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Chapter 2.4.1 : Introduction to Microbial Community Analysis of Environmental Samples with Next-Generation Sequencing

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Introduction to Microbial Community Analysis of Environmental Samples with Next-Generation Sequencing, Page 1 of 2

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Abstract:

In this introduction, we briefly survey developments in next-generation sequencing that have been applied to environmental microbiology, consider both major advances and areas where progress has been slow, and highlight chapters in this and other sections of the MEM4 relevant to nucleic acid-based molecular analyses of microbial communities. Experts on various aspects of next-generation sequencing have contributed to this section, including chapters addressing the analysis of microbial communities through the study of (a) ribosomal RNA gene amplicons (Ionescu); (b) shotgun metagenomic sequence data (Lal and Sangwan); and (c) shotgun metatranscriptomic sequence data (Sarode et al.). In addition, this section includes a chapter reviewing functional metagenomics (Marchesi and Morris) and sequencing platforms for environmental microbiologists (Green).

Citation: Green S, Neufeld J. 2016. Introduction to Microbial Community Analysis of Environmental Samples with Next-Generation Sequencing, p 2.4.1-1-2.4.1-6. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch2.4.1
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References

/content/book/10.1128/9781555818821.ch2.4.1
1. Brisson VL, West KA, Lee PK, Tringe SG, Brodie EL, Alvarez-Cohen L. 2012. Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6:17021714.[PubMed][CrossRef]
2. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK. 2011. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480:368371.[PubMed][CrossRef]
3. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Jian M, Zhou Y, Li Y, Zhang X, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:5965.[PubMed][CrossRef]
4. Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE. 2011. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol 77:80718079.[PubMed][CrossRef]
5. Neufeld JD, Dumont MG, Vohra J, Murrell JC. 2007. Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53:435442.[PubMed][CrossRef]
6. Ramette A. 2007. Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62:142160.[PubMed][CrossRef]
7. Iverson V, Morris RM, Frazar CD, Berthiaume CT, Morales RL, Armbrust EV. 2012. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335:587590.[PubMed][CrossRef]
8. Scholz MB, Lo CC, Chain PS. 2012. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr Opin Biotechnol 23:915.[PubMed][CrossRef]
9. Hoshino T, Inagaki F. 2012. Molecular quantification of environmental DNA using microfluidics and digital PCR. Syst Appl Microbiol 35:390395.[PubMed][CrossRef]
10. Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. 2011. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl Environ Microbiol 77:38463852.[PubMed][CrossRef]
11. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 108: 45164522.[CrossRef]
12. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7:335336.[CrossRef]
13. Green SJ, Leigh MB, Neufeld JD,. 2009. Denaturing gradient gel electrophoresis (DGGE) for microbial community analysis, p 41374158. In Timmis KN (ed.), Handbook of Hydrocarbon and Lipid Microbiology. Springer, Heidelberg.
14. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kampfer P, Maiden MCJ, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Micr 52:10431047.[CrossRef]
15. Stackebrandt E, Goebel BM. 1994. A place for DNA-DNA reassociation and 16s ribosomal RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846849.[CrossRef]
16. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249266.[PubMed][CrossRef]
17. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:8191.[PubMed][CrossRef]
18. Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo C, Poretsky R, Konstantinidis KT. 2011. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77:60006011.[PubMed][CrossRef]
19. Zomorrodi AR, Maranas CD. 2012. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol 8:e1002363.[PubMed][CrossRef]
20. Edwards JS, Covert M, Palsson B. 2002. Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4:133140.[PubMed][CrossRef]
21. Park JH, Lee KH, Kim TY, Lee SY. 2007. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci USA 104:77977802.[PubMed][CrossRef]
22. Nealson KH, Venter JC. 2007. Metagenomics and the global ocean survey: what's in it for us, and why should we care? ISME J 1:185187.[PubMed][CrossRef]
23. 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 312:13551359.[PubMed][CrossRef]
24. Mocali S, Benedetti A. 2010. Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497505.[PubMed][CrossRef]
25. Schloss PD, Handelsman J. 2005. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 6:229.[PubMed][CrossRef]
26. Croucher NJ, Thomson NR. 2010. Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 13:619624.[PubMed][CrossRef]
27. Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, Joint I. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS One 3:e3042.[PubMed][CrossRef]
28. Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, Pickering M, Pate WM, Moran MA, Hollibaugh JT. 2005. Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71:41214126.[PubMed][CrossRef]
29. Liang P, Pardee AB. 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967971.[PubMed][CrossRef]
30. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. 1995. Serial analysis of gene expression. Science 270:484487.[PubMed][CrossRef]
31. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC. 2008. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLOS ONE 3:e2527.[PubMed][CrossRef]
32. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB. 2007. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:70597066.[PubMed][CrossRef]
33. Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F. 2010. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010:pdb prot5368.[CrossRef]
34. Willner D, Hugenholtz P. 2013. Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clin Microbiol Newsl 35:19.[CrossRef]
35. Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R. 2003. Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl Environ Microbiol 69:14081416.[PubMed][CrossRef]
36. Woyke T, Xie G, Copeland A, Gonzalez 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.[PubMed][CrossRef]
37. Suenaga H. 2012. Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ Microbiol 14:1322.[PubMed][CrossRef]
38. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. 2011. UniFrac: an effective distance metric for microbial community comparison. ISME J 5:169172.[PubMed][CrossRef]
39. Warwick RM, Clarke KR. 2006. Primer 6. Primer-E, Plymouth.
40. Prosser JI, Bohannan BJ, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JP. 2007. The role of ecological theory in microbial ecology. Nat Rev Microbiol 5:384392.[PubMed][CrossRef]
41. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12:118123.[PubMed][CrossRef]
42. Prosser JI. 2010. Replicate or lie. Environ Microbiol 12:18061810.[PubMed][CrossRef]
43. Eisenstein M. 2012. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30:295296.[PubMed][CrossRef]
44. Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE. 2012. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 30:701707.[PubMed][CrossRef]
45. Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S. 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278288.[PubMed][CrossRef]
46. Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. 2001. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181184.[PubMed][CrossRef]
47. Kembel SW, Wu M, Eisen JA, Green JL. 2012. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol 8:e1002743.[PubMed][CrossRef]
48. Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. 2012. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13:1.[PubMed][CrossRef]
49. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:75377541.[PubMed][CrossRef]
50. He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1:6777.[PubMed][CrossRef]
51. DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL. 2011. PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol 77:63136322.[PubMed][CrossRef]

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