Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

PeerJ

Volumn 2016, Issue 9, 2016, Pages

  Rinke, Christian ^a   Low, Serene ^a   Woodcroft, Ben J ^a   Raina, Jean Baptiste ^b   Skarshewski, Adam ^a   Le, Xuyen H ^a   Butler, Margaret K ^a   Stocker, Roman ^c   Seymour, Justin ^b   Tyson, Gene W ^a   Hugenholtz, Philip ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF TECHNOLOGY SYDNEY   (Australia)

^c ETH ZURICH   (Switzerland)

Author keywords

100 fg; Illumina; Low biomass; Low input DNA library; Low volume; Marine microheterogeneity; Microscale metagenomics; Nextera XT; Picogram; Reagent contamination

Indexed keywords

ACTINOBACTERIA; ANALYTIC METHOD; ARTICLE; BACTERIUM ISOLATE; BIOMASS; CONTROLLED STUDY; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; ECOSYSTEM MONITORING; FEMTOGRAPHY; FIRMICUTES; GEL ELECTROPHORESIS; HIGH THROUGHPUT SEQUENCING; MARINE BIOLOGY; METAGENOMICS; MICROBIAL COMMUNITY; NONHUMAN; PICOGRAPHY; POLYMERASE CHAIN REACTION; POSITION WEIGHT MATRIX; PROTEOBACTERIA; VALIDATION PROCESS;

EID: 84991293701     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.2486     Document Type: Article

References (58)

1. Adey A, Morrison HG, Asan, Xun X, Kitzman JO, Turner EH, Stackhouse B, MacKenzie AP, Caruccio NC, Zhang X, Shendure J. 2010. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biology 11(12):R119 DOI 10.1186/gb-2010-11-12-r119.
2. Azam F. 1998. Microbial control of oceanic carbon flux: the plot thickens. Science 280(5364):694-696 DOI 10.1126/science.280.5364.694.
3. Azam F, Malfatti F. 2007. Microbial structuring of marine ecosystems. Nature Reviews Microbiology 5(10):782-791 DOI 10.1038/nrmicro1747.
4. Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, Ngan CY, Cheng J-F, Tringe SG, Woyke T. 2015. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics 16(1):856 DOI 10.1186/s12864-015-2063-6.
5. Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12(1):59-60 DOI 10.1038/nmeth.3176.
6. Button DK, Robertson BR. 2001. Determination of DNA content of aquatic bacteria by flow cytometry. Applied and Environmental Microbiology 67(4):1636-1645 DOI 10.1128/AEM.67.4.1636-1645.2001.
7. Caruccio N. 2011. Preparation of next-generation sequencing libraries using NexteraTM technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. In: Kwon YM, Ricke SC, eds. High-Throughput Next Generation Sequencing. New York: Humana Press.
8. Chafee M, Maignien L, Simmons SL. 2015. The effects of variable sample biomass on comparative metagenomics. Environmental Microbiology 17(7):2239-2253 DOI 10.1111/1462-2920.12668.
9. Chen Y-C, Liu T, Yu C-H, Chiang T-Y, Hwang C-C. 2013. Effects of GC bias in next-generationsequencing data on de novo genome assembly. PLoS ONE 8(4):e62856 DOI 10.1371/journal.pone.0062856.
10. Clingenpeel S, Clum A, Schwientek P, Rinke C, Woyke T. 2015. Reconstructing each cell's genome within complex microbial communities-dream or reality? Microbial Physiology and Metabolism 5:771 DOI 10.3389/fmicb.2014.00771.
11. Crooks GE, Hon G, Chandonia J-M, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Research 14(6):1188-1190 DOI 10.1101/gr.849004.
12. de la Cruz NB,Weinreich MD,Wiegand TW, Krebs MP, Reznikoff WS. 1993. Characterization of the Tn5 transposase and inhibitor proteins: a model for the inhibition of transposition. Journal of Bacteriology 175(21):6932-6938.
13. Dröge J, McHardy AC. 2012. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Briefings in Bioinformatics 13(6):646-655 DOI 10.1093/bib/bbs031.
14. Duhaime MB, Deng L, Poulos BT, Sullivan MB. 2012. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environmental Microbiology 14(9):2526-2537 DOI 10.1111/j.1462-2920.2012.02791.x.
15. Ekblom R,Wolf JBW. 2014. A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications 7(9):1026-1042 DOI 10.1111/eva.12178.
16. Gilbert JA, Dupont CL. 2011. Microbial metagenomics: beyond the genome. Annual Review of Marine Science 3(1):347-371 DOI 10.1146/annurev-marine-120709-142811.
17. Gomez-Alvarez V, Teal TK, Schmidt TM. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME Journal 3(11):1314-1317 DOI 10.1038/ismej.2009.72.
18. Goryshin IY, Miller JA, Kil YV, Lanzov VA, Reznikoff WS. 1998. Tn5/IS50 target recognition. Proceedings of the National Academy of Sciences of the United States of America 95(18):10716-10721 DOI 10.1073/pnas.95.18.10716.
19. Kallmeyer J, Pockalny R, Adhikari RR, Smith DC, D'Hondt S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America 109(40):16213-16216 DOI 10.1073/pnas.1203849109.
20. Kang DD, Froula J, Egan R, Wang Z. 2015. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3(8):e1165 DOI 10.7717/peerj.1165.
21. Kircher M, Sawyer S, Meyer M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40(1):e3 DOI 10.1093/nar/gkr771.
22. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nature Methods 6(4):291-295 DOI 10.1038/nmeth.1311.
23. Lamble S, Batty E, Attar M, Buck D, Bowden R, Lunter G, Crook D, El-Fahmawi B, Piazza P. 2013. Improved workflows for high throughput library preparation using the transposomebased nextera system. BMC Biotechnology 13(1):104 DOI 10.1186/1472-6750-13-104.
24. Leung HCM, Wang Y, Yiu SM, Chin FYL. 2013. Next-generation sequencing on metagenomic data: assembly and binning. In: Nelson KE, ed. Encyclopedia of Metagenomics. New York: Springer, 1-7.
25. Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Available at http://arxiv.org/abs/1303.3997 [q-bio].
26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078-2079 DOI 10.1093/bioinformatics/btp352.
27. Long RA, Azam F. 2001. Microscale patchiness of bacterioplankton assemblage richness in seawater. Aquatic Microbial Ecology 26:103-113 DOI 10.3354/ame026103.
28. Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15(12):550 DOI 10.1186/s13059-014-0550-8.
29. Lusk RW. 2014. Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. PLoS ONE 9(10):e110808 DOI 10.1371/journal.pone.0110808.
30. 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. Applied and Environmental Microbiology 77(22):8071-8079 DOI 10.1128/AEM.05610-11.
31. 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(6):495-500 DOI 10.1038/nmeth1043.
32. Otto M. 2010. Staphylococcus colonization of the skin and antimicrobial peptides. Expert Review of Dermatology 5(2):183-195 DOI 10.1586/edm.10.6.
33. Paerl HW, Pinckney JL. 1996. A mini-review of microbial consortia: their roles in aquatic production and biogeochemical cycling. Microbial Ecology 31(3):225-247 DOI 10.1007/BF00171569.
34. Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, Buck D, Ragoussis J, Ponting CP, Fischer MD. 2012. Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Research 22(1):125-133 DOI 10.1101/gr.124016.111.
35. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. PeerJ PrePrints 2:e554v1 DOI 10.7287/peerj.preprints.554v1.
36. Probst AJ, Auerbach AK, Moissl-Eichinger C. 2013. Archaea on human skin. PLoS ONE 8(6): e65388 DOI 10.1371/journal.pone.0065388.
37. Probst AJ, Weinmaier T, DeSantis TZ, Santo Domingo JW, Ashbolt N. 2015. New perspectives on microbial community distortion after whole-genome amplification. PLoS ONE 10(5): e124158 DOI 10.1371/journal.pone.0124158.
38. Raghunathan A, Ferguson HR, Bornarth CJ, Song W, Driscoll M, Lasken RS. 2005. Genomic DNA amplification from a single bacterium. Applied and Environmental Microbiology 71(6):3342-3347 DOI 10.1128/AEM.71.6.3342-3347.2005.
39. Rappe MS, Giovannoni SJ. 2003. The uncultured microbial majority. Annual Review of Microbiology 57(1):369-394 DOI 10.1146/annurev.micro.57.030502.090759.
40. Reddy TBK, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos EA, Kyrpides NC. 2015. The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta) genome project classification. Nucleic Acids Research 43(D1):D1099-D1106 DOI 10.1093/nar/gku950.
41. Risso D, Schwartz K, Sherlock G, Dudoit S. 2011. GC-content normalization for RNA-Seq data. BMC Bioinformatics 12(1):480 DOI 10.1186/1471-2105-12-480.
42. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. 2014. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology 12(1):87 DOI 10.1186/s12915-014-0087-z.
43. Schneider TD, Stephens RM. 1990. Sequence logos: a new way to display consensus sequences. Nucleic Acids Research 18(20):6097-6100 DOI 10.1093/nar/18.20.6097.
44. Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M. 2013. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environmental Microbiology 15(6):1882-1899 DOI 10.1111/1462-2920.12086.
45. Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. 2014. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biology 15:420 DOI 10.1186/s13059-014-0420-4.
46. Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB. 2013. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 14(1):320 DOI 10.1186/1471-2164-14-320.
47. Steiniger M, Adams CD, Marko JF, Reznikoff WS. 2006. Defining characteristics of Tn5 Transposase non-specific DNA binding. Nucleic Acids Research 34(9):2820-2832 DOI 10.1093/nar/gkl179.
48. Stocker R. 2012. Marine microbes see a sea of gradients. Science 338(6107):628-633 DOI 10.1126/science.1208929.
49. Stocker R, Seymour JR. 2012. Ecology and physics of bacterial chemotaxis in the ocean. Microbiology and Molecular Biology Reviews 76(4):792-812 DOI 10.1128/MMBR.00029-12.
50. Strong MJ, Xu G, Morici L, Bon-Durant SS, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK. 2014. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathogens 10(11):e1004437 DOI 10.1371/journal.ppat.1004437.
51. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10):1282-1288 DOI 10.1093/bioinformatics/btm098.
52. Syed F, Grunenwald H, Caruccio N. 2009. Next-generation sequencing library preparation: simultaneous fragmentation and tagging using in vitro transposition. Nature Methods 6:1-2.
53. Vaishampayan P, Probst AJ, La Duc MT, Bargoma E, Benardini JN, Andersen GL, Venkateswaran K. 2013. New perspectives on viable microbial communities in low-biomass cleanroom environments. ISME Journal 7(2):312-324 DOI 10.1038/ismej.2012.114.
54. Weon H-Y, Kim B-Y, Joa J-H, Son J-A, Song M-H, Kwon S-W, Go S-J, Yoon S-H. 2008. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. International Journal of Systematic and Evolutionary Microbiology 58(1):93-96 DOI 10.1099/ijs.0.65047-0.
55. Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D, Clingenpeel S, Malmstrom R, Stepanauskas R, Cheng J-F. 2011. Decontamination of MDA reagents for single cell whole genome amplification. PLoS ONE 6(10):e26161 DOI 10.1371/journal.pone.0026161.
56. Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S. 2012. FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS ONE 7(12):e52249 DOI 10.1371/journal.pone.0052249.7.
57. Yilmaz S, Allgaier M, Hugenholtz P. 2010. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods 7(12):943-944 DOI 10.1038/nmeth1210-943.
58. Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. 2014. Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics 30(8):1073-1080 DOI 10.1093/bioinformatics/btt771.