Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray

Applied and Environmental Microbiology

Volumn 76, Issue 16, 2010, Pages 5636-5638

  Schatz, Michael C ^a,b   Phillippy, Adam M ^a,b   Gajer, Pawel ^a   DeSantis, Todd Z ^c   Andersen, Gary L ^c   Ravel, Jacques ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b University of Maryland   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL; DESKTOP APPLICATIONS; ENVIRONMENTAL SAMPLE; MICROARRAY DATA; OPERATING SYSTEMS;

COMPUTER OPERATING SYSTEMS;

EXPERIMENTAL STUDY; MICROBIAL ACTIVITY; PROKARYOTE; SAMPLING;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIOLOGY; CLASSIFICATION; COMPUTER PROGRAM; DNA MICROARRAY; GENETICS; METHODOLOGY; MICROARRAY ANALYSIS; MICROBIOLOGY; ARCHAEON; BACTERIA; PROCEDURES;

ARCHAEA; BACTERIA; COMPUTATIONAL BIOLOGY; ENVIRONMENTAL MICROBIOLOGY; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

ARCHAEA; BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 77955934408     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00303-10     Document Type: Article

References (9)

1. Brodie, E. L., T. Z. Desantis, D. C. Joyner, S. M. Baek, J. T. Larsen, G. L. Andersen, T. C. Hazen, P. M. Richardson, D. J. Herman, T. K. Tokunaga, J. M. Wan, andM. K. Firestone. 2006. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Environ. Microbiol. 72:6288-6298.
2. Brodie, E. L., T. Z. DeSantis, J. P. Parker, I. X. Zubietta, Y. M. Piceno, andG. L. Andersen. 2007. Urban aerosols harbor diverse and dynamic bacterial populations. Proc. Natl. Acad. Sci. U. S. A. 104:299-304.
3. de Hoon, M. J., S. Imoto, J. Nolan, andS. Miyano. 2004. Open source clustering software. Bioinformatics 20:1453-1454.
4. DeSantis, T. Z., E. L. Brodie, J. P. Moberg, I. X. Zubieta, Y. M. Piceno, andG. L. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371-383.
5. DeSantis, T. Z., C. E. Stone, S. R. Murray, J. P. Moberg, andG. L. Andersen. 2005. Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol. Lett. 245:271-278.
6. Flanagan, J. L., E. L. Brodie, L. Weng, S. V. Lynch, O. Garcia, R. Brown, P. Hugenholtz, T. Z. DeSantis, G. L. Andersen, J. P. Wiener-Kronish, andJ. Bristow. 2007. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45:1954-1962.
7. Gentleman, R. C., V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Jacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, andJ. Zhang. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
8. Hamady, M., C. Lozupone, andR. Knight. 2010. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J. 4:17-27.
9. Ivanov, I.I., K. Atarashi, N. Manel, E. L. Brodie, T. Shima, U. Karaoz, D. Wei, K. C. Goldfarb, C. A. Santee, S. V. Lynch, T. Tanoue, A. Imaoka, K. Itoh, K. Takeda, Y. Umesaki, K. Honda, andD. R. Littman. 2009. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485-498.