Data analysis for 16S microbial profiling from different benchtop sequencing platforms

Journal of Microbiological Methods

Volumn 107, Issue , 2014, Pages 30-37

  Pylro, Victor S ^a,c   Roesch, Luiz Fernando W ^b   Morais, Daniel K ^a,c   Clark, Ian M ^c   Hirsch, Penny R ^c   Tótola, Marcos R ^a  

^a FEDERAL UNIVERSITY OF VIÇOSA   (Brazil)

^b UNIVERSIDADE FEDERAL DO PAMPA   (Brazil)

^c ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

Alpha diversity; Amplicons; Beta diversity; Microbial community analysis; Next generation sequencing

Indexed keywords

RNA 16S;

16S RRNA GENE; ALPHA DIVERSITY; ARTICLE; BETA DIVERSITY; BRAZIL; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; HIGH THROUGHPUT SEQUENCING; ILLUMINA MISEQ PLATFORM; MEASUREMENT; MICROBIAL COMMUNITY; NONHUMAN; PERSONAL GENOME MACHINE PLATFORM; PHYLOGENETIC DIVERSITY WHOLE TREE; PHYLOGENY; PROCRUSTES ANALYSIS; QIIME PIPELINE; RNA GENE; SHANNON INDEX; SIMPSON INDEX; SPECIES DIVERSITY; STATISTICAL ANALYSIS; UPARSE PIPELINE; ARCHAEON; BACTERIUM; BIOLOGY; CLASSIFICATION; GENETICS; METAGENOME; MICROBIOLOGY; PROCEDURES;

ARCHAEA; BACTERIA; BRAZIL; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84907525758     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2014.08.018     Document Type: Article

References (27)

1. Angiuoli S.V., Matalka M., Gussman G., Galens K., Vangala M., Riley D.R., et al. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinforma. 2011, 12:356. 10.1186/1471-2105-12-356.
2. Aronesty E. Comparison of sequencing utility programs. Open Bioinforma. J. 2013, 7:1-8. 10.2174/1875036201307010001.
3. Bokulich N.A., Subramanian S., Fait J.J., Gevers D., Gordon J.I., Knight R., Mills D.A., Caporaso J.G. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 2013, 10:57-59.
4. Bragg L.M., Stone G., Butler M.K., Hugenholtz P., Tyson G.W. Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput. Biol. 2013, 9:e1003031. 10.1371/journal.pcbi.1003031.
5. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7(5):335-336.
6. Caporaso J.G., Lauber C.L., Costello E.K., Berg-Lyons D., Gonzalez A., Stombaugh J., et al. Moving pictures of the human microbiome. Genome Biol. 2011, 12(5):R50. 10.1186/gb-2011-12-5-r50.
7. Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
8. Chao A., Chiu C., Jost L. Phylogenetic diversity measures based on Hill numbers. Philos. Trans. R. Soc. B 2010, 365(1558):3599-3609.
9. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460-2461. 10.1093/bioinformatics/btq461.
10. Edgar R.C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 2013, 10:996-998.
11. Group Jumpstart Consortium Human Microbiome Project Data Generation Working Group Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS ONE 2012, 7(6):e39315. 10.1371/journal.pone.0039315.
12. Hayden E.C. Technology: the $1000 genome. Nature 2014, 507:294-295. 10.1038/507294a.
13. Holmes S., McMurdie P.J. Statistical data analysis challenges from the microbiome. The Social Biology of Microbial Communities 2012, 275-303. L. Olsen, E.R. Choffnes, A. Mack (Eds.).
14. Jünemann S., Sedlazeck F.J., Prior K., Albersmeier A., John U., Kalinowski J., et al. Updating benchtop sequencing performance comparison. Nat. Biotechnol. 2013, 31:294-296.
15. Koeppel A.F., Wu M. Surprisingly extensive mixed phylogenetic and ecological signals among bacterial operational taxonomic units. Nucleic Acids Res. 2013, 41(10):5175-5188.
16. Krzanowski W.J. Between-group analysis with heterogeneous covariance matrices: the common principal component model. J. Classif. 1990, 7:81-98.
17. Liu Z., Lozupone C., Hamady M., Bushman F.D., Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007, 35:e120.
18. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012, 30:434-439.
19. Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 2005, 71:8228-8235.
20. Pallen M.J. Updating benchtop sequencing performance comparison reply. Nat. Biotechnol. 2013, 31. (296-296).
21. Pylro V.S., Roesch L.F., Ortega J.M., Amaral A.M., Tótola M.R., Hirsch P.R., et al. Brazilian microbiome project: revealing the unexplored microbial diversity - challenges and prospects. Microb. Ecol. 2014, 67:237-241.
22. Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013, 41(D1):D590-D596.
23. Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475:348-352.
24. Schloss P.D. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput. Biol. 2010, 6(7):e1000844. 10.1371/journal.pcbi.1000844.
25. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
26. Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 2011, 6:e27310.
27. Simpson E.H. Measurement of diversity. Nature 1949, 163:688.