Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

PeerJ

Volumn 2014, Issue 1, 2014, Pages

  Rideout, Jai Ram ^a,b   He, Yan ^c   Navas Molina, Jose A ^d   Walters, William A ^e   Ursell, Luke K ^e   Gibbons, Sean M ^f,g   Chase, John ^a   McDonald, Daniel ^d,e   Gonzalez, Antonio ^e   Robbins Pianka, Adam ^d,e   Clemente, Jose C ^b   Gilbert, Jack A ^f,g   Huse, Susan M ^h   Zhou, Hong Wei ^c   Knight, Rob ^e,i   Gregory Caporaso, J ^a  

^a NORTHERN ARIZONA UNIVERSITY   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c SOUTHERN MEDICAL UNIVERSITY   (China)

^d University of Colorado at Boulder   (United States)

^e UNIVERSITY OF COLORADO   (United States)

^f UNIVERSITY OF CHICAGO   (United States)

^g ARGONNE NATIONAL LABORATORY   (United States)

^h BROWN UNIVERSITY   (United States)

ⁱ HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Bioinformatics; Microbial ecology; Microbiome; OTU picking; Qiime

Indexed keywords

RNA 16S;

AMPLICON; ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; CORRELATION COEFFICIENT; DNA SEQUENCE; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC VARIABILITY; HUMAN; MARKER GENE; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TAXONOMIC IDENTIFICATION;

EID: 84920714710     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.545     Document Type: Article

References (19)

1. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña 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, WaltersWA,Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7(5):335-336 DOI 10.1038/nmeth.f.303.
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. 2011. Moving pictures of the human microbiome. Genome Biology 12(5):R50 DOI 10.1186/gb-2011-12-5-r50.
3. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326(5960):1694-1697 DOI 10.1126/science.1177486.
4. Cutting DR, Karger DR, Pedersen JO, Tukey JW. 1992. Scatter/gather: a cluster-based approach to browsing large document collections. In: Proceedings of the 15th annual international ACM SIGIR conference on research and development in information retrieval, SIGIR'92. New York, NY: ACM, 318-329 DOI 10.1145/133160.133214.
5. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology 72(7):5069-5072 DOI 10.1128/AEM.03006-05.
6. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460-2461 DOI 10.1093/bioinformatics/btq461.
7. Eren AM,Maignien L, Sul WJ,Murphy LG, Grim SL,Morrison HG, Sogin ML. 2013. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods in Ecology and Evolution/British Ecological Society 4(12):1111-1119 DOI 10.1111/2041-210X.12114.
8. Faith DP. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61(1):1-10 DOI 10.1016/0006-3207(92)91201-3.
9. Gilbert JA,Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Gevers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N,Mackelprang R,McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R. 2010. Meeting report: the terabase metagenomics workshop and the vision of an Earth Microbiome Project. Standards in Genomic Sciences 3(3):243-248 DOI 10.4056/sigs.1433550.
10. Jensen EC, Beitzel SM, Pilotto AJ, Goharian N, Frieder O. 2002. Parallelizing the buckshot algorithm for efficient document clustering. In: Proceedings of the eleventh international conference on information and knowledge management, CIKM '02. New York, NY: ACM, 684-686 DOI 10.1145/584792.584919.
11. Lauber CL, Hamady M, Knight R, Fierer N. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75(15):5111-5120 DOI 10.1128/AEM.00335-09.
12. Li W, Godzik A. 2006. Cd-Hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658-1659 DOI 10.1093/bioinformatics/btl158.
13. Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 71(12):8228-8235 DOI 10.1128/AEM.71.12.8228-8235.2005.
14. Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27(2):209-220.
15. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J,Wendel D,Wilke A, Huse S, Hufnagle J,Meyer F, Knight R, Caporaso JG. 2012a. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience 1(1):7 DOI 10.1186/2047-217X-1-7.
16. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. 2012b. An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. The ISME Journal 6(3):610-618 DOI 10.1038/ismej.2011.139.
17. Navas-Molina JA, Peralta-Sánchez JM, González A,McMurdie PJ, Vázquez-Baeza Y, Xu Z, Ursell LK, Lauber C, Zhou H, Song SJ, Huntley J, Ackermann GL, Berg-Lyons D, Holmes S, Caporaso JG, Knight R. 2013. Advancing our understanding of the human microbiome using QIIME. Methods in Enzymology 531:371-444 DOI 10.1016/B978-0-12-407863-5.00019-8.
18. Schloss PD,Westcott SL. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Applied and Environmental Microbiology 77(10):3219-3226 DOI 10.1128/AEM.02810-10.
19. Yatsunenko T, Rey FE,Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M,Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC,Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. 2012. Human gut microbiome viewed across age and geography. Nature 486(7402):222-227 DOI 10.1038/nature11053.