Getting started with microbiome analysis: Sample acquisition to bioinformatics

Current Protocols in Human Genetics

Volumn 2014, Issue , 2014, Pages 18.8.1-18.8.29

  Kumar, Ranjit ^a   Eipers, Peter ^b   Little, Rebecca B ^c   Crowley, Michael ^d   Crossman, David K ^d   Lefkowitz, Elliot J ^e   Morrow, Casey D ^b  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^d UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^e University of Alabama at Birmingham   (United States)

Author keywords

16S rrna genes; Microbe communities; Microbiome analysis pipeline; QWRAP bioinformatics analysis

Indexed keywords

DNA; RNA 16S;

AMPLICON; ARTICLE; BIOINFORMATICS; CHEEK MUCOSA; CONTROLLED STUDY; DATA ANALYSIS; DNA ISOLATION; DNA SEQUENCE; FECES ANALYSIS; FECES CULTURE; HIGH THROUGHPUT SEQUENCING; HUMAN; MICROBIAL COMMUNITY; MICROBIOME; MOUTH FLORA; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA GENE; SALIVA ANALYSIS; SKIN CULTURE; VAGINA FLORA; VAGINA SMEAR; BIOLOGY; FECES; FEMALE; GENETICS; MICROBIOLOGY; MICROFLORA;

COMPUTATIONAL BIOLOGY; FECES; FEMALE; HUMANS; MICROBIOTA; RNA, RIBOSOMAL, 16S;

EID: 84917701407     PISSN: 19348266     EISSN: 19348258     Source Type: Journal    
DOI: 10.1002/0471142905.hg1808s82     Document Type: Article

References (50)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Antolin, M., Artiguenave, F., Blottiere, H.M., Almeida, M., Brechot, C., Cara, C., Chervaux, C., Cultrone, A., Delorme, C., Denariaz, G., Dervyn, R., Foerstner, K.U., Friss, C., van de Guchte, M., Guedon, E., Haimet, F., Huber, W., van Hylckama-Vlieg, J., Jamet, A., Juste, C., Kaci, G., Knol, J., Lakhdari, O., Layec, S., Le Roux, K., Maguin, E., Merieux, A., Melo Minardi, R., M'Rini, C., Muller, J., Oozeer, R., Parkhill, J., Renault, P., Rescigno, M., Sanchez, N., Sunagawa, S., Torrejon, A., Turner, K., Vandemeulebrouck, G., Varela, E., Winogradsky, Y., Zeller, G., Weissenbach, J., Ehrlich, S.D., and Bork, P. 2011. Enterotypes of the human gut microbiome. Nature 473:174-180.
3. Bokulich, N.A., Subramanian, S., Faith, J.J., Gevers, D., Gordon, J.I., Knight, R., Mills, D.A., and Caporaso, J.G. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10:57-59.
4. Caporaso, J.G., Bittinger, K., Bushman, F.D., De-Santis, T.Z., Andersen, G.L., and Knight, R. 2010a. PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266-267.
5. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Pena, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., and Knight, R. 2010b. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336.
6. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A., Turnbaugh, P.J., Fierer, N., and Knight, R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. U.S.A. 108:4516-4522.
7. Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S.M., Betley, J., Fraser, L., Bauer, M., Gormley, N., Gilbert, J.A., Smith, G., and Knight, R. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6:1621-1624.
8. Cho, I. and Blaser, M.J. 2012. The human microbiome: At the interface of health and disease. Nat. Rev. Genet. 13:260-270.
9. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M., and Tiedje, J.M. 2009. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-145.
10. Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., Sun, Y., Brown, C.T., Porras-Alfaro, A., Kuske, C.R., and Tiedje, J.M. 2014. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 41:D633-D642.
11. Coussens, L.M. and Werb, Z. 2002. Inflammation and cancer. Nature 420:860-867.
12. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., and Andersen, G.L. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
13. Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S.R., Nelson, K.E., and Relman, D.A. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
14. Edgar, R.C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
15. Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.
16. Evans, J., Sheneman, L., and Foster, J. 2006. Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62:785-792.
17. Faith, J.J., Guruge, J.L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A.L., Clemente, J.C., Knight, R., Heath, A.C., Leibel, R.L., Rosenbaum, M., and Gordon, J.I. 2013. The long-term stability of the human gut microbiota. Science 341:1237439.
18. Goodman, A.L., Kallstrom, G., Faith, J.J., Reyes, A., Moore, A., Dantas, G., and Gordon, J.I. 2011. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl. Acad. Sci. U.S.A. 108:6252-6257.
19. Haas, B.J., Garges, S., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S.K., Sodergren, E., Methe, B., DeSantis, T.Z., Consotium, H.M., Petrosino, J.F., Knight, R., and Birren, B.W. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494-504.
20. Huse, S.M., Mark Welch, D.B., Voorhis, A., Shipunova, A., Morrison, H.G., Eren, A.M., and Sogin, M.L. 2014. VAMPS: A website for visualization and analysis of microbial population structures. BMC Bioinformatics doi: 10.1186/1471-2105-15-41.
21. Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J.H., Chinwalla, A.T., Creasy, H.H., Earl, A.M., FitzGerald, M.G., Fulton, R.S., Giglio, M.G., Hallsworth-Pepin, K., Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J.H., Chinwalla, A.T., Creasy, H.H., Earl, A.M., FitzGerald, M.G., Fulton, R.S., Giglio, M.G., Hallsworth-Pepin, K., Lobos, E.A., Madupu, R., Magrini, F., Martin, J.C., Mitreva, M., Muzny, D.M., Sodergren, E.J., Versalovic, J., Wollam, A.M., Worley, K.C., Wortman, J.R., Young, S.K., Zeng, Q., Aagaard, K.M., Abolude, O.O., Allen-Vercoe, E., Alm, E.J., Alvarado, L., Andersen, G.L., Anderson, S., Appelbaum, E., Arachchi, H.M., Armitage, G., Arze, C.A., Ayvaz, T., Baker, C.C., Begg, L., Belachew, T., Bhonagiri, V., Bihan, M., Blaser, M.J., Bloom, T., Bonazzi, V., Brooks, J.P., Buck, G.A., Buhay, C.J., Busam, D.A., Campbell, J.L., Canon, S.R., Cantarel, B.L., Chain, P.S.G., Chen, I.A., Chen, L., Chhibba, S., Chu, K., Ciulla, D.M., Clemente, J.C., Clifton, S.W., Conlan, S., Crabtree, J., Cutting, M.A., Davidovics, N.J., Davis, C.C., DeSantis, T.Z., Deal, C., Delehaunty, K.D., Dewhirst, F.E., Deych, E., Ding, Y., Dooling, D.J., Dugan, S.P., Dunne, W.M., Durkin, A.S., Edgar, R.C., Erlich, R.L., Farmer, C.N., Farrell, R.M., Faust, K., Feldgarden, M., Felix, V.M., Fisher, S., Fodor, A.A., Forney, L.J., Foster, L., Di Francesco, V., Friedman, J., Friedrich, D.C., Fronick, C.C., Fulton, L.L., Gao, H., Garcia, N., Giannoukos, G., Giblin, C., Giovanni, M.Y., Goldberg, J.M., Goll, J., Gonzalez, A., Griggs, A., Gujja, S., Kinder Haake, S., Haas, B.J., Hamilton, H.A., Harris, E.L., Hepburn, T.A., Herter, B., Hoffmann, D.E., Holder, M.E., Howarth, C., Huang, K.H., Huse, S.M., Izard, J., Jansson, J.K., Jiang, H., Jordan, C., Joshi, V., Katancik, J.A., Keitel, W.A., Kelley, S.T., Kells, C., King, N.B., Knights, D., Kong, H.H., Koren, O., Koren, S., Kota, K.C., Kovar, C.L., Kyrpides, N.C., La Rosa, P.S., Lee, S.L., Lemon, K.P., Lennon, N., Lewis, C.M., Lewis, L., Ley, R.E., Li, K., Liolios, K., Liu, B., Liu, Y., Lo, C.-C., Lozupone, C.A., Lunsford, R.D., Madden, T., Mahurkar, A.A., Mannon, P.J., Mardis, E.R., Markowitz, V.M., Mavromatis, K., McCorrison, J.M., McDonald, D., McEwen, J., McGuire, A.L., McInnes, P., Mehta, T., Mihindukulasuriya, K.A., Miller, J.R., Minx, P.J., Newsham, I., Nusbaum, C., O'Laughlin, M., Orvis, J., Pagani, I., Palaniappan, K., Patel, S.M., Pearson, M., Peterson, J., Podar, M., Pohl, C., Pollard, K.S., Pop, M., Priest, M.E., Proctor, L.M., Qin, X., Raes, J., Ravel, J., Reid, J.G., Rho, M., Rhodes, R., Riehle, K.P., Rivera, M.C., Rodriguez-Mueller, B., Rogers, Y.-H., Ross, M.C., Russ, C., Sanka, R.K., Sankar, P., Sathirapongsasuti, J.F., Schloss, J.A., Schloss, P.D., Schmidt, T.M., Scholz, M., Schriml, L., Schubert, A.M., Segata, N., Segre, J.A., Shannon, W.D., Sharp, R.R., Sharpton, T.J., Shenoy, N., Sheth, N.U., Simone, G.A., Singh, I., Smillie, C.S., Sobel, J.D., Sommer, D.D., Spicer, P., Sutton, G.G., Sykes, S.M., Tabbaa, D.G., Thiagarajan, M., Tomlinson, C.M., Torralba, M., Treangen, T.J., Truty, R.M., Vishnivetskaya, T.A., Walker, J., Wang, L., Wang, Z., Ward, D.V., Warren, W., Watson, M.A., Wellington, C., Wetterstrand, K.A., White, J.R., Wilczek-Boney, K., Wu, Y.Q., Wylie, K.M., Wylie, T., Yandava, C., Ye, L., Ye, Y., Yooseph, S., Youmans, B.P., Zhang, L., Zhou, Y., Zhu, Y., Zoloth, L., Zucker, J.D., Birren, B.W., Gibbs, R.A., Highlander, S.K., Methé, B.A., Nelson, K.E., Petrosino, J.F., Weinstock, G.M., Wilson, R.K., and White, O. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
22. Jost, L. 2007. Partitioning diversity into independent alpha and beta components. Ecology 88:2427-2439.
23. Kozich, J.J., Westcott, S.L., Baxter, N.T., Highlander, S.K., and Schloss, P.D. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79:5112-5120.
24. Kuczynski, J., Stombaugh, J., Walters, W.A., Gonzalez, A., Caporaso, J.G., and Knight, R. 2011. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Bioinform. 36:10.7.1-10.7.20.
25. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J., and Higgins, D.G. 2007. ClustalWand Clustal X version 2.0. Bioinformatics 23:2947-2948.
26. Ley, R.E. 2010. Obesity and the human microbiome. Curr. Opin. Gastroenterol. 26:5-11.
27. Li, W. and Godzik, A. 2006. Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659.
28. Littman, D.R. and Pamer, E.G., 2011. Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe 10:311-323.
29. Lozupone, C., Hamady, M., and Knight, R. 2006. UniFrac-An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform. 7:371.
30. Lozupone, C.A., Hamady, M., Kelley, S.T., and Knight, R. 2007. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73:1576-1585.
31. Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K., and Knight, R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220-230.
32. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüssmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., and Schleifer, K.H. 2004. ARB: A software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
33. Magoc, T. and Salzberg, S.L. 2011. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957-2963.
34. McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., DeSantis, T.Z., Probst, A., Andersen, G.L., Knight, R., and Hugenholtz, P. 2012. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6:610-618.
35. Musso, G., Gambino, R., and Cassader, M. 2011. Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annu. Rev. Med. 62:361-380.
36. Navas-Molina, J.A., Peralta-Sanchez, J.M., Gonzalez, A., McMurdie, P.J., Vazquez-Baeza, Y., Xu, Z., Ursell, L.K., Lauber, C., Zhou, H., Song, S.J., Huntley, J., Ackermann, G.L., Berg-Lyons, D., Holmes, S., Caporaso, J.G., and Knight, R. 2013. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol. 531:371-444.
37. Nawrocki, E.P., Kolbe, D.L., and Eddy, S.R. 2009. Infernal 1.0: Inference of RNA alignments. Bioinformatics 25:1335-1337.
38. Nechvatal, J.M., Ram, J.L., Basson, M.D., Namprachan, P., Niec, S.R., Badsha, K.Z., Matherly, L.H., Majumdar, A.P., and Kato, I. 2008. Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J. Microbiol. Methods 72:124-132.
39. Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J.A., Bonazzi, V., McEwen, J.E., Wetterstrand, K.A., Deal, C., Baker, C.C., Di Francesco, V., Howcroft, T.K., Karp, R.W., Lunsford, R.D., Wellington, C.R., 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., Little, A.R., Peavy, H., Pontzer, C., Portnoy, M., Sayre, M.H., Starke-Reed, P., Zakhari, S., Read, J., Watson, B., and Guyer, M. 2009. The NIH Human Microbiome Project. Genome Res. 19:2317-2323.
40. Price, M.N., Dehal, P.S., andArkin, A.P. 2009. Fast-Tree: Computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26:1641-1650.
41. Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B., Lesniewski, R.A., Oakley, B.B., Parks, D.H., Robinson, C.J., Sahl, J.W., Stres, B., Thallinger, G.G., Van Horn, D.J., and Weber, C.F. 2009. Introducing MOTHUR: Open-source, platformindependent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
42. Stackebrandt, E. and Goebel, B.M. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bact. 44:846-849.
43. Stamatakis, A., Ludwig, T., and Meier, H. 2005. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
44. Tilg, H. and Kaser, A. 2011. Gut microbiome, obesity, and metabolic dysfunction. J. Clin. Invest. 121:2126-2132.
45. Tlaskalova-Hogenova, H., Stepankova, R., Kozakova, H., Hudcovic, T., Vannucci, L., Tuckova, L., Rossmann, P., Hrncir, T., Kverka, M., Zakostelska, Z., Klimesova, K., Pribylova, J., Bartova, J., Sanchez, D., Fundova, P., Borovska, D., Srutkova, D., Zidek, Z., Schwarzer, M., Drastich, P., and Funda, D.P. 2011. The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: Contribution of germ-free and gnotobiotic animal models of human diseases. Cell. Mol. Immunol. 8:110-120.
46. Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R., and Gordon, J.I. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031.
47. Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., Sogin, M.L., Jones, W.J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R., and Gordon, J.I. 2009a. A core gut microbiome in obese and lean twins. Nature 457:480-484.
48. Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., Rey, F.E., Knight, R., and Gordon, J.I. 2009b. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1:6ra14.
49. Woese, C.R. and Gutell, R.R. 1989. Evidence for several higher order structural elements in ribosomal RNA. Proc. Natl. Acad. Sci. U.S.A. 86:3119-3122.
50. Wu, G.D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.Y., Keilbaugh, S.A., Bewtra, M., Knights, D., Walters, W.A., Knight, R., Sinha, R., Gilroy, E., Gupta, K., Baldassano, R., Nessel, L., Li, H., Bushman, F.D., and Lewis, J.D. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105-108.