Two-stage microbial community experimental design

ISME Journal

Volumn 7, Issue 12, 2013, Pages 2330-2339

  Tickle, Timothy L ^a,b   Segata, Nicola ^a   Waldron, Levi ^a,c   Weingart, Uri ^a   Huttenhower, Curtis ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

16S; microbial; microbiome; sampling; sequencing; two stage

Indexed keywords

RNA 16S;

ACCURACY ASSESSMENT; CLADISTICS; EXPERIMENTAL DESIGN; GENETIC MARKER; MICROBIAL COMMUNITY; OPTIMIZATION; PHENOTYPE; RNA; SAMPLING; SIMULATION; SOFTWARE;

ARTICLE; ECOLOGY; GENETICS; HUMAN; METAGENOMICS; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; REPRODUCIBILITY; STANDARD; STATISTICAL BIAS;

BIAS (EPIDEMIOLOGY); ECOLOGY; HUMANS; METAGENOMICS; MICROBIOLOGICAL TECHNIQUES; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; RNA, RIBOSOMAL, 16S;

EID: 84888203198     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2013.139     Document Type: Article

References (31)

1. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL et al. (2012). Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8: e1002358
2. Albanese D, Visintainer R, Merler S, Riccadonna S, Jurman G, Furlanello C. (2012). mlpy: Machine Learning Python arXiv:1202.6548
3. Baillargeon S, Rivest L. (2011). the construction of stratified designs in R with the package stratification. Survey Methodology 37: 53-65
4. Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. (2011). Generation of multimillionsequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads. Appl Environ Microbiol 77: 3846-3852
5. Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, Mangan M et al. (2001). Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Current Protocols in Molecular Biology. John Wiley & Sons, Inc..
6. Brown J, Salehi MM, Moradi M, Bell G, Smith D. (2008). An adaptive two-stage sequential design for sampling rare and clustered populations. Popul Ecol 50: 239-245
7. Claesson MJ, Jeffery IB, Conde S, Power SE, O?Connor EM, Cusack S et al. (2012). Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178-184
8. Danz NP, Regal RR, Niemi GJ, Brady VJ, Hollenhorst T, Johnson LB et al. (2005). Environmentally stratified sampling design for the development of Great Lakes environmental indicators. Environ Monit Assess 102: 41-65 (Pubitemid 40409483)
9. Frank DN, St. Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 104: 13780-13785 (Pubitemid 350003397)
10. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW et al. (2012). the human microbiome project: a community resource for the healthy human microbiome. PLoS Biol 10: e1001377
11. Hamady M, Knight R. (2009). Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res 19: 1141-1152
12. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC et al. (2007). PyCogent: a toolkit for making sense from sequence. Genome Biol 8: R171
13. Knights D, Costello EK, Knight R. (2011). Supervised classification of human microbiota. FEMS Microbiol Rev 35: 343-359
14. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D et al. (2012). Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13: 47-58
15. Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ et al. (2011). Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480: 368-371
16. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV et al. (2012). Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13: R79
17. Olsen A, Sedransk J, Edwards D, Gotway C, Liggett W, Rathbun S et al. (1999). Statistical issues for monitoring ecological and natural resources in the United States. Environ Monit Assess 54: 1-45 (Pubitemid 29067271)
18. Pace NR, Stahl DA, Lane DJ, Olsen GJ. (1986). the analysis of natural microbial populations by ribosomal RNA sequences. Adv Microbial Ecol 9: 1-55
19. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65
20. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL et al. (2011). Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA 108(Suppl): 4680-4687
21. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: open-source, platform-independent, community- supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541
22. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS et al. (2011). Metagenomic biomarker discovery and explanation. Genome Biol 12: R60
23. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Meth advance online publication 9: 811-814
24. Simpson EH. (1949). Measurement of diversity. Nature 163: 1
25. the Human Microbiome Project Consortium. (2012a). A framework for human microbiome research. Nature 486: 215-221
26. the Human Microbiome Project Consortium. (2012b). Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214
27. Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT. (2012). Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys. ISME J 6: 1273-1276
28. Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z et al. (2010). A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139: 1844-1854, e1841
29. Yamaguchi-Kabata Y, Nakazono K, Takahashi A, Saito S, Hosono N, Kubo M et al. (2008). Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am J Hum Genet 83: 445-456
30. Yang F, Zeng X, Ning K, Liu KL, Lo CC, Wang W et al. (2012). Saliva microbiomes distinguish cariesactive from healthy human populations. ISME J 6: 1-10
31. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez- Bello MG, Contreras M et al. (2012). Human gut microbiome viewed across age and geography. Nature 486: 222-227.