16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles

Microbiome

Volumn 2, Issue 1, 2014, Pages

  Hang, Jun ^a   Desai, Valmik ^b   Zavaljevski, Nela ^b   Yang, Yu ^a   Lin, Xiaoxu ^a   Satya, Ravi V ^b,d   Martinez, Luis J ^a   Blaylock, Jason M ^a,c   Jarman, Richard G ^a   Thomas, Stephen J ^a   Kuschner, Robert A ^a  

^a WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^b U S ARMY MEDICAL RESEARCH AND MATERIEL COMMAND   (United States)

^c Department of Pulmonary and Critical Care Medicine   (United States)

^d Qiagen Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RNA 16S;

ARTICLE; CONTROLLED STUDY; CYTOLYSIS; DNA EXTRACTION; DNA PURIFICATION; GENE SEQUENCE; HUMAN; INCUBATION TEMPERATURE; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; POLYMERASE CHAIN REACTION; PRINCIPAL COORDINATE ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; PYROSEQUENCING; SAMPLING; THERMOSTABILITY;

BACTERIA (MICROORGANISMS);

EID: 84938484290     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-2-31     Document Type: Article

References (54)

1. Blaser M, Bork P, Fraser C, Knight R, Wang J. The microbiome explored: recent insights and future challenges. Nat Rev Microbiol 2013, 11(3):213-217. 10.1038/nrmicro2973, 23377500.
2. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. Moving pictures of the human microbiome. Genome Biol 2011, 12(5):R50. 10.1186/gb-2011-12-5-r50, 3271711, 21624126.
3. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009, 326(5960):1694-1697. 10.1126/science.1177486, 3602444, 19892944.
4. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM. Biogeography of the ecosystems of the healthy human body. Genome Biol 2013, 14(1):R1. 10.1186/gb-2013-14-1-r1, 4054670, 23316946.
5. Human Microbiome Project C A framework for human microbiome research. Nature 2012, 486(7402):215-221. 10.1038/nature11209, 3377744, 22699610, Human Microbiome Project C.
6. Human Microbiome Project C Structure, function and diversity of the healthy human microbiome. Nature 2012, 486(7402):207-214. 10.1038/nature11234, 3564958, 22699609, Human Microbiome Project C.
7. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, et al. Human Microbiome Jumpstart Reference Strains Consortium A catalog of reference genomes from the human microbiome. Science 2010, 328(5981):994-999. 2940224, 20489017, Human Microbiome Jumpstart Reference Strains Consortium.
8. Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol 2012, 7:99-122. 10.1146/annurev-pathol-011811-132421, 21910623.
9. Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature 2014, 509(7500):357-360. 10.1038/nature13178, 24739969.
10. Ren T, Glatt DU, Nguyen TN, Allen EK, Early SV, Sale M, Winther B, Wu M. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids. Environ Microbiol 2013, 15(2):535-547. 10.1111/1462-2920.12000, 23113966.
11. Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H. Towards the human colorectal cancer microbiome. PloS one 2011, 6(5):e20447. 10.1371/journal.pone.0020447, 3101260, 21647227.
12. Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L. Human gut microbiome and risk for colorectal cancer. J Natl Canc Inst 2013, 105(24):1907-1911.
13. Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, Schloss PD. The gut microbiome modulates colon tumorigenesis. mBio 2013, 4(6):e00692-00613. 3892781, 24194538.
14. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444(7122):1027-1031. 10.1038/nature05414, 17183312.
15. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PloS one 2014, 9(1):e84689. 10.1371/journal.pone.0084689, 3885756, 24416266.
16. Naseer MI, Bibi F, Alqahtani MH, Chaudhary AG, Azhar EI, Kamal MA, Yasir M. Role of gut microbiota in obesity, type 2 diabetes and Alzheimer's disease. CNS Neurol Disord Drug Targets 2014, 13(2):305-311. 10.2174/18715273113126660147, 24059313.
17. Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PloS one 2010, 5(2):e9085. 10.1371/journal.pone.0009085, 2816710, 20140211.
18. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2012, 13(1):47-58.
19. Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The " most wanted" taxa from the human microbiome for whole genome sequencing. PloS one 2012, 7(7):e41294. 10.1371/journal.pone.0041294, 3406062, 22848458.
20. Group NHW, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, et al. The NIH Human Microbiome Project. Genome Res 2009, 19(12):2317-2323. 2792171, 19819907.
21. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J 2010, 4(5):642-647. 10.1038/ismej.2009.153, 20090784.
22. Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 2009, 19(7):1141-1152. 10.1101/gr.085464.108, 3776646, 19383763.
23. Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 2010, 307(1):80-86. 10.1111/j.1574-6968.2010.01965.x, 3148093, 20412303.
24. Biesbroek G, Sanders EA, Roeselers G, Wang X, Caspers MP, Trzcinski K, Bogaert D, Keijser BJ. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PloS one 2012, 7(3):e32942. 10.1371/journal.pone.0032942, 3295791, 22412957.
25. Lozupone C, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, Jansson JK, Gordon JI, Knight R. Meta-analyses of studies of the human microbiota. Genome Res 2013, 23(10):1704-1714. 10.1101/gr.151803.112, 3787266, 23861384.
26. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, Hwang J, Chen J, Berkowsky R, Nessel L, Li H, Bushman FD. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 2010, 10:206. 10.1186/1471-2180-10-206, 2921404, 20673359.
27. Jumpstart Consortium Human Microbiome Project Data Generation Working G Evaluation of 16S rDNA-based community profiling for human microbiome research. PloS one 2012, 7(6):e39315. 10.1371/journal.pone.0039315, 3374619, 22720093, Jumpstart Consortium Human Microbiome Project Data Generation Working G.
28. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PloS one 2011, 6(12):e27310. 10.1371/journal.pone.0027310, 3237409, 22194782.
29. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3-new capabilities and interfaces. Nucleic Acids Res 2012, 40(15):e115. 10.1093/nar/gks596, 3424584, 22730293.
30. Sacchi CT, Whitney AM, Mayer LW, Morey R, Steigerwalt A, Boras A, Weyant RS, Popovic T. Sequencing of 16S rRNA gene: a rapid tool for identification of Bacillus anthracis. Emerg Infect Dis 2002, 8(10):1117-1123. 10.3201/eid0810.020391, 2730316, 12396926.
31. Wang Y, Qian PY. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PloS one 2009, 4(10):e7401. 10.1371/journal.pone.0007401, 2754607, 19816594.
32. Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z. Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol 2010, 16(33):4135-4144. 10.3748/wjg.v16.i33.4135, 2932916, 20806429.
33. Amplification primers. [http://vamps.mbl.edu/resources/primers.php].
34. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73(16):5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.
35. Group HDGW: 16S 454 Default Protocol Version 4.2-Pilot Study P.1 (15). [http://www.hmpdacc.org/doc/HMP_MDG_454_16S_Protocol.pdf].
36. 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. QIIME allows analysis of high-throughput community sequencing data. Br J Pharmacol 2010, 7(5):335-336.
37. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27(16):2194-2200. 10.1093/bioinformatics/btr381, 3150044, 21700674.
38. Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J 2011, 5(2):169-172. 10.1038/ismej.2010.133, 3105689, 20827291.
39. HMP: hypothesis testing and power calculations for comparing metagenomic samples from HMP. R-package. [http://cran.r-project.org/web/packages/HMP/index.html].
40. La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PloS one 2012, 7(12):e52078. 10.1371/journal.pone.0052078, 3527355, 23284876.
41. metagenomeSeq: statistical analysis for sparse high-throughput sequencing. [http://www.bioconductor.org/packages/devel/bioc/vignettes/metagenomeSeq/inst/doc/metagenomeSeq.pdf].
42. Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods 2013, 10(12):1200-1202. 10.1038/nmeth.2658, 4010126, 24076764.
43. Cabrera-Rubio R, Garcia-Nunez M, Seto L, Anto JM, Moya A, Monso E, Mira A. Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J Clin Microbiol 2012, 50(11):3562-3568. 10.1128/JCM.00767-12, 3486223, 22915614.
44. Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PloS one 2012, 7(8):e43093. 10.1371/journal.pone.0043093, 3419673, 22905208.
45. 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. 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, 2786419, 19801464.
46. Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38. 10.1186/1471-2105-12-38, 3045300, 21276213.
47. Willner D, Daly J, Whiley D, Grimwood K, Wainwright CE, Hugenholtz P. Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PloS one 2012, 7(4):e34605. 10.1371/journal.pone.0034605, 3326054, 22514642.
48. Zhao J, Li J, Schloss PD, Kalikin LM, Raymond TA, Petrosino JF, Young VB, LiPuma JJ. Effect of sample storage conditions on culture-independent bacterial community measures in cystic fibrosis sputum specimens. J Clin Microbiol 2011, 49(10):3717-3718. 10.1128/JCM.01189-11, 3187318, 21865433.
49. Cardona S, Eck A, Cassellas M, Gallart M, Alastrue C, Dore J, Azpiroz F, Roca J, Guarner F, Manichanh C. Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol 2012, 12:158. 10.1186/1471-2180-12-158, 3489833, 22846661.
50. Rubin BE, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA. Investigating the impact of storage conditions on microbial community composition in soil samples. PloS one 2013, 8(7):e70460. 10.1371/journal.pone.0070460, 3729949, 23936206.
51. Carroll IM, Ringel-Kulka T, Siddle JP, Klaenhammer TR, Ringel Y. Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage. PloS one 2012, 7(10):e46953. 10.1371/journal.pone.0046953, 3465312, 23071673.
52. Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PloS one 2012, 7(9):e42786. 10.1371/journal.pone.0042786, 3435383, 22970118.
53. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011, 184(8):957-963. 10.1164/rccm.201104-0655OC, 3208663, 21680950.
54. Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R. Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio 2010, 1(3):e00129-10. 2925076, 20802827.