ublast and blastx for metagenomic sequences annotation of specific functional genes PLoS One 2014, 9 (10) e110947 10.1371/journal.pone.0110947
117. Yu, K.; Zhang, T. Construction of customized sub-databases from ncbi-nr database for rapid annotation of huge metagenomic datasets using a combined blast and megan approach PLoS One 2013, 8 (4) e59831 10.1371/journal.pone.0059831
118. Qin, J.; Li, Y.; Cai, Z.; Li, S.; Zhu, J.; Zhang, F.; Liang, S.; Zhang, W.; Guan, Y.; Shen, D. A metagenome-wide association study of gut microbiota in type 2 diabetes Nature 2012, 490 (7418) 55-60 10.1038/nature11450
119. Markowitz, V. M.; Mavromatis, K.; Ivanova, N. N.; Chen, I. M. A.; Chu, K.; Kyrpides, N. C. IMG ER: a system for microbial genome annotation expert review and curation Bioinformatics 2009, 25 (17) 2271-2278 10.1093/bioinformatics/btp393
120. Aziz, R. K.; Bartels, D.; Best, A. A.; DeJongh, M.; Disz, T.; Edwards, R. A.; Formsma, K.; Gerdes, S.; Glass, E. M.; Kubal, M. The RAST Server: rapid annotations using subsystems technology BMC Genomics 2008, 9 (1) 75-89 10.1186/1471-2164-9-75
121. Wu, S.; Zhu, Z.; Fu, L.; Niu, B.; Li, W. WebMGA: a customizable web server for fast metagenomic sequence analysis BMC Genomics 2011, 12 (1) 444-452 10.1186/1471-2164-12-444
122. Hyatt, D.; Chen, G. L.; LoCascio, P.; Land, M.; Larimer, F.; Hauser, L. Prodigal: prokaryotic gene recognition and translation initiation site identification BMC Bioinf. 2010, 11 (1) 119-129 10.1186/1471-2105-11-119
123. Noguchi, H.; Taniguchi, T.; Itoh, T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes DNA Res. 2008, 15 (6) 387-396 10.1093/dnares/dsn027
124. Zhu, W.; Lomsadze, A.; Borodovsky, M. Ab initio gene identification in metagenomic sequences Nucleic Acids Res. 2010, 38 (12) 132-146 10.1093/nar/gkq275
125. Rho, M.; Tang, H.; Ye, Y. FragGeneScan: predicting genes in short and error-prone reads Nucleic Acids Res. 2010, 38 (20) e191-e191 10.1093/nar/gkq747
126. Hoff, K. J.; Lingner, T.; Meinicke, P.; Tech, M. Orphelia: predicting genes in metagenomic sequencing reads Nucleic Acids Res. 2009, 37 (2) 101-105 10.1093/nar/gkp327
127. Mortazavi, A.; Williams, B. A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 2008, 5 (7) 621-628 10.1038/nmeth.1226
128. Trapnell, C.; Williams, B. A.; Pertea, G.; Mortazavi, A.; Kwan, G.; van Baren, M. J.; Salzberg, S. L.; Wold, B. J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 2010, 28 (5) 511-515 10.1038/nbt.1621
129. Langmead, B.; Salzberg, S. L. Fast gapped-read alignment with Bowtie 2 Nat. Methods 2012, 9 (4) 357-359 10.1038/nmeth.1923
130. Langmead, B.; Trapnell, C.; Pop, M.; Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 2009, 10 (3) R25-R34 10.1186/gb-2009-10-3-r25
131. Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 2009, 25 (14) 1754-1760 10.1093/bioinformatics/btp324
132. Li, H.; Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 2010, 26 (5) 589-595 10.1093/bioinformatics/btp698
133. Kim, D.; Langmead, B.; Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements Nat. Methods 2015, 12 (4) 357-360 10.1038/nmeth.3317
134. Quevillon, E.; Silventoinen, V.; Pillai, S.; Harte, N.; Mulder, N.; Apweiler, R.; Lopez, R. InterProScan: protein domains identifier Nucleic Acids Res. 2005, 33 (suppl 2) W116-W120 10.1093/nar/gki442
135. Finn, R. D.; Clements, J.; Eddy, S. R. HMMER web server: interactive sequence similarity searching Nucleic Acids Res. 2011, 39, 29-37 10.1093/nar/gkr367
136. Marchler-Bauer, A.; Bryant, S. H. CD-Search: protein domain annotations on the fly Nucleic Acids Res. 2004, 32 (2) 327-331 10.1093/nar/gkh454
137. Consortium, U. The universal protein resource (UniProt) Nucleic Acids Res. 2008, 36 (1) 190-195 10.1093/nar/gki070
138. Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M. C.; Estreicher, A.; Gasteiger, E.; Martin, M. J.; Michoud, K.; ODonovan, C.; Phan, I. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 2003, 31 (1) 365-370 10.1093/nar/gkg095
139. Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J. The Pfam protein families database Nucleic Acids Res. 2012, 40, 290-301 10.1093/nar/gkr1065
140. Selengut, J. D.; Haft, D. H.; Davidsen, T.; Ganapathy, A.; Gwinn-Giglio, M.; Nelson, W. C.; Richter, A. R.; White, O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes Nucleic Acids Res. 2007, 35 (1) 260-264 10.1093/nar/gkl1043
141. Powell, S.; Szklarczyk, D.; Trachana, K.; Roth, A.; Kuhn, M.; Muller, J.; Arnold, R.; Rattei, T.; Letunic, I.; Doerks, T. eggNOG v3. 0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges Nucleic Acids Res. 2012, 40 (1) 284-289 10.1093/nar/gkr1060
142. Tatusov, R. L.; Fedorova, N. D.; Jackson, J. D.; Jacobs, A. R.; Kiryutin, B.; Koonin, E. V.; Krylov, D. M.; Mazumder, R.; Mekhedov, S. L.; Nikolskaya, A. N. The COG database: an updated version includes eukaryotes BMC Bioinf. 2003, 4 (1) 41-54 10.1186/1471-2105-4-41
143. Marchler-Bauer, A.; Lu, S.; Anderson, J. B.; Chitsaz, F.; Derbyshire, M. K.; DeWeese-Scott, C.; Fong, J. H.; Geer, L. Y.; Geer, R. C.; Gonzales, N. R. CDD: a Conserved Domain Database for the functional annotation of proteins Nucleic Acids Res. 2011, 39 (1) 225-229 10.1093/nar/gki069
144. Letunic, I.; Doerks, T.; Bork, P. SMART 7: recent updates to the protein domain annotation resource Nucleic Acids Res. 2012, 40 (1) 302-305 10.1093/nar/gkr931
145. Prestat, E.; David, M. M.; Hultman, J.; Taş, N.; Lamendella, R.; Dvornik, J.; Mackelprang, R.; Myrold, D. D.; Jumpponen, A.; Tringe, S. G. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus Nucleic Acids Res. 2014, 42 (19) e145 10.1093/nar/gku702
146. Ju, F.; Xia, Y.; Guo, F.; Wang, Z.; Zhang, T. Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants Environ. Microbiol. 2014, 16 (8) 2421-2432 10.1111/1462-2920.12355
147. Ju, F.; Zhang, T. Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant ISME J. 2015, 9 (3) 683-695 10.1038/ismej.2014.162
148. Peng, X.; Guo, F.; Ju, F.; Zhang, T. Shifts in the Microbial Community, Nitrifiers and Denitrifiers in the Biofilm in a Full-scale Rotating Biological Contactor Environ. Sci. Technol. 2014, 48 (14) 8044-8052 10.1021/es5017087
149. FU, X.; SUN, Y.; WANG, J.; XING, Q.; ZOU, J.; LI, R.; WANG, Z.; WANG, S.; HU, X.; ZHANG, L. Sequencing-based gene network analysis provides a core set of gene resource for understanding thermal adaptation in Zhikong scallop Chlamys farreri Mol. Ecol. Resour. 2014, 14 (1) 184-198 10.1111/1755-0998.12169
150. Vinayagam, A.; Zirin, J.; Roesel, C.; Hu, Y.; Yilmazel, B.; Samsonova, A. A.; Neumüller, R. A.; Mohr, S. E.; Perrimon, N. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions Nat. Methods 2013, 11 (1) 94-99 10.1038/nmeth.2733
151. Chao, Y.; Ma, L.; Yang, Y.; Ju, F.; Zhang, X. X.; Wu, W. M.; Zhang, T. Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment Sci. Rep. 2013, 10.1038/srep03550
152. Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N. S.; Wang, J. T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 2003, 13 (11) 2498-2504 10.1101/gr.1239303
153. Bastian, M.; Heymann, S.; Jacomy, M. Gephi: An Open Source Software for Exploring and Manipulating Networks, International AAAI conference on weblogs and social media, 2009; AAAI Press: Menlo Park, CA, 2009.
154. Langfelder, P.; Horvath, S. WGCNA: an R package for weighted correlation network analysis BMC Bioinf. 2008, 9 (1) 559-571 10.1186/1471-2105-9-559
155. Reddy, T.; Thomas, A. D.; Stamatis, D.; Bertsch, J.; Isbandi, M.; Jansson, J.; Mallajosyula, J.; Pagani, I.; Lobos, E. A.; Kyrpides, N. C. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta) genome project classification Nucleic Acids Res. 2015, 43, 1099-1106 10.1093/nar/gku950
156. Wang, Y.; Xia, Y.; Ju, F.; Zhang, T. Metagenome approaches revealed a biological prospect for improvement on mesophilic cellulose degradation Appl. Microbiol. Biotechnol. 2015, 10.1007/s00253-015-6945-y
157. Yang, Y.; Li, B.; Zou, S.; Fang, H. H.; Zhang, T. Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach Water Res. 2014, 62, 97-106 10.1016/j.watres.2014.05.019
158. Chao, Y.; Mao, Y.; Wang, Z.; Zhang, T. Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing Sci. Rep. 2015, 5, 10044 10.1038/srep10044
159. Guo, F.; Wang, Z. P.; Yu, K.; Zhang, T. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers Sci. Rep. 2015, 5, 7637 10.1038/srep07637
160. Tsementzi, D.; Poretsky, R.; Rodriguez-R, L. M.; Luo, C.; Konstantinidis, K. T. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities Environ. Microbiol. Rep. 2014, 6 (6) 640-655 10.1111/1758-2229.12180
161. Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing Science 2008, 320 (5881) 1344-1349 10.1126/science.1158441
162. Delmont, T. O.; Eren, A. M.; Maccario, L.; Prestat, E.; Esen, Ö. C.; Pelletier, E.; Le Paslier, D.; Simonet, P.; Vogel, T. M. Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics Front. Microbiol. 2015, 6, 358-373 10.3389/fmicb.2015.00358
163. Benndorf, D.; Balcke, G. U.; Harms, H.; Von Bergen, M. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater ISME J. 2007, 1 (3) 224-234 10.1038/ismej.2007.39
164. Rotaru, A.-E.; Shrestha, P. M.; Liu, F.; Shrestha, M.; Shrestha, D.; Embree, M.; Zengler, K.; Wardman, C.; Nevin, K. P.; Lovley, D. R. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane Energy Environ. Sci. 2014, 7 (1) 408-415 10.1039/C3EE42189A
165. Hess, M.; Sczyrba, A.; Egan, R.; Kim, T.-W.; Chokhawala, H.; Schroth, G.; Luo, S.; Clark, D. S.; Chen, F.; Zhang, T. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen Science 2011, 331 (6016) 463-467 10.1126/science.1200387
166. Li, L. G.; Cai, L.; Zhang, X. X.; Zhang, T. Potentially novel copper resistance genes in copper-enriched activated sludge revealed by metagenomic analysis Appl. Microbiol. Biotechnol. 2014, 99 (18) 7771-7779
167. Wang, Z. P.; Guo, F.; Liu, L. L.; Zhang, T. Evidence of carbon fixation pathway in a bacterium from Candidate Phylum SBR1093 revealed with genomic analysis PLoS One 2014, 9 (10) e109571 10.1371/journal.pone.0109571